Entering edit mode
6.3 years ago
c.clarido
▴
110
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'
what does it mean ?
(do you know how to use a cmd-line ?)