GATK Index Feature FIle No suitable codecs found
Answered
I am trying to get my Index Feature File from my bed file. I have used the command before and it worked but when I changed the bed file it stopped working.
My GATK version used: 4.4.0.0.
My Exact command used:
- Where the `bed_file` is a variable containing the path to the Agilent Version 6 hg19 bed file.
- Where `singularity_image` contains the path to the GATK 4.4.0.0 singularity image.
singularityexec$singularity_image/gatk/gatk--java-options-Xms8000m\
IndexFeatureFile\
--input ${bed_file}
My Entire program log/error:
21:44:13.751 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
21:44:13.788 INFO IndexFeatureFile - ------------------------------------------------------------
21:44:13.791 INFO IndexFeatureFile - The Genome Analysis Toolkit (GATK) v4.4.0.0
21:44:13.792 INFO IndexFeatureFile - For support and documentation go to https://software.broadinstitute.org/gatk/
21:44:13.792 INFO IndexFeatureFile - Executing as Name@Node on Linux v4.19.0-23-amd64 amd64
21:44:13.793 INFO IndexFeatureFile - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10-Ubuntu-0ubuntu118.04.1
21:44:13.794 INFO IndexFeatureFile - Start Date/Time: August 28, 2023 at 9:44:13 PM GMT
21:44:13.794 INFO IndexFeatureFile - ------------------------------------------------------------
21:44:13.794 INFO IndexFeatureFile - ------------------------------------------------------------
21:44:13.795 INFO IndexFeatureFile - HTSJDK Version: 3.0.5
21:44:13.796 INFO IndexFeatureFile - Picard Version: 3.0.0
21:44:13.797 INFO IndexFeatureFile - Built for Spark Version: 3.3.1
21:44:13.797 INFO IndexFeatureFile - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:44:13.798 INFO IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:44:13.799 INFO IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:44:13.799 INFO IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:44:13.800 INFO IndexFeatureFile - Deflater: IntelDeflater
21:44:13.812 INFO IndexFeatureFile - Inflater: IntelInflater
21:44:13.814 INFO IndexFeatureFile - GCS max retries/reopens: 20
21:44:13.815 INFO IndexFeatureFile - Requester pays: disabled
21:44:13.815 INFO IndexFeatureFile - Initializing engine
21:44:13.816 INFO IndexFeatureFile - Done initializing engine
21:44:13.890 INFO IndexFeatureFile - Shutting down engine
[August 28, 2023 at 9:44:13 PM GMT] org.broadinstitute.hellbender.tools.IndexFeatureFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=8388608000
***********************************************************************
A USER ERROR has occurred: Cannot read file:///path/to/Agilent/version/6/bed/file/for/hg19/ because no suitable codecs found
***********************************************************************
Paths have been removed in accordance with my HPCs guidelines. How can I fix this?
-
Hi
Can you send the first ~50 lines of your bed file as an example? I cannot seem to replicate the issue and unmodified fresh downloaded bed files from agilent earray seems to get indexed without any issues.
-
If I do `head -n 50 file.bed` for the bed file to get the first 50 lines I get the following:
browser position chr1:12190-12227
track name="Target Regions" description="Agilent SureSelect DNA - SureSelect Human All Exon V6" color=0,0,128 db=hg19
chr1 12189 12227
chr1 12594 12721
chr1 13402 13639
chr1 17368 17436
chr1 30365 30503
chr1 35137 35174
chr1 35276 35481
chr1 35720 35736
chr1 69088 69970
chr1 138529 139696
chr1 139789 139792
chr1 324342 324345
chr1 324438 325588
chr1 327745 328186
chr1 367656 368599
chr1 621093 622036
chr1 664484 665108
chr1 721405 721909
chr1 762079 762571
chr1 861319 861395
chr1 865532 865718
chr1 866416 866471
chr1 871149 871278
chr1 874417 874511
chr1 874651 874842
chr1 876521 876688
chr1 877513 877633
chr1 877787 877870
chr1 877936 878440
chr1 878630 878759
chr1 879075 879706
chr1 880071 880182
chr1 880421 880528
chr1 880895 881035
chr1 881550 881668
chr1 881779 881970
chr1 883508 883614
chr1 883867 883985
chr1 886504 886620
chr1 887377 887521
chr1 887789 887982
chr1 888552 888670
chr1 889159 889274
chr1 889381 889551
chr1 891300 891395
chr1 891472 891597
chr1 892271 892407
chr1 892476 892655This looks normal to me. Why is this not working?
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Hi Y R
Your path to bed file is just the folder but not the bed file itself. Input for this tool must be the absolute path of the bed file like
/path/to/bedfile.bed
I hope this helps.
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I have - I am not sure why but it seems that a clean run worked.
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