Hello, I've tried running Monopogen with the below parameters and run into an error where there is a
Incorrect number of FORMAT fields at chr20:2998993 .. DP, 0 vs 1 of the chr20.gl.vcf file that gets generated.
bcftools view chr20.gl.vcf.gz -r chr20:2998993 shows me that that position does not have the correct # of columns (see below)
##FILTER=<ID=PASS,Description="All filters passed">
##samtoolsVersion=1.8+htslib-1.8
##samtoolsCommand=samtools mpileup -f /tmp/Monopogen/example/chr20_2Mb.hg38.fa -r chr20 -q 20 -Q 20 -t DP -d 10000000 -v /dbfs/FileStore/2023-h1-ancestry/data/monopogen_output/80_test/Bam/chr20.filter.bam
##reference=file:///tmp/Monopogen/example/chr20_2Mb.hg38.fa
##contig=<ID=chr1,length=248956422>
##contig=<ID=chr10,length=133797422>
##contig=<ID=chr11,length=135086622>
##contig=<ID=chr12,length=133275309>
##contig=<ID=chr13,length=114364328>
##contig=<ID=chr14,length=107043718>
##contig=<ID=chr15,length=101991189>
##contig=<ID=chr16,length=90338345>
##contig=<ID=chr17,length=83257441>
##contig=<ID=chr18,length=80373285>
##contig=<ID=chr19,length=58617616>
##contig=<ID=chr2,length=242193529>
##contig=<ID=chr20,length=64444167>
##contig=<ID=chr21,length=46709983>
##contig=<ID=chr22,length=50818468>
##contig=<ID=chr3,length=198295559>
##contig=<ID=chr4,length=190214555>
##contig=<ID=chr5,length=181538259>
##contig=<ID=chr6,length=170805979>
##contig=<ID=chr7,length=159345973>
##contig=<ID=chr8,length=145138636>
##contig=<ID=chr9,length=138394717>
##contig=<ID=chrM,length=16569>
##contig=<ID=chrX,length=156040895>
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##contig=<ID=KI270362.1,length=3530>
##contig=<ID=KI270517.1,length=3253>
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##contig=<ID=KI270528.1,length=2983>
##contig=<ID=KI270587.1,length=2969>
##contig=<ID=KI270364.1,length=2855>
##contig=<ID=KI270371.1,length=2805>
##contig=<ID=KI270333.1,length=2699>
##contig=<ID=KI270374.1,length=2656>
##contig=<ID=KI270411.1,length=2646>
##contig=<ID=KI270414.1,length=2489>
##contig=<ID=KI270510.1,length=2415>
##contig=<ID=KI270390.1,length=2387>
##contig=<ID=KI270375.1,length=2378>
##contig=<ID=KI270420.1,length=2321>
##contig=<ID=KI270509.1,length=2318>
##contig=<ID=KI270315.1,length=2276>
##contig=<ID=KI270302.1,length=2274>
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##contig=<ID=KI270530.1,length=2168>
##contig=<ID=KI270304.1,length=2165>
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##contig=<ID=KI270417.1,length=2043>
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##contig=<ID=KI270303.1,length=1942>
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##contig=<ID=KI270529.1,length=1899>
##contig=<ID=KI270425.1,length=1884>
##contig=<ID=KI270396.1,length=1880>
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##contig=<ID=KI270386.1,length=1788>
##contig=<ID=KI270465.1,length=1774>
##contig=<ID=KI270383.1,length=1750>
##contig=<ID=KI270384.1,length=1658>
##contig=<ID=KI270330.1,length=1652>
##contig=<ID=KI270372.1,length=1650>
##contig=<ID=KI270548.1,length=1599>
##contig=<ID=KI270580.1,length=1553>
##contig=<ID=KI270387.1,length=1537>
##contig=<ID=KI270391.1,length=1484>
##contig=<ID=KI270305.1,length=1472>
##contig=<ID=KI270373.1,length=1451>
##contig=<ID=KI270422.1,length=1445>
##contig=<ID=KI270316.1,length=1444>
##contig=<ID=KI270340.1,length=1428>
##contig=<ID=KI270338.1,length=1428>
##contig=<ID=KI270583.1,length=1400>
##contig=<ID=KI270334.1,length=1368>
##contig=<ID=KI270429.1,length=1361>
##contig=<ID=KI270393.1,length=1308>
##contig=<ID=KI270516.1,length=1300>
##contig=<ID=KI270389.1,length=1298>
##contig=<ID=KI270466.1,length=1233>
##contig=<ID=KI270388.1,length=1216>
##contig=<ID=KI270544.1,length=1202>
##contig=<ID=KI270310.1,length=1201>
##contig=<ID=KI270412.1,length=1179>
##contig=<ID=KI270395.1,length=1143>
##contig=<ID=KI270376.1,length=1136>
##contig=<ID=KI270337.1,length=1121>
##contig=<ID=KI270335.1,length=1048>
##contig=<ID=KI270378.1,length=1048>
##contig=<ID=KI270379.1,length=1045>
##contig=<ID=KI270329.1,length=1040>
##contig=<ID=KI270419.1,length=1029>
##contig=<ID=KI270336.1,length=1026>
##contig=<ID=KI270312.1,length=998>
##contig=<ID=KI270539.1,length=993>
##contig=<ID=KI270385.1,length=990>
##contig=<ID=KI270423.1,length=981>
##contig=<ID=KI270392.1,length=971>
##contig=<ID=KI270394.1,length=970>
##ALT=<ID=*,Description="Represents allele(s) other than observed.">
##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">
##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
##bcftools_viewVersion=1.8+htslib-1.8
##bcftools_viewCommand=view; Date=Wed Mar 15 02:47:19 2023
##bcftools_normVersion=1.8+htslib-1.8
##bcftools_normCommand=norm -m-both -f /tmp/Monopogen/example/chr20_2Mb.hg38.fa; Date=Wed Mar 15 02:47:19 2023
##bcftools_viewCommand=view -r chr20:2998993 /dbfs/FileStore/2023-h1-ancestry/data/monopogen_output/80_test/SCvarCall/chr20.gl.vcf.gz; Date=Wed Mar 15 03:18:53 2023
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 10x3_Lobe_19_D006_NeuN_4
[E::bcf_write] Broken VCF record, the number of columns at chr20:2998993 does not match the number of samples (0 vs 1)```
**Here's the output log**
[2023-03-15 20:01:59,456] INFO Monopogen.py Preparing varint calling pipeline...
[2023-03-15 20:01:59,457] INFO Monopogen.py Parameters in effect:
[2023-03-15 20:01:59,457] INFO Monopogen.py --subcommand = [SCvarCall]
[2023-03-15 20:01:59,457] INFO Monopogen.py --bamFile = [/dbfs/FileStore/2023-h1-ancestry/data/lattice/80.bam]
[2023-03-15 20:01:59,457] INFO Monopogen.py --step = [germline]
[2023-03-15 20:01:59,457] INFO Monopogen.py --mode = [single]
[2023-03-15 20:01:59,457] INFO Monopogen.py --chr = [chr20]
[2023-03-15 20:01:59,458] INFO Monopogen.py --out = [/dbfs/FileStore/2023-h1-ancestry/data/monopogen_output/80_test]
[2023-03-15 20:01:59,458] INFO Monopogen.py --reference = [/tmp/Monopogen/example/chr20_2Mb.hg38.fa]
[2023-03-15 20:01:59,458] INFO Monopogen.py --imputation_panel = [/tmp/Monopogen/example/CCDG_14151_B01_GRM_WGS_2020-08-05_chr20.filtered.shapeit2-duohmm-phased.vcf.gz]
[2023-03-15 20:01:59,458] INFO Monopogen.py --depth_filter = [200]
[2023-03-15 20:01:59,458] INFO Monopogen.py --depth_filter_monovar = [50]
[2023-03-15 20:01:59,458] INFO Monopogen.py --alt_ratio = [0.1]
[2023-03-15 20:01:59,458] INFO Monopogen.py --wildCluster = [2]
[2023-03-15 20:01:59,458] INFO Monopogen.py --mutationCluster = [1]
[2023-03-15 20:01:59,458] INFO Monopogen.py --max_mismatch = [3]
[2023-03-15 20:01:59,458] INFO Monopogen.py --max_softClipped = [5]
[2023-03-15 20:01:59,459] INFO Monopogen.py --app_path = [/tmp/Monopogen/apps]
[2023-03-15 20:01:59,459] INFO Monopogen.py --cell_cluster = [/tmp/Monopogen/example/cell_cluster.csv]
[2023-03-15 20:01:59,459] INFO Monopogen.py --logfile = [/dbfs/FileStore/2023-h1-ancestry/data/monopogen_output/80_test_chr20.log]
[2023-03-15 20:01:59,459] INFO Monopogen.py --samtools = [/tmp/Monopogen/apps/samtools]
[2023-03-15 20:01:59,459] INFO Monopogen.py --bcftools = [/tmp/Monopogen/apps/bcftools]
[2023-03-15 20:01:59,459] INFO Monopogen.py --bgzip = [/tmp/Monopogen/apps/bgzip]
[2023-03-15 20:01:59,459] INFO Monopogen.py --java = [java]
[2023-03-15 20:01:59,459] INFO Monopogen.py --beagle = [/tmp/Monopogen/apps/beagle.27Jul16.86a.jar]
[2023-03-15 20:01:59,459] INFO Monopogen.py Checking existence of essenstial resource files...
[2023-03-15 20:01:59,460] INFO Monopogen.py Checking dependencies...
[2023-03-15 20:01:59,566] INFO Monopogen.py Filtering bam files...
[2023-03-15 20:03:06,093] INFO Monopogen.py Performing Variant Calling...
[W::hts_idx_load2] The index file is older than the data file: /dbfs/FileStore/2023-h1-ancestry/data/monopogen_output/80_test/Bam/chr20.filter.bam.bai
[mpileup] 1 samples in 1 input files
(mpileup) Max depth is above 1M. Potential memory hog!
Reference allele mismatch at chr20:3000001 .. REF_SEQ:'A' vs VCF:'N'
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
Incorrect number of FORMAT fields at chr20:2998993 .. DP, 0 vs 1
Exception in thread "main" java.lang.IllegalArgumentException: VCF header line has 10 fields, but data line has 8 fields
File source:File source: /dbfs/FileStore/2023-h1-ancestry/data/monopogen_output/80_test/SCvarCall/chr20.gl.vcf.gz
[chr20, 2998993, ., T, <*>, 0, ., DP=9;I16=6,3,0,0,333]
at vcf.VcfRecord.fieldCountError(VcfRecord.java:221)
at vcf.VcfRecord.delimiters(VcfRecord.java:203)
at vcf.VcfRecord.(VcfRecord.java:87)
at vcf.VcfRecord.fromGTGL(VcfRecord.java:193)
at vcf.VcfIt.lambda$static$5(VcfIt.java:76)
at vcf.VcfIt.lambda$new$8(VcfIt.java:192)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Spliterators$ArraySpliterator.forEachRemaining(Spliterators.java:948)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
at java.util.stream.ReduceOps$ReduceTask.doLeaf(ReduceOps.java:747)
at java.util.stream.ReduceOps$ReduceTask.doLeaf(ReduceOps.java:721)
at java.util.stream.AbstractTask.compute(AbstractTask.java:327)
at java.util.concurrent.CountedCompleter.exec(CountedCompleter.java:731)
at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
at java.util.concurrent.ForkJoinPool$WorkQueue.pollAndExecCC(ForkJoinPool.java:1190)
at java.util.concurrent.ForkJoinPool.helpComplete(ForkJoinPool.java:1879)
at java.util.concurrent.ForkJoinPool.externalHelpComplete(ForkJoinPool.java:2467)
at java.util.concurrent.ForkJoinTask.externalAwaitDone(ForkJoinTask.java:324)
at java.util.concurrent.ForkJoinTask.doInvoke(ForkJoinTask.java:405)
at java.util.concurrent.ForkJoinTask.invoke(ForkJoinTask.java:734)
at java.util.stream.ReduceOps$ReduceOp.evaluateParallel(ReduceOps.java:714)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:233)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:566)
at vcf.VcfIt.fillEmissionBuffer(VcfIt.java:307)
at vcf.VcfIt.next(VcfIt.java:363)
at vcf.VcfIt.next(VcfIt.java:52)
at vcf.IntervalVcfIt.readNextRecord(IntervalVcfIt.java:110)
at vcf.IntervalVcfIt.next(IntervalVcfIt.java:92)
at vcf.IntervalVcfIt.next(IntervalVcfIt.java:36)
at main.Main.restrictToVcfMarkers(Main.java:343)
at main.Main.allData(Main.java:313)
at main.Main.main(Main.java:111)
gzip: /dbfs/FileStore/2023-h1-ancestry/data/monopogen_output/80_test/SCvarCall/chr20.gp.vcf.gz: No such file or directory
/dbfs/FileStore/2023-h1-ancestry/data/monopogen_output/80_test/SCvarCall/chr20.gp.vcf.gz: No such file or directory
[2023-03-15 20:26:35,885] INFO Monopogen.py Generating variant statistical information ...
[E::hts_open_format] Failed to open file "/dbfs/FileStore/2023-h1-ancestry/data/monopogen_output/80_test/SCvarCall/chr20.gp.vcf.gz" : No such file or directory
Traceback (most recent call last):
File "/tmp/Monopogen/src/Monopogen.py", line 519, in
main()
File "/tmp/Monopogen/src/Monopogen.py", line 514, in main
args.func(args)
File "/tmp/Monopogen/src/Monopogen.py", line 398, in SCvarCall
getDPinfo(args)
File "/tmp/Monopogen/src/Monopogen.py", line 152, in getDPinfo
gp_vcf_in = VariantFile(out + "/SCvarCall/" + args.chr + ".gp.vcf.gz")
File "pysam/libcbcf.pyx", line 4119, in pysam.libcbcf.VariantFile.init
File "pysam/libcbcf.pyx", line 4344, in pysam.libcbcf.VariantFile.open
FileNotFoundError: [Errno 2] could not open variant file b'/dbfs/FileStore/2023-h1-ancestry/data/monopogen_output/80_test/SCvarCall/chr20.gp.vcf.gz': No such file or directory
Hello, I've tried running Monopogen with the below parameters and run into an error where there is a
Incorrect number of FORMAT fields at chr20:2998993 .. DP, 0 vs 1
of the chr20.gl.vcf file that gets generated.bcftools view chr20.gl.vcf.gz -r chr20:2998993
shows me that that position does not have the correct # of columns (see below)[2023-03-15 20:01:59,456] INFO Monopogen.py Preparing varint calling pipeline... [2023-03-15 20:01:59,457] INFO Monopogen.py Parameters in effect: [2023-03-15 20:01:59,457] INFO Monopogen.py --subcommand = [SCvarCall] [2023-03-15 20:01:59,457] INFO Monopogen.py --bamFile = [/dbfs/FileStore/2023-h1-ancestry/data/lattice/80.bam] [2023-03-15 20:01:59,457] INFO Monopogen.py --step = [germline] [2023-03-15 20:01:59,457] INFO Monopogen.py --mode = [single] [2023-03-15 20:01:59,457] INFO Monopogen.py --chr = [chr20] [2023-03-15 20:01:59,458] INFO Monopogen.py --out =(VcfRecord.java:87)
at vcf.VcfRecord.fromGTGL(VcfRecord.java:193)
at vcf.VcfIt.lambda$static$5(VcfIt.java:76)
at vcf.VcfIt.lambda$new$8(VcfIt.java:192)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Spliterators$ArraySpliterator.forEachRemaining(Spliterators.java:948)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
at java.util.stream.ReduceOps$ReduceTask.doLeaf(ReduceOps.java:747)
at java.util.stream.ReduceOps$ReduceTask.doLeaf(ReduceOps.java:721)
at java.util.stream.AbstractTask.compute(AbstractTask.java:327)
at java.util.concurrent.CountedCompleter.exec(CountedCompleter.java:731)
at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
at java.util.concurrent.ForkJoinPool$WorkQueue.pollAndExecCC(ForkJoinPool.java:1190)
at java.util.concurrent.ForkJoinPool.helpComplete(ForkJoinPool.java:1879)
at java.util.concurrent.ForkJoinPool.externalHelpComplete(ForkJoinPool.java:2467)
at java.util.concurrent.ForkJoinTask.externalAwaitDone(ForkJoinTask.java:324)
at java.util.concurrent.ForkJoinTask.doInvoke(ForkJoinTask.java:405)
at java.util.concurrent.ForkJoinTask.invoke(ForkJoinTask.java:734)
at java.util.stream.ReduceOps$ReduceOp.evaluateParallel(ReduceOps.java:714)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:233)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:566)
at vcf.VcfIt.fillEmissionBuffer(VcfIt.java:307)
at vcf.VcfIt.next(VcfIt.java:363)
at vcf.VcfIt.next(VcfIt.java:52)
at vcf.IntervalVcfIt.readNextRecord(IntervalVcfIt.java:110)
at vcf.IntervalVcfIt.next(IntervalVcfIt.java:92)
at vcf.IntervalVcfIt.next(IntervalVcfIt.java:36)
at main.Main.restrictToVcfMarkers(Main.java:343)
at main.Main.allData(Main.java:313)
at main.Main.main(Main.java:111)
gzip: /dbfs/FileStore/2023-h1-ancestry/data/monopogen_output/80_test/SCvarCall/chr20.gp.vcf.gz: No such file or directory
/dbfs/FileStore/2023-h1-ancestry/data/monopogen_output/80_test/SCvarCall/chr20.gp.vcf.gz: No such file or directory
[2023-03-15 20:26:35,885] INFO Monopogen.py Generating variant statistical information ...
[E::hts_open_format] Failed to open file "/dbfs/FileStore/2023-h1-ancestry/data/monopogen_output/80_test/SCvarCall/chr20.gp.vcf.gz" : No such file or directory
Traceback (most recent call last):
File "/tmp/Monopogen/src/Monopogen.py", line 519, in
main()
File "/tmp/Monopogen/src/Monopogen.py", line 514, in main
args.func(args)
File "/tmp/Monopogen/src/Monopogen.py", line 398, in SCvarCall
getDPinfo(args)
File "/tmp/Monopogen/src/Monopogen.py", line 152, in getDPinfo
gp_vcf_in = VariantFile(out + "/SCvarCall/" + args.chr + ".gp.vcf.gz")
File "pysam/libcbcf.pyx", line 4119, in pysam.libcbcf.VariantFile.init
File "pysam/libcbcf.pyx", line 4344, in pysam.libcbcf.VariantFile.open
FileNotFoundError: [Errno 2] could not open variant file
[/dbfs/FileStore/2023-h1-ancestry/data/monopogen_output/80_test]
[2023-03-15 20:01:59,458] INFO Monopogen.py --reference = [/tmp/Monopogen/example/chr20_2Mb.hg38.fa] [2023-03-15 20:01:59,458] INFO Monopogen.py --imputation_panel = [/tmp/Monopogen/example/CCDG_14151_B01_GRM_WGS_2020-08-05_chr20.filtered.shapeit2-duohmm-phased.vcf.gz] [2023-03-15 20:01:59,458] INFO Monopogen.py --depth_filter = [200] [2023-03-15 20:01:59,458] INFO Monopogen.py --depth_filter_monovar = [50] [2023-03-15 20:01:59,458] INFO Monopogen.py --alt_ratio = [0.1] [2023-03-15 20:01:59,458] INFO Monopogen.py --wildCluster = [2] [2023-03-15 20:01:59,458] INFO Monopogen.py --mutationCluster = [1] [2023-03-15 20:01:59,458] INFO Monopogen.py --max_mismatch = [3] [2023-03-15 20:01:59,458] INFO Monopogen.py --max_softClipped = [5] [2023-03-15 20:01:59,459] INFO Monopogen.py --app_path = [/tmp/Monopogen/apps] [2023-03-15 20:01:59,459] INFO Monopogen.py --cell_cluster = [/tmp/Monopogen/example/cell_cluster.csv] [2023-03-15 20:01:59,459] INFO Monopogen.py --logfile = [/dbfs/FileStore/2023-h1-ancestry/data/monopogen_output/80_test_chr20.log] [2023-03-15 20:01:59,459] INFO Monopogen.py --samtools = [/tmp/Monopogen/apps/samtools] [2023-03-15 20:01:59,459] INFO Monopogen.py --bcftools = [/tmp/Monopogen/apps/bcftools] [2023-03-15 20:01:59,459] INFO Monopogen.py --bgzip = [/tmp/Monopogen/apps/bgzip] [2023-03-15 20:01:59,459] INFO Monopogen.py --java = [java] [2023-03-15 20:01:59,459] INFO Monopogen.py --beagle = [/tmp/Monopogen/apps/beagle.27Jul16.86a.jar] [2023-03-15 20:01:59,459] INFO Monopogen.py Checking existence of essenstial resource files... [2023-03-15 20:01:59,460] INFO Monopogen.py Checking dependencies... [2023-03-15 20:01:59,566] INFO Monopogen.py Filtering bam files... [2023-03-15 20:03:06,093] INFO Monopogen.py Performing Variant Calling... [W::hts_idx_load2] The index file is older than the data file: /dbfs/FileStore/2023-h1-ancestry/data/monopogen_output/80_test/Bam/chr20.filter.bam.bai [mpileup] 1 samples in 1 input files (mpileup) Max depth is above 1M. Potential memory hog! Reference allele mismatch at chr20:3000001 .. REF_SEQ:'A' vs VCF:'N' Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid Incorrect number of FORMAT fields at chr20:2998993 .. DP, 0 vs 1 Exception in thread "main" java.lang.IllegalArgumentException: VCF header line has 10 fields, but data line has 8 fields File source:File source: /dbfs/FileStore/2023-h1-ancestry/data/monopogen_output/80_test/SCvarCall/chr20.gl.vcf.gz [chr20, 2998993, ., T, <*>, 0, ., DP=9;I16=6,3,0,0,333] at vcf.VcfRecord.fieldCountError(VcfRecord.java:221) at vcf.VcfRecord.delimiters(VcfRecord.java:203) at vcf.VcfRecord.b'/dbfs/FileStore/2023-h1-ancestry/data/monopogen_output/80_test/SCvarCall/chr20.gp.vcf.gz'
: No such file or directory