Entering edit mode
4.9 years ago
ahammedy02
▴
10
I'm trying to run some quality control on aligned RNA Sequence reads, these were aligned and merged into single files using STAR and SAMTOOLS. I've noticed the file name of QC.xxxxxxxxxxxx.log changes to random values and the program is trying to find this random file for whatever reason which of course doesn't exist.
$ java -Xmx4g -jar /gpfs/ts0/home/mya205/packages/QoRTs/qortsstable/QoRTs-STABLE.jar QC \ /gpfs/ts0/projects/Research_Project-T113519/ftp1.sequencing.exeter.ac.uk/H0243/24_rna_alignment/ftp3013_KOA_xAligned.sortedByCoord.out.bam \ /gpfs/ts0/projects/Research_Project-T113519/STAR_files/referenceGenomes/GRCh38/Homo_sapiens_GRCh38_98.gtf \ /gpfs/ts0/projects/Research_Project-T113519/qc_collection/QoRTs_output
OUTPUT:
Starting QoRTs v1.3.6 (Compiled Tue Sep 25 11:21:46 EDT 2018)
Starting time: (Mon Nov 25 10:12:03 GMT 2019)
INPUT_COMMAND(QC)
INPUT_ARG(infile)= /gpfs/ts0/projects/Research_Project-T113519/ftp1.sequencing.exeter.ac.uk/H0243/24_rna_alignment/ftp3013_KOA_xAligned.sortedByCoord.out.bam
INPUT_ARG(gtffile)= /gpfs/ts0/projects/Research_Project-T113519/STAR_files/referenceGenomes/GRCh38/Homo_sapiens_GRCh38_98.gtf
INPUT_ARG(outdir)= /gpfs/ts0/projects/Research_Project-T113519/qc_collection/QoRTs_output
Creating Directory: /gpfs/ts0/projects/Research_Project-T113519/qc_collection/QoRTs_output
============================FATAL_ERROR============================
QoRTs encountered a FATAL ERROR. For general help, use command:
java -jar path/to/jar/QoRTs.jar --man
============================FATAL_ERROR============================
Error info:
Exception in thread "main" java.io.FileNotFoundException: /gpfs/ts0/projects/Research_Project-T113519/qc_collection/QoRTs_output/QC.9gZCUFz5rnuA.log (No such file or directory)
at java.io.FileOutputStream.open0(Native Method)
at java.io.FileOutputStream.open(FileOutputStream.java:270)
at java.io.FileOutputStream.(FileOutputStream.java:213)
at java.io.FileOutputStream.(FileOutputStream.java:101)
at java.io.FileWriter.(FileWriter.java:63)
at internalUtils.fileUtils$.openWriter(fileUtils.scala:64)
at internalUtils.Reporter$AddedFileReportLogger.(Reporter.scala:123)
at internalUtils.Reporter$.init_completeLogFile(Reporter.scala:215)
at qcUtils.runAllQC$.run(runAllQC.scala:748)
at qcUtils.runAllQC$allQC_runner.run(runAllQC.scala:680)
at runner.runner$.main(runner.scala:98)
at runner.runner.main(runner.scala)
