Hi, I met an error when processing repeatmask:
nextflow run .../Software/GraffiTE/main.nf \
--assemblies assemblies.csv \
--TE_library Libraries/RepbaseforRepeatMasker.fasta \
--reference gadMor3.0_shorten.fa \
--reads reads.csv \
--cores 16
executor > local (3)
[e6/7ef80e] process > svim_asm (1) [100%] 1 of 1 ✔
[e6/ad812a] process > survivor_merge [100%] 1 of 1 ✔
[13/56bd72] process > repeatmask_VCF (1) [ 0%] 0 of 1
[- ] process > tsd_prep -
[- ] process > tsd_search -
[- ] process > tsd_report -
[- ] process > pangenie -
[- ] process > merge_VCFs -
Error executing process > 'repeatmask_VCF (1)'
Caused by:
Process repeatmask_VCF (1)
terminated with an error exit status (255)
Command executed:
repmask_vcf.sh genotypes.vcf genotypes_repmasked.vcf.gz RepbaseForRepeatMasker.fasta
bcftools view -G genotypes_repmasked.vcf.gz | awk -v FS=' ' -v OFS=' ' '{if($0 ~ /#CHROM/) {$9 = "FORMAT"; $10 = "ref"; print $0} else if(substr($0, 1, 1) == "#") {print $0} else {$9 = "GT"; $10 = "1|0"; print $0}}' | awk 'NR==1{print; print "##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">"} NR!=1' | bcftools view -i 'INFO/total_match_span > 0.80' -o genotypes_repmasked_temp.vcf
fix_vcf.py --ref gadMor3.0_shorten.fa --vcf_in genotypes_repmasked_temp.vcf --vcf_out genotypes_repmasked_filtered.vcf
Command exit status:
255
Command output:
column count: 10
Meta line 260 read in.
All meta lines processed.
gt matrix initialized.
Character matrix gt created.
Character matrix gt rows: 31290
Character matrix gt cols: 10
skip: 0
nrows: 31290
row_num: 0
Processed variant 1000
Processed variant 2000
Processed variant 3000
Processed variant 4000
Processed variant 5000
Processed variant 6000
Processed variant 7000
Processed variant 8000
Processed variant 9000
Processed variant 10000
Processed variant 11000
Processed variant 12000
Processed variant 13000
Processed variant 14000
Processed variant 15000
Processed variant 16000
Processed variant 17000
Processed variant 18000
Processed variant 19000
Processed variant 20000
Processed variant 21000
Processed variant 22000
Processed variant 23000
Processed variant 24000
Processed variant 25000
Processed variant 26000
Processed variant 27000
Processed variant 28000
Processed variant 29000
Processed variant 30000
Processed variant 31000
Processed variant: 31290
All variants processed
[1] "CHROM" "POS" "qry_id" "n_hits"
[5] "fragmts" "match_lengths" "repeat_ids" "matching_classes"
[9] "strands" "RM_id"
compute repeat proportion for each SVs...
Mammalian filters OFF, writing vcf...
Command error:
Phase 1 : exact matches
#################################
85 matches found in non-fuzzy phase
#################################
4680 elements found without match
#################################
#################################
Output file should be manually edited to take into account all specificities of the considered organism!
#################################
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
***** *** vcfR *** *****
This is vcfR 1.13.0
browseVignettes('vcfR') # Documentation
citation('vcfR') # Citation
***** ***** ***** *****
Warning message:
The x
argument of as_tibble.matrix()
must have unique column names if
.name_repair
is omitted as of tibble 2.0.0.
i Using compatibility .name_repair
.
awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted
mktemp: failed to create file via template '/scratch/SlurmTMP/user.7524169/tmp.XXXXXXXXXX': No such file or directory
.../Software/GraffiTE/bin/repmask_vcf.sh: line 146: ${HDR_FILE}: ambiguous redirect
.../Software/GraffiTE/bin/repmask_vcf.sh: line 147: ${HDR_FILE}: ambiguous redirect
.../Software/GraffiTE/bin/repmask_vcf.sh: line 148: ${HDR_FILE}: ambiguous redirect
.../Software/GraffiTE/bin/repmask_vcf.sh: line 149: ${HDR_FILE}: ambiguous redirect
.../Software/GraffiTE/bin/repmask_vcf.sh: line 150: ${HDR_FILE}: ambiguous redirect
.../Software/GraffiTE/bin/repmask_vcf.sh: line 151: ${HDR_FILE}: ambiguous redirect
.../Software/GraffiTE/bin/repmask_vcf.sh: line 152: ${HDR_FILE}: ambiguous redirect
.../Software/GraffiTE/bin/repmask_vcf.sh: line 153: ${HDR_FILE}: ambiguous redirect
.../Software/GraffiTE/bin/repmask_vcf.sh: line 154: ${HDR_FILE}: ambiguous redirect
.../Software/GraffiTE/bin/repmask_vcf.sh: line 155: ${HDR_FILE}: ambiguous redirect
sort: cannot create temporary file in '/scratch/SlurmTMP/user.7524169': No such file or directory
[E::hts_open_format] Failed to open file "CHROM,POS,~ID,INFO/n_hits,INFO/fragmts,INFO/match_lengths,INFO/repeat_ids,INFO/matching_classes,INFO/RM_hit_strands,INFO/RM_hit_IDs,INFO/total_match_length,INFO/total_match_span" : No such file or directory
Failed to read from CHROM,POS,~ID,INFO/n_hits,INFO/fragmts,INFO/match_lengths,INFO/repeat_ids,INFO/matching_classes,INFO/RM_hit_strands,INFO/RM_hit_IDs,INFO/total_match_length,INFO/total_match_span: No such file or directory
Failed to read from standard input: unknown file type
Work dir:
/.../work/13/56bd72c9c56695ebc011428b61aac4
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh
.command.sh:
#!/bin/bash -ue repmask_vcf.sh genotypes.vcf genotypes_repmasked.vcf.gz RepbaseForRepeatMasker.fasta bcftools view -G genotypes_repmasked.vcf.gz | awk -v FS=' ' -v OFS=' ' '{if($0 ~ /#CHROM/) {$9 = "FORMAT"; $10 = "ref"; print $0} else if(substr($0, 1, 1) == "#") {print $0} else {$9 = "GT"; $10 = "1|0"; print $0}}' | awk 'NR==1{print; print "##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">"} NR!=1' | bcftools view -i 'INFO/total_match_span > 0.80' -o genotypes_repmasked_temp.vcf fix_vcf.py --ref gadMor3.0_shorten.fa --vcf_in genotypes_repmasked_temp.vcf --vcf_out genotypes_repmasked_filtered.vcf