Failed to open or file not indexed:

[colinhercus]

I'm getting an error while trying to run hap.py. This is using a script I've successfully run many times.

This is the stderr log from the run.

${HAPPY} $GIABSNPS q0.recode.vcf -f $GIABBED -T $TARGETS -o q0.hap.py --scratch-prefix tmp --keep-scratch [I] Total VCF records: 3775119 [I] Non-reference VCF records: 3775119 [W] variant at chr1:914414 has more than one base of reference padding [W] Variants that have >1 base of reference padding: 5528 [I] Total VCF records: 105704 [I] Non-reference VCF records: 39408 2022-05-23 17:25:13,378 ERROR [stderr] Added region file '/st2/benchmarking.qa/na12878/NextSeq/Rep1/V4.03.05.Rep1.070/tmp/tmpz8v8xf.bed' as 'CONF' (29676 intervals) 2022-05-23 17:25:13,378 ERROR [stderr] Added region file '/st2/benchmarking.qa/na12878/GIAB/HG001_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdelUCSC.bed' as 'CONF' (599232 intervals) 2022-05-23 17:25:13,378 ERROR [stderr] Failed to open or file not indexed: /st2/benchmarking.qa/na12878/NextSeq/Rep1/V4.03.05.Rep1.070/tmp/hap.py.result.3zy2Wr.vcf.gz 2022-05-23 17:25:13,378 ERROR [stderr] 2022-05-23 17:25:13,378 ERROR Command 'quantify /st2/benchmarking.qa/na12878/NextSeq/Rep1/V4.03.05.Rep1.070/tmp/hap.py.result.3zy2Wr.vcf.gz -o q0.hap.py.roc.tsv -r /st2/sq/grch37decoy/hs37d5.fa --threads 32 --output-vtc 0 --output-rocs 1 --type xcmp --qq IQQ --qq-header QUAL --roc-delta 0.500000 --clean-info 1 --fix-chr-regions 0 -v q0.hap.py.vcf.gz -R 'CONF_VARS:/st2/benchmarking.qa/na12878/NextSeq/Rep1/V4.03.05.Rep1.070/tmp/tmpz8v8xf.bed' -R 'CONF:/st2/benchmarking.qa/na12878/GIAB/HG001_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdelUCSC.bed' --roc-regions ''' returned non-zero exit status 1 2022-05-23 17:25:13,378 ERROR Traceback (most recent call last): 2022-05-23 17:25:13,378 ERROR File "/st2/downloads/hap.py/pysam/bin/hap.py", line 460, in 2022-05-23 17:25:13,379 ERROR main() 2022-05-23 17:25:13,379 ERROR File "/st2/downloads/hap.py/pysam/bin/hap.py", line 445, in main 2022-05-23 17:25:13,379 ERROR qfy.quantify(args) 2022-05-23 17:25:13,379 ERROR File "/st2/downloads/hap.py/pysam/bin/qfy.py", line 129, in quantify 2022-05-23 17:25:13,379 ERROR strat_fixchr=args.strat_fixchr) 2022-05-23 17:25:13,379 ERROR File "/st2/downloads/hap.py/pysam/lib/python27/Haplo/quantify.py", line 178, in run_quantify 2022-05-23 17:25:13,379 ERROR subprocess.check_call(run_str, shell=True, stdout=tfo, stderr=tfe) 2022-05-23 17:25:13,379 ERROR File "/usr/lib/python2.7/subprocess.py", line 190, in check_call 2022-05-23 17:25:13,379 ERROR raise CalledProcessError(retcode, cmd) 2022-05-23 17:25:13,379 ERROR CalledProcessError: Command 'quantify /st2/benchmarking.qa/na12878/NextSeq/Rep1/V4.03.05.Rep1.070/tmp/hap.py.result.3zy2Wr.vcf.gz -o q0.hap.py.roc.tsv -r /st2/sq/grch37decoy/hs37d5.fa --threads 32 --output-vtc 0 --output-rocs 1 --type xcmp --qq IQQ --qq-header QUAL --roc-delta 0.500000 --clean-info 1 --fix-chr-regions 0 -v q0.hap.py.vcf.gz -R 'CONF_VARS:/st2/benchmarking.qa/na12878/NextSeq/Rep1/V4.03.05.Rep1.070/tmp/tmpz8v8xf.bed' -R 'CONF:/st2/benchmarking.qa/na12878/GIAB/HG001_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdelUCSC.bed' --roc-regions ''' returned non-zero exit status 1

tabix is in the PATH.

Any ideas what might cause this?

Thanks, Colin