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How do I read a logfile?
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16 months ago
c.clarido • 50
Netherlands/Rotterdam/Leiden University…

Hello.

I was given a project to translate an existing pipeline to GALAXY. I was given a logfile and I have no idea how to read it. I have here the first two lines of the logfile.

'/usr/local/FastQC/FastQC-0.11.2/fastqc'  '--java' 'java'  '--threads' '4'  '--contaminants' '/usr/local/FastQC/FastQC-0.11.2/Configuration/contaminant_list.txt'  '--adapters' '/usr/local/FastQC/FastQC-0.11.2/Configuration/adapter_list.txt'  '--extract'  '-o' '/exports/sasc/project-259-RNAseqChantalOSCC/analysis/01_HSL_student/samples/H68_clone_64_CD161_negative/lib_lib1/flexiprep/CLD4_S7_L008_R1_001.fastq.fastqc'  '/exports/lgtc/equipment/HiSeq/HS4000/180528_K00296_0322_AHVM7YBBXX/103398/Fastqs/CDuurland/CLD4_S7_L008_R1_001.fastq.gz' 

'/usr/local/sasc/programs/miniconda3/bin/java'  '-Xmx4096m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/exports/sasc/project-259-RNAseqChantalOSCC/src/01_student_test/.queue/tmp'  '-Dscala.concurrent.context.numThreads=1'  '-Dscala.concurrent.context.maxThreads=1'  '-cp' '/usr/local/sasc/programs/biopet/Biopet-v0.9.0.jar'  'nl.lumc.sasc.biopet.tools.ValidateFastq'  '-i' '/exports/lgtc/equipment/HiSeq/HS4000/180528_K00296_0322_AHVM7YBBXX/103398/Fastqs/CDuurland/CLD4_S7_L008_R1_001.fastq.gz'  '-j' '/exports/lgtc/equipment/HiSeq/HS4000/180528_K00296_0322_AHVM7YBBXX/103398/Fastqs/CDuurland/CLD4_S7_L008_R2_001.fastq.gz'
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I have no idea how to read it

what does it mean ?

(do you know how to use a cmd-line ?)

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14 months ago
Freiburg, Germany

You have commands on each line. Ignore the extraneous quoting. The first line is trivial, since FastQC is already available in Galaxy. The second command is ValidateFastq, which is not something I've ever seen someone actually use (it should be completely unnecessary).

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