GatherBQSRReports OSError: [Errno 2] No such file or directory, but does not show which is missing
I am currently using GATK 4.1.2 for analysis and encountered error 'OSError: [Errno 2] No such file or directory, but does not show which is missing ' when running GatherBQSRReports.
With the error log, I was not able to detect what file or directory is missing. Therefore, I have checked all the input files are at the right path and if the files are truncated, where found nothing is wrong.
Would there be something that I might be missing??
Thank you!
REQUIRED for all errors and issues:
a) GATK version used:
gatk-4.1.2.0
b) Exact command used:
$ /gpfs/gibbs/pi/ycga/mane/ycga_bioinfo/programs/gatk-4.1.2.0/gatk
GatherBQSRReports -I TWE0815.3/gatkExome_working/TWE0815.3.recal.1.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.2.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.3.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.4.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.5.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.6.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.7.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.8.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.9.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.10.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.11.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.12.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.13.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.14.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.15.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.16.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.17.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.18.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.19.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.20.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.21.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.22.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.23.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.24.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.25.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.26.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.27.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.28.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.29.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.30.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.31.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.32.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.33.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.34.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.35.table -I TWE0815.3/gatkExome_working/TWE0815.3.recal.36.table -O TWE0815.3/gatkExome_working/TWE0815.3.recal.table
c) Entire program log:
-
This error message is not specific to GATK related tool but the installation of GATK itself. Looks like gatk python script is unable to find the proper jar files in the path to start the run. Can you check your GATK installation folder?
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