How do I read a logfile?
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'
• 1,389 views
•
link
updated
by
Devon Ryan
•
written
by
c.clarido
•
written
by
c.clarido
1 answer
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).
• 1 views
•
link
written
by
Devon Ryan
Log in to answer this question.
what does it mean ?
(do you know how to use a cmd-line ?)