Question: FileNotFoundException for QoRTs QC program?
0
gravatar for ahammedy02
6 months ago by
ahammedy0210
ahammedy0210 wrote:

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)
rna-seq qorts • 134 views
ADD COMMENTlink modified 6 months ago by lakhujanivijay5.0k • written 6 months ago by ahammedy0210
1
gravatar for ahammedy02
6 months ago by
ahammedy0210
ahammedy0210 wrote:

Figured out the error, anyone else wondering, do not include any spaces after specifiying file directory with "\".

ADD COMMENTlink written 6 months ago by ahammedy0210
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