phyluce_assembly_get_trinity_coverage gatk issue

[mprebus]

I have been getting the following error when trying to run the phyluce_assembly_get_trinity_coverage script:

2019-12-10 11:01:00,484 - phyluce_assembly_get_trinity_coverage - INFO - ========= Starting phyluce_assembly_get_trinity_coverage ======== 2019-12-10 11:01:00,484 - phyluce_assembly_get_trinity_coverage - INFO - Version: git fatal: Not a git repository: '/home/mborowiec/phyluce-master/.git' 2019-12-10 11:01:00,484 - phyluce_assembly_get_trinity_coverage - INFO - Argument --assembler: trinity 2019-12-10 11:01:00,484 - phyluce_assembly_get_trinity_coverage - INFO - Argument --assemblies: /home/mborowiec/Matt/16173R/trinity-assembly 2019-12-10 11:01:00,484 - phyluce_assembly_get_trinity_coverage - INFO - Argument --assemblo_config: /home/mborowiec/Matt/16173R/trinity.conf 2019-12-10 11:01:00,484 - phyluce_assembly_get_trinity_coverage - INFO - Argument --bwa_mem: False 2019-12-10 11:01:00,484 - phyluce_assembly_get_trinity_coverage - INFO - Argument --clean: False 2019-12-10 11:01:00,484 - phyluce_assembly_get_trinity_coverage - INFO - Argument --cores: 9 2019-12-10 11:01:00,484 - phyluce_assembly_get_trinity_coverage - INFO - Argument --log_path: /home/mborowiec/Matt/16173R 2019-12-10 11:01:00,485 - phyluce_assembly_get_trinity_coverage - INFO - Argument --subfolder: raw-reads 2019-12-10 11:01:00,485 - phyluce_assembly_get_trinity_coverage - INFO - Argument --trim: False 2019-12-10 11:01:00,485 - phyluce_assembly_get_trinity_coverage - INFO - Argument --verbosity: INFO 2019-12-10 11:01:00,485 - phyluce_assembly_get_trinity_coverage - INFO - Getting input filenames 2019-12-10 11:01:00,487 - phyluce_assembly_get_trinity_coverage - INFO - ---------- Processing Leptothorax_wilsoni_P378_trinity ---------- 2019-12-10 11:01:00,487 - phyluce_assembly_get_trinity_coverage - INFO - Finding fastq/fasta files 2019-12-10 11:01:00,489 - phyluce_assembly_get_trinity_coverage - INFO - File type is fastq 2019-12-10 11:01:00,490 - phyluce_assembly_get_trinity_coverage - INFO - Running bwa indexing against /home/mborowiec/Matt/16173R/trinity-assembly/Leptothorax_wilsoni_P378_trinity/contigs.fasta 2019-12-10 11:01:04,568 - phyluce_assembly_get_trinity_coverage - INFO - Indexing fasta for Leptothorax_wilsoni_P378_trinity 2019-12-10 11:01:04,693 - phyluce_assembly_get_trinity_coverage - INFO - Creating FASTA dict for Leptothorax_wilsoni_P378_trinity 2019-12-10 11:01:05,465 - phyluce_assembly_get_trinity_coverage - INFO - Creating read index file for Leptothorax_wilsoni_P378-READ1.fastq.gz 2019-12-10 11:01:20,633 - phyluce_assembly_get_trinity_coverage - INFO - Creating read index file for Leptothorax_wilsoni_P378-READ2.fastq.gz 2019-12-10 11:01:37,741 - phyluce_assembly_get_trinity_coverage - INFO - Building BAM for Leptothorax_wilsoni_P378_trinity 2019-12-10 11:02:12,203 - phyluce_assembly_get_trinity_coverage - INFO - Cleaning BAM for Leptothorax_wilsoni_P378_trinity 2019-12-10 11:02:31,722 - phyluce_assembly_get_trinity_coverage - INFO - Adding RG header to BAM for Leptothorax_wilsoni_P378_trinity 2019-12-10 11:03:09,891 - phyluce_assembly_get_trinity_coverage - INFO - Marking read duplicates from BAM for Leptothorax_wilsoni_P378_trinity 2019-12-10 11:03:40,379 - phyluce_assembly_get_trinity_coverage - INFO - Indexing BAM for Leptothorax_wilsoni_P378_trinity 2019-12-10 11:03:42,107 - phyluce_assembly_get_trinity_coverage - INFO - Computing coverage with GATK for Leptothorax_wilsoni_P378_trinity 2019-12-10 11:03:42,867 - phyluce_assembly_get_trinity_coverage - INFO - Screening contigs for coverage Traceback (most recent call last): File "/home/mborowiec/anaconda2/envs/phyluce/bin/phyluce_assembly_get_trinity_coverage", line 238, in main() File "/home/mborowiec/anaconda2/envs/phyluce/bin/phyluce_assembly_get_trinity_coverage", line 228, in main overall_contigs = gatk.get_untrimmed_coverage_from_output(log, sample, assembly_pth, coverage, args.assembler) File "/home/mborowiec/phyluce-master/phyluce/gatk.py", line 216, in get_untrimmed_coverage_from_output with open(coverage, 'rU') as infile: IOError: [Errno 2] No such file or directory: '/home/mborowiec/Matt/16173R/trinity-assembly/Leptothorax_wilsoni_P378_trinity/Leptothorax_wilsoni_P378_trinity-coverage'

The GATK-coverage-out.log file contains the following:

ERROR ------------------------------------------------------------------------------------------

ERROR stack trace

java.lang.ExceptionInInitializerError at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.(GenomeAnalysisEngine.java:160) at org.broadinstitute.sting.gatk.CommandLineExecutable.(CommandLineExecutable.java:53) at org.broadinstitute.sting.gatk.CommandLineGATK.(CommandLineGATK.java:54) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:90) Caused by: java.lang.NullPointerException at org.reflections.Reflections.scan(Reflections.java:220) at org.reflections.Reflections.scan(Reflections.java:166) at org.reflections.Reflections.(Reflections.java:94) at org.broadinstitute.sting.utils.classloader.PluginManager.(PluginManager.java:77) ... 4 more

ERROR ------------------------------------------------------------------------------------------

ERROR A GATK RUNTIME ERROR has occurred (version 2.3-9-gdcdccbb):

ERROR

ERROR Please visit the wiki to see if this is a known problem

ERROR If not, please post the error, with stack trace, to the GATK forum

ERROR Visit our website and forum for extensive documentation and answers to

ERROR commonly asked questions http://www.broadinstitute.org/gatk

ERROR

ERROR MESSAGE: Code exception (see stack trace for error itself)

ERROR ------------------------------------------------------------------------------------------

[brantfaircloth]

have you checked compatibility between java and this version of GATK by any chance? The error appears to be in GATK and not in phyluce...

[mprebus]

I was able to resolve this issue by using GATK v3.8 with java 8. Thanks very much!