The makeflow command for md5sum is too long for the cluster

The command for md5sum sent by Makeflow contains the paths of all samples. In 2 of our workflows, there are 672 samples, that is far too long to be accepted for the cluster.

2018/12/04 12:47:55.67 makeflow[46806] notice: job submission failed: no output from slurm couldn't submit batch job, still trying...

Script en erreur lancé par la commande

submitting job: /work/ng6/jflow/work/illumina_diversity_qc/wf000877/.working/ba0c311bd6/_Stash/0/0/0/w0000541 /work/ng6/jflow/work/data/run/91dc3bed5/md5sum.txt /work/ng6/jflow/work/data/run/91dc3bed5/RZ4P3-Be19_CAGAGAGG-CATAACTG-C286B_L001_R2.fastq.gz ...1342 files further...  /work/ng6/jflow/work/data/run/91dc3bed5/RZ3P1-J12_AAAGGCAG-TAGATCGC-C286B_L001_R1.fastq.gz
submitted job 2072387

#!/tools/python/3.4.3/bin/python3.4
import pickle
import os, sys

sys.path.insert(0, '/usr/local/bioinfo/src/nG6/workflows/lib')
sys.path.insert(0, '/usr/local/bioinfo/src/ng6_sources/V3.2/src/weaver/..')
sys.path.insert(0, '/usr/local/bioinfo/src/ng6_sources/V3.2/src/weaver/../..')

from jflow.parameter import IOObject 
def prepare_arguments(*args):

    ioobj_ext = IOObject.IOOBJECT_EXT
    new_args = []
    output_path = []
    # load input object
    for i, arg in enumerate(args):
        if arg.endswith(ioobj_ext):
            if os.path.exists(arg):
                ioobjh = open(arg, 'rb')
                try:
                    ioobj = pickle.load(ioobjh)
                    if isinstance(ioobj, list):
                        for j, cioobj in enumerate(ioobj):
                            if (hasattr(cioobj, "is_ioobject")):
                                cioobjh = open(cioobj.dump_path, 'rb')
                                ioobj[j] = pickle.load(cioobjh)
                                cioobjh.close()
                finally:
                    ioobjh.close()
                new_args.append(ioobj)
            else :
                output_path.append(arg)
        else :
            new_args.append(arg)     
    return (new_args, output_path)
    
def md5sum(md5_file_out, *files_to_md5sum):
    import jflow.seqio as seqio
    import logging
    import os
    from subprocess import Popen, PIPE
    logging.getLogger("AddRawFiles").debug("md5sum. entering")
    logging.getLogger("AddRawFiles").debug("md5sum. files_to_md5sum in "+os.path.dirname(md5_file_out)+" 
= " + ",".join(files_to_md5sum))
    p = Popen("md5sum " + " ".join(files_to_md5sum) +"|awk -F/ {'print $1$NF'} 
> "+ md5_file_out   ,shell=True,stdout=PIPE,stderr=PIPE,universal_newlines=True)
    stdout,stderr = p.communicate()
    logging.getLogger("AddRawFiles").debug("md5sum. finished")

if __name__ == '__main__':
    (new_args, output_path) = prepare_arguments(*sys.argv[1:])
    outputs = md5sum(*new_args)
    
    if not isinstance(outputs, list): outputs = [outputs]
    # in case the returned object is a table
    if len(output_path) == 1 and len(outputs) != len(output_path):
        outputs = [outputs]
    # otherwise the number does not match
    elif len(outputs) != len(output_path) and len (output_path) != 0:
        raise Exception( "The number of object returned by the function is different from the number 
of outputs specified!")
    if len (output_path) > 0 :
        for i, obj in enumerate(outputs):
            objh = open(output_path[i], "wb")
            pickle.dump(obj, objh)
            objh.close()

assigned to @augibert

This p = Popen("md5sum " + os.path.commonprefix(files_to_md5sum)+"/* " +"| awk -F/ {'print $1$NF'} > "+ md5_file_out ,shell=True,stdout=PIPE,stderr=PIPE,universal_newlines=True) was tested without success : Makeflow details the "*"...

ajouter des python fonctions!

def md5sum(md5_file_out, files_to_md5sum):
   p = Popen("md5sum " + os.path.dirname(files_to_md5sum)+"/* " +"| awk -F/ {'print $1$NF'} > "+ md5_file_out   ,shell=True,stdout=PIPE,stderr=PIPE,universal_newlines=True)
# End of function
# ...
# Lot of  code
# Then at the end
        if (len(files_to_md5_ori)>0):
            md5_file = os.path.join(self.runobj.get_work_directory(), "md5sum.txt")
            self.add_python_execution(md5sum,cmd_format="{EXE} {OUT} {IN}",
                                      inputs = files_to_md5[0], outputs = md5_file, map=False)
                                      #inputs = files_to_md5, outputs = md5_file, map=False)

-> Does not work because a line with the md5sum of md5sum.txt file appears in the md5sum.txt file..

okey! Le problème du md5sum est reglé!

La fonction md5sum

def md5sum(md5_file_out, files_to_md5sum):    
    import jflow.seqio as seqio
    import logging
    import os
    from subprocess import Popen, PIPE
    logging.getLogger("AddRawFiles").debug("md5sum. entering")
    logging.getLogger("AddRawFiles").debug("md5sum. files_to_md5sum in "+os.path.dirname(md5_file_out)+" = "+
                                           "find " + os.path.dirname(files_to_md5sum)  + " -maxdepth 1 -type f -not -name " + md5_file_out + " -exec md5sum {} \;" + 
                                           "| awk -F/ {'print $1$NF'} > "+ md5_file_out)
    p = Popen("find " + os.path.dirname(files_to_md5sum)  + "-maxdepth 1 -type f -not -name " + md5_file_out + " -exec md5sum {} \;" + 
              "| awk -F/ {'print $1$NF'} > "+ md5_file_out,
              shell = True, stdout = PIPE, stderr = PIPE, universal_newlines = True)
    stdout,stderr = p.communicate()
    logging.getLogger("AddRawFiles").debug("md5sum. finished")

Son appel :

        if (len(files_to_md5_ori)>0):
            md5_file = os.path.join(self.runobj.get_work_directory(), "md5sum.txt")
            self.add_python_execution(md5sum, cmd_format="{EXE} {OUT} {IN}",
                                      inputs = files_to_md5[0], outputs = md5_file, map=False)  

Fonctionne pour le workflow de test, cette fonction là est passée sur le run de 672 échantillons.

Nouveau problème identifié :

submitting job: /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/.working/669fdc6d84/_Stash/0/0/0/w0000540 /work/ng6-test/jflow_augibert/tmp/tmpupic8fv4.dump /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P1-09_TAGGCATG-GATCGCTA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P1-J8-1_GCGATAAG-TCGCTAGA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P2-26_GCTACGCT-AAGGAGGT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P3-Be24_CTAGCGTA-AAGCCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P2-R99-1_TAAGGCGA-GGAGGTAA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P3-B30_TCCTGGAC-AGTAAAGG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P3-B37_CTGGACTC-AAGGAGTA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P3-31_TGCGAGGC-GCCTCTAA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P3-10_GCTGCGAG-TGCATAAC-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P2-08-3_GAGTAGAG-AGTAGAAG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P2-17-1_GCGATAAG-GGAGGTAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P3-01_GCTCCTGA-CATAACTG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P3-Be21_CGAGGCTG-CATAACTG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P2-25_CAGAGAGG-AAGGAGGT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P2-27_CGAGGCTG-AAGGAGGT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P2-R15-3_ACCTCTCT-AGTAGAAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P1-06_AGGCAGAA-GATCGCTA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P2-14_GCTGCGAG-TAGAAGAG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/Vid26_CAGAGAGG-GCCTCTAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P3-B16_GGCAGAGA-GTAAGGAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P1-13_CGAGGCTG-GATCGCTA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P1-16_GAGCTCCT-CTATCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P2-R78_AGGCAGAA-TAGAAGAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P1-02_AGCGTACT-TCGCTAGA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P1-18_TGTAGGCA-CTATCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ2P3-B88-3_TGTAGGCA-AAGCCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P3-B13_CTGGACTC-GTAAGGAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P1-14_CTAGCGTA-CTCTATCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P2-26_CTACCTCT-AAGGAGGT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P3-18_CTGCTACG-AGTAAAGG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P2-09_CTGGACTC-TAGAAGAG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J47_AGGCAGAA-TCGCTAGA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P1-22_TGCGAGGC-CTATCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P3-03_CATGTAGG-CATAACTG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P2-18-1_TAAGGCGA-AAGGAGGT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P3-29_GCTACGCT-AAGCCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/MZ2P1-19-3_GCTCCTGA-AAGGAGGT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P2-R66_AGGCAGAA-CTCTTATC-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P3-B33-1_GATAAGGC-AAGGAGTA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P3-B17_CTGCTACG-GTAAGGAG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P2-24_CTCTCTAC-AAGGAGGT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P3-Be22_AAGAGGCA-CATAACTG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P3-Be13_CGTACTAG-CATAACTG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P3-19_TGCGAGGC-AGTAAAGG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P2-07_CGTACTAG-AGTAGAAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P2-19_AAAGGCAG-GGAGGTAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P3-B38_TGTAGGCA-AAGGAGTA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P2-R29_AAAGGCAG-GTAAGGAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/MZ3P3-30-3_GCTCCTGA-AGTAGAAG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ2P3-B76-3_TGTAGGCA-GGAGTAAA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P2-R87_AAGAGGCA-TAGAAGAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P1-10_GCTGCGAG-GATCGCTA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/LZ3P3-J240-3_GATAAGGC-GGAGTAAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P1-14_AAGAGGCA-GATCGCTA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P3-12_AGAAAGGC-AGTAAAGG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P2-04_CGCTGCTA-TCCTCTTA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P1-10_GCTGCGAG-TCGCTAGA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P3-Be1_CGTACTAG-GGAGGTAA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P2-R19_CTGGACTC-AGAGTAGA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P1-10_GCTGCGAG-GATCGCTA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P3-Be25_CGTACTAG-AGTAAAGG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ2P3-B76-3_TGTAGGCA-GGAGTAAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P2-19_CGTACTAG-AAGGAGGT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J33-1_GATAAGGC-CTAAGCCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P2-05-1_GCGATAAG-TAGAAGAG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J57-3_GGCAGAGA-CTCTATCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P2-R52_GCTACGCT-TCCTCTTA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P2-R28_AGCGTACT-GTAAGGAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P1-25-1_GATAAGGC-CTCTTATC-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P3-30_CATGTAGG-AAGCCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P3-21_GAGTAGAG-AGTAAAGG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P3-13-1_GCGATAAG-GGAGTAAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P1-18_CATGTAGG-CTATCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P2-20_GAGCTCCT-GGAGGTAA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P2-15_CAAAGAGG-TAGAAGAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P1-05_TCCTGGAC-GATCGCTA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J51_CTCTCTAC-TCGCTAGA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P3-20_CAAAGAGG-AGTAAAGG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P3-Be55-3_GAGTAGAG-AAGCCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P3-20_GAGGCAGA-GGAGTAAA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P3-08_CAAAGAGG-CATAACTG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P3-05_TCCTGGAC-TGCATAAC-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P3-09-1_TAAGGCGA-GGAGTAAA-C286B_L001_R2.count 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/work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P1-25_CGAGGCTG-CTCTATCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/Vid7-3_GATAAGGC-AAGCCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P1-04_GAGCTCCT-TCGCTAGA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P3-20_GGCAAAGA-AGTAAAGG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P3-Be17_TAGGCATG-CATAACTG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P2-30-3_CAAAGAGG-TGCATAAC-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P1-11_CAAAGAGG-TCGCTAGA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P3-18_CGAGGCTG-GGAGTAAA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/Vid16_CGAGGCTG-AGTAAAGG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P2-16_AGGAGTAG-TAGAAGAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P2-R13_CAAAGAGG-TATCCTCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P1-J41_GAGGCAGA-CTCTATCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P2-15_CGAGGCTG-AGTAGAAG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P1-17_TCCTGGAC-CTATCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P3-B29_CAGAGAGG-GGAGTAAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P2-09_TCCTGAGC-AGTAGAAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P2-12_GAGGCAGA-TAGAAGAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P1-14_CTAGCGTA-CTATCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P1-24_GAGTAGAG-CTATCTCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P3-Be9_CGAGGCTG-GGAGGTAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P1-06_CATGTAGG-TCGCTAGA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ1P3-B24-3_CTGGACTC-AAGCCTCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P3-13_GCTCCTGA-AGTAAAGG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P2-R75_GTAGAGGA-CTCTTATC-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J46_CGTACTAG-TCGCTAGA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P2-R86_CGAGGCTG-TAGAAGAG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J41_CTGCTACG-CTAAGCCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/Vid24_TAGGCATG-GCCTCTAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P2-04_AGGAGTAG-CTCTTATC-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P1-J50-3_TGCGAGGC-GATCGCTA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J49_GGACTCCT-TCGCTAGA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P3-B19_CAAAGAGG-GTAAGGAG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P3-Be55-3_GAGTAGAG-AAGCCTCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P2-24_GAGGCAGA-GGAGGTAA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P3-19_CTACCTCT-GGAGTAAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P2-R67_TCCTGAGC-CTCTTATC-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P3-Be3_TCCTGAGC-GGAGGTAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J60_TCCTGAGC-CTATCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P1-J44-3_GAGTAGAG-GATCGCTA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P3-21_AGGAGTAG-AGTAAAGG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P2-05-3_TGCGAGGC-AGTAGAAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P2-05-3_TGCGAGGC-AGTAGAAG-C286B_L001_R1.count 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/work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P3-26_TCCTGGAC-GCCTCTAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P2-24_GGCAGAGA-GGAGGTAA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ1P1-J14-3_CTGGACTC-CTCTATCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/Vid21_AGGCAGAA-GCCTCTAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P2-25_CATGTAGG-AAGGAGGT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P3-B21-1_GATAAGGC-ACTGCATA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J47_AGGCAGAA-TCGCTAGA-C286B_L001_R1.count 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/work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P1-J22-3_ACCTCTCT-CTCTATCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P1-11_CAGAGAGG-GATCGCTA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/Vid15_GCTACGCT-AGTAAAGG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P1-08_GGACTCCT-GATCGCTA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/Vid32_GGCAAAGA-AAGCCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P2-21_TCCTGGAC-GGAGGTAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J62_TAGGCATG-CTATCTCT-C286B_L001_R2.count 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/work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P2-R58_CTCTCTAC-CTATCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P3-03_TGTAGGCA-CATAACTG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P1-23_GGCAAAGA-CTATCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P3-B40_GGCAGAGA-AAGGAGTA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P3-16_ACCTCTCT-AGTAAAGG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P2-08_GCTCCTGA-TAGAAGAG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P1-15_GTAGAGGA-GATCGCTA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P1-24_AGGAGTAG-CTCTATCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P2-R84_CAGAGAGG-TAGAAGAG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/MZ3P1-05-3_AAAGGCAG-AAGGAGGT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/LZ3P3-J240-3_GATAAGGC-GGAGTAAA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P1-04_GCTCCTGA-TCGCTAGA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P3-B36_GCTCCTGA-AAGGAGTA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P2-19_AAAGGCAG-GGAGGTAA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P2-30_AGCGTACT-CATAACTG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/MZ3P3-31-3_AAAGGCAG-GATCGCTA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/MZ3P3-18-3_GCTCCTGA-TCCTCTTA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P1-03_AGAAAGGC-GATCGCTA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P1-16-1_TAAGGCGA-CTCTATCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P1-22_CTCTCTAC-CTCTATCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P2-R52bis_AAGAGGCA-AAGGAGGT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P2-R61_CGAGGCTG-CTATCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P2-14_GCTACGCT-AGTAGAAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P3-25_GGACTCCT-AAGCCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P2-02_CTACCTCT-TCCTCTTA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P3-34_GCTGCGAG-AAGCCTCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P3-10-1_GCGATAAG-AGTAAAGG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P1-15_AAAGGCAG-CTATCTCT-C286B_L001_R2.count 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/work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P2-20_GCTCCTGA-GGAGGTAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/LZ3P1-B19-3_AGCGTACT-AAGCCTCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P2-R74_AAGAGGCA-CTCTTATC-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P2-04_GAGTAGAG-CTCTTATC-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P1-05_TCCTGGAC-GATCGCTA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P2-04_CGCTGCTA-TCCTCTTA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P3-11_CTAGCGTA-AGTAAAGG-C286B_L001_R1.count 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/work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/LZ3P3-J228-3_GATAAGGC-TGCATAAC-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P1-J14_CTGGACTC-TAGATCGC-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P1-J53_GGCAGAGA-TCGCTAGA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P1-07_ACCTCTCT-TCGCTAGA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P3-01-1_GCGATAAG-TGCATAAC-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/LZ3P3-J216-3_GATAAGGC-AAGGAGGT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P2-06_AGCGTACT-TAGAAGAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P1-J52_AGAAAGGC-TCCTCTTA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P3-Be2_AGGCAGAA-GGAGGTAA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P2-31_AAAGGCAG-CATAACTG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P2-R63_GTAGAGGA-CTATCTCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P1-28_GAGCTCCT-CTCTTATC-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P1-22_GCTGCGAG-CTATCTCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P2-07_CGTACTAG-AGTAGAAG-C286B_L001_R1.count 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/work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P3-23_GGCAAAGA-GGAGTAAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P3-22-3_CTGCTACG-AAGCCTCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P2-30_AGAAAGGC-CATAACTG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/LZ2P3-V92-3_AGCGTACT-TGCATAAC-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P3-16_ACCTCTCT-AGTAAAGG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P1-J18_CTGCTACG-TAGATCGC-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/LZ3P3-J216-3_GATAAGGC-AAGGAGGT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P1-09_CGCTGCTA-TCGCTAGA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P3-Be11_GTAGAGGA-GGAGGTAA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P3-22-3_CTGCTACG-AAGCCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J36_GCTCCTGA-CTAAGCCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P2-R79_TCCTGAGC-TAGAAGAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P1-21_CTGCTACG-CTATCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P3-B15_ACCTCTCT-GTAAGGAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/MZ3P3-31-3_AAAGGCAG-GATCGCTA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P2-08_GCTCCTGA-TAGAAGAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P3-28_ACCTCTCT-GCCTCTAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P1-07_CTACCTCT-TCGCTAGA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P3-15_CATGTAGG-AGTAAAGG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/Vid14_CAGAGAGG-AGTAAAGG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/LZ3P1-B19-3_AGCGTACT-AAGCCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P1-19_ACCTCTCT-CTATCTCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P3-28_CAGAGAGG-AAGCCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/MZ3P2-27-3_GCTCCTGA-CTCTATCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J50_TAGGCATG-TCGCTAGA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/Vid33_AGGAGTAG-AAGCCTCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P1-31_TCCTGAGC-TCCTCTTA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/MZ2P2-05-3_AAAGGCAG-CTCTATCT-C286B_L001_R1.count 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/work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P2-R82_AGAAAGGC-AGTAGAAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P3-B20_TCCTGGAC-CATAACTG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P3-30_CGCTGCTA-GCCTCTAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P2-25_CTGCTACG-GGAGGTAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P1-31_TCCTGAGC-TCCTCTTA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P3-B18_TGCGAGGC-GTAAGGAG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P3-17_TCCTGGAC-GGAGTAAA-C286B_L001_R1.count 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/work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J49_GGACTCCT-TCGCTAGA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P2-03_GAGGCAGA-TCCTCTTA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P3-21_GAGTAGAG-AGTAAAGG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P2-R26_GAGTAGAG-AGAGTAGA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P2-R63_GTAGAGGA-CTATCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P3-B30_TCCTGGAC-AGTAAAGG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P1-13-3_TGCGAGGC-CTCTATCT-C286B_L001_R1.count 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/work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P1-17_CTGGACTC-CTATCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P3-B60_TGCGAGGC-AAGGAGTA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P2-R52_GCTACGCT-TCCTCTTA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P2-05_GTAGAGGA-TCCTCTTA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J45-3_GGCAGAGA-GATCGCTA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P2-R13_CAAAGAGG-TATCCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/LZ2P3-V4-3_AGCGTACT-GGAGTAAA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P1-17_TCCTGGAC-CTCTATCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P2-R27-1_GATAAGGC-GTAAGGAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/Vid21_AGGCAGAA-GCCTCTAA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P3-B25_CTGGACTC-ACTGCATA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P3-28_CTACCTCT-GCCTCTAA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P1-J20_CAAAGAGG-TAGATCGC-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P1-31_ACCTCTCT-CTCTTATC-C286B_L001_R2.count 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/work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P2-01_CAGAGAGG-TCCTCTTA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P1-05_CGTACTAG-GATCGCTA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P2-R68_GGACTCCT-CTCTTATC-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P3-27_CATGTAGG-GCCTCTAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P1-09_TAGGCATG-GATCGCTA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P1-J21_GAGTAGAG-TAGATCGC-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ2P2-R55-3_TGTAGGCA-AGTAGAAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P1-22_TGCGAGGC-CTATCTCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P2-11_GAGCTCCT-AGTAGAAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P2-23_CTACCTCT-GGAGGTAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P1-32_GAGGCAGA-CTCTTATC-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P2-12_GAGGCAGA-TAGAAGAG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P3-Be26_AGGCAGAA-AGTAAAGG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J37_CTGGACTC-CTAAGCCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/Vid18_GTAGAGGA-AGTAAAGG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P2-R41_TCCTGAGC-TGCATAAC-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P2-R67_TCCTGAGC-CTCTTATC-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P3-09_AGGAGTAG-CATAACTG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J52_CAGAGAGG-TCGCTAGA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P3-01_GCTCCTGA-CATAACTG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P2-01_CGCTGCTA-CTCTTATC-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P2-R85_GCTACGCT-TAGAAGAG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/MZ3P1-05-3_AAAGGCAG-AAGGAGGT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P1-J50-1_GATAAGGC-TCGCTAGA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P1-32_GGCAGAGA-CTCTTATC-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P3-Be14_AGGCAGAA-CATAACTG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P2-06_GGCAAAGA-TCCTCTTA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P1-26_AGCGTACT-CTCTTATC-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P1-21_CGCTGCTA-CTATCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P2-R27-3_ACCTCTCT-AAGGAGGT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P3-Be18_CTCTCTAC-CATAACTG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P2-10_GGACTCCT-AGTAGAAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P2-R99-3_GGCAGAGA-AAGGAGGT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/LZ3P2-Be21-3_GATAAGGC-TCCTCTTA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P3-B20_GAGTAGAG-GTAAGGAG-C286B_L001_R1.count 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/work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P3-20_GTAGAGGA-GGAGTAAA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P2-R27-3_ACCTCTCT-AAGGAGGT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P2-29-1_GATAAGGC-CATAACTG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P3-21_CGCTGCTA-GGAGTAAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/LZ2P3-V4-3_AGCGTACT-GGAGTAAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P3-B34_AGCGTACT-AAGGAGTA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J54_CGAGGCTG-TCGCTAGA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P2-19_AGAAAGGC-GGAGGTAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J57-3_GGCAGAGA-CTCTATCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P1-J10-3_ACCTCTCT-GATCGCTA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/Vid7-3_GATAAGGC-AAGCCTCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P3-02_TAGGCATG-TGCATAAC-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P1-J2_AGAAAGGC-CTCTTATC-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P1-16_GCTCCTGA-CTATCTCT-C286B_L001_R1.count 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/work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P2-31_AGGAGTAG-AAGGAGGT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P3-19_TGCGAGGC-AGTAAAGG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P2-22_CATGTAGG-GGAGGTAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P1-13-3_GAGTAGAG-CTCTATCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P3-Be26_AGGCAGAA-AGTAAAGG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P1-J31_TGCGAGGC-CTCTCTAT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P2-R88_GTAGAGGA-TAGAAGAG-C286B_L001_R2.count 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/work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P1-04_GAGCTCCT-GATCGCTA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P3-33_CGCTGCTA-AAGCCTCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J45-1_TAAGGCGA-TCGCTAGA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P3-Be18_CTCTCTAC-CATAACTG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P3-02_CTAGCGTA-TGCATAAC-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P1-26_AAGAGGCA-CTCTATCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P2-13_CATGTAGG-AGTAGAAG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P3-B23_AAAGGCAG-ACTGCATA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P3-03_CATGTAGG-CATAACTG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P3-08_GAGGCAGA-TGCATAAC-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P2-08-1_GCGATAAG-AGTAGAAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P2-13_CAGAGAGG-AGTAGAAG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/MZ3P1-17-3_GCTCCTGA-GATCGCTA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P1-22_GCTGCGAG-CTATCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P2-01_CAGAGAGG-TCCTCTTA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P1-16_GCTCCTGA-CTATCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J56_GTAGAGGA-TCGCTAGA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P1-J25_GCTCCTGA-CTCTCTAT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P2-R69_TAGGCATG-CTCTTATC-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P2-11_ACCTCTCT-TAGAAGAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/Vid26_CAGAGAGG-GCCTCTAA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P3-04_GAGCTCCT-TGCATAAC-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P3-Be3_TCCTGAGC-GGAGGTAA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/LZ3P3-J228-3_GATAAGGC-TGCATAAC-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P2-24_CTCTCTAC-AAGGAGGT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P3-16_CTACCTCT-AGTAAAGG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P3-31_CTACCTCT-AAGCCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P3-B60_TGCGAGGC-AAGGAGTA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P2-16_GAGTAGAG-TAGAAGAG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/MZ3P3-09-3_AAAGGCAG-AAGCCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P2-R84_CAGAGAGG-TAGAAGAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P1-19_TCCTGAGC-CTCTATCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P1-20_GAGGCAGA-CTATCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P1-18_AGGCAGAA-CTCTATCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P2-R5_AAAGGCAG-TATCCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P2-R17_AAAGGCAG-AGAGTAGA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P1-15_AGAAAGGC-CTCTATCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P1-24_AGGAGTAG-CTATCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P1-12_AGGAGTAG-TCGCTAGA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P3-09_AGGAGTAG-CATAACTG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P3-B35_AAAGGCAG-AAGGAGTA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P3-Be20_GCTACGCT-CATAACTG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ1P2-R7-3_CTGGACTC-AGTAGAAG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P2-13_CTGCTACG-TAGAAGAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P3-07_AAGAGGCA-TGCATAAC-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J61_GGACTCCT-CTATCTCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P1-32_GGACTCCT-TCCTCTTA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P1-20_GGACTCCT-CTCTATCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P3-B18_TGCGAGGC-GTAAGGAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P1-03_AGAAAGGC-TCGCTAGA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P3-22_GCTGCGAG-GGAGTAAA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J59_AGGCAGAA-CTATCTCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P2-R28_AGCGTACT-GTAAGGAG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P2-05_GTAGAGGA-TCCTCTTA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J33-3_ACCTCTCT-AAGCCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P2-R22_GGCAGAGA-AGAGTAGA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P1-16_GAGCTCCT-CTATCTCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P1-29_CGTACTAG-TCCTCTTA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P3-04_CAGAGAGG-TGCATAAC-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P2-31_AGGAGTAG-AAGGAGGT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P3-23_CTAGCGTA-GCCTCTAA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P1-10_CTCTCTAC-GATCGCTA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P1-18_CATGTAGG-CTATCTCT-C286B_L001_R1.count 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/work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P1-J30_CTACCTCT-CTATCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P3-02_CTGGACTC-CATAACTG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P3-B33-3_ACCTCTCT-GGAGTAAA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/LZ2P2-J68-3_AGCGTACT-AAGGAGGT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/Vid19-1_TAAGGCGA-GCCTCTAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P2-28-3_CTGCTACG-TGCATAAC-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P2-13_CAGAGAGG-AGTAGAAG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P2-R78_AGGCAGAA-TAGAAGAG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P3-09_GAGTAGAG-CATAACTG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P2-17-3_TGCGAGGC-AAGGAGGT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P1-J21_GAGTAGAG-TAGATCGC-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/MZ3P2-27-3_GCTCCTGA-CTCTATCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ2P1-J52-3_TGTAGGCA-GATCGCTA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P2-R73_CGAGGCTG-CTCTTATC-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J36_GCTCCTGA-CTAAGCCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ2P3-B64-3_TGTAGGCA-TGCATAAC-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P1-06_CATGTAGG-GATCGCTA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P3-28_ACCTCTCT-GCCTCTAA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/LZ2P3-V92-3_AGCGTACT-TGCATAAC-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P3-B20_TCCTGGAC-CATAACTG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P2-11_GAGCTCCT-AGTAGAAG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P3-06_CATGTAGG-TGCATAAC-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J48_TCCTGAGC-TCGCTAGA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P3-03_AGAAAGGC-TGCATAAC-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ3P1-27_GTAGAGGA-CTCTATCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P3-19_GCTGCGAG-AGTAAAGG-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P2-R7_CTGGACTC-TATCCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/Vid29_AAGAGGCA-GCCTCTAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ3P1-J26_CTGGACTC-CTCTCTAT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ4P3-27_AGAAAGGC-AAGCCTCT-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J45-1_TAAGGCGA-TCGCTAGA-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P3-Be4_GGACTCCT-GGAGGTAA-C286B_L001_R2.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P2-11_CTACCTCT-TAGAAGAG-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ1P1-13-3_CTGCTACG-CTCTATCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/SZ2P1-17_CTGGACTC-CTATCTCT-C286B_L001_R1.count /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/RZ4P1-J35_AAAGGCAG-CTAAGCCT-C286B_L001_R1.count > /work/ng6-test/jflow_augibert/work/illumina_diversity_qc/wf000038/AddRawFiles_default/addRawFiles.stdout

La fonction

def add_stats_to_run (run_dump_path,*files):
    import pickle
    import logging
    total_nb_seq = 0
    total_size = 0
    for curr_stat_file in files:
        logging.getLogger("AddRawFiles").debug("add_stats_to_run. Content of " + curr_stat_file)
        with open(curr_stat_file, 'r') as myfile:
            nb_seq,size=myfile.read().split(':')
            logging.getLogger("AddRawFiles").debug("add_stats_to_run. Content of " + curr_stat_file + " nb_seq = " + str(nb_seq) + ", size = " + str(size))
        size= int(size)
        nb_seq= int(nb_seq)
        total_size+=size
        total_nb_seq+=nb_seq
    # load the analysis object
    run_dump = open(run_dump_path, "rb")
    my_run = pickle.load(run_dump)
    run_dump.close()
    logging.getLogger("AddRawFiles").debug("add_stats_to_run. Before my_run.process_raw_files total_nb_seq = " + str(total_nb_seq) + ", total_size = " + str(total_size))
    logging.getLogger("AddRawFiles").debug("add_stats_to_run. work_directory of the run "+ my_run.get_work_directory())
    my_run.process_raw_files(total_size,total_nb_seq)
    logging.getLogger("AddRawFiles").debug("add_stats_to_run. after my_run.process_raw_files, does the work dir ("+my_run.get_work_directory()+") exist? "+ str(os.path.isdir(my_run.get_work_directory())))
    logging.getLogger("AddRawFiles").debug("add_stats_to_run. Content of the folder ("+my_run.get_work_directory()+" = " + ",".join(os.listdir(my_run.get_work_directory())))

Son appel

        logging.getLogger("AddRawFiles").debug("process. Before self.add_stats_to_run(extract_stats_from_seq_file")
        #Add number of reads and total length in base for each seq file and add these data to the run in the database
        self.add_python_execution(add_stats_to_run, cmd_format='{EXE} {ARG} {IN} > {OUT}', map=False,
                                 outputs=self.stdout, inputs=files_to_save_stats,includes=self.files_to_save, arguments=[run_dump_path])

Corrigée par

Fonction :

def add_stats_to_run (run_dump_path,file):
    import pickle
    import logging
    total_nb_seq = 0
    total_size = 0
    logging.getLogger("AddRawFiles").debug("add_stats_to_run. Working on files of the directory containing this one : " + file)
    file_list = [ f for f in os.listdir(os.path.dirname(file)) if f.endswith('.count')]
    logging.getLogger("AddRawFiles").debug("add_stats_to_run. Length on the file_list : " + str(len(file_list)))
    logging.getLogger("AddRawFiles").debug("add_stats_to_run. Files on the file_list : " + str(file_list))
    for curr_stat_file in file_list:
        logging.getLogger("AddRawFiles").debug("add_stats_to_run. Content of " + os.path.dirname(file) + "/" + curr_stat_file)
        with open(os.path.dirname(file) + "/" + curr_stat_file, 'r') as myfile:
            nb_seq,size=myfile.read().split(':')
            logging.getLogger("AddRawFiles").debug("add_stats_to_run. Content of " + curr_stat_file + " nb_seq = " + str(nb_seq) + ", size = " + str(size))
        size= int(size)
        nb_seq= int(nb_seq)
        total_size+=size
        total_nb_seq+=nb_seq
    # load the analysis object
    run_dump = open(run_dump_path, "rb")
    my_run = pickle.load(run_dump)
    run_dump.close()
    logging.getLogger("AddRawFiles").debug("add_stats_to_run. Before my_run.process_raw_files total_nb_seq = " + str(total_nb_seq) + ", total_size = " + str(total_size))
    logging.getLogger("AddRawFiles").debug("add_stats_to_run. work_directory of the run "+ my_run.get_work_directory())
    my_run.process_raw_files(total_size,total_nb_seq)
    logging.getLogger("AddRawFiles").debug("add_stats_to_run. after my_run.process_raw_files, does the work dir ("+my_run.get_work_directory()+") exist? "+ str(os.path.isdir(my_run.get_work_directory())))
    logging.getLogger("AddRawFiles").debug("add_stats_to_run. Content of the folder ("+my_run.get_work_directory()+" = " + ",".join(os.listdir(my_run.get_work_directory())))

Appel :

        files_to_save_stats = self.get_outputs( '{basename_woext}.count', self.files_to_save)
        logging.getLogger("AddRawFiles").debug("process. Before self.add_python_execution(extract_stats_from_seq_file")
        #count number of reads and total length in base for each seq file
        for i,o in zip(self.files_to_save, files_to_save_stats ):
                self.add_python_execution(extract_stats_from_seq_file,cmd_format="{EXE} {IN} {OUT}",
                                      inputs = i, outputs = o, map=False)

ATTENTION : pas de bug de syntaxe, mais le fichier md5sum.txt est vide..

... Ce fichier vide était dû à

    p = Popen("find " + os.path.dirname(files_to_md5sum)  + "-maxdepth 1 -type f -not -name " + os.path.basename(md5_file_out) + " -exec md5sum {} \;" + 
              "| awk -F/ {'print $1$NF'} > "+ md5_file_out, shell = True, stdout = PIPE, stderr = PIPE, universal_newlines = True)

au lieu de

    p = Popen("find " + os.path.dirname(files_to_md5sum)  + " -maxdepth 1 -type f -not -name " + os.path.basename(md5_file_out) + " -exec md5sum {} \;" + 
              "| awk -F/ {'print $1$NF'} > "+ md5_file_out, shell = True, stdout = PIPE, stderr = PIPE, universal_newlines = True)

Oui il y a un espace de différence au niveau du maxdepth...

closed

mentioned in commit 992a5b3b

mentioned in merge request !14 (merged)

reopened

Ajout de log dans src>ng6>analysis.py

changed milestone to %V3.2.1

closed

mentioned in issue #100 (closed)