alnusmeinata
commented
3 months ago I use Pop0BJ_Teak049.F.fq.gz file format and I enclose reference genome in the directory. for reference genome it was originally .fa format and I change the name to .fasta. I am new to this field and need help. thank you very much.
dDocent version 2.9.4 started Tue Mar 26 16:27:46 JST 2024
804 individuals are detected. Is this correct? Enter yes or no and press [ENTER] Proceeding with 804 individuals dDocent detects 28 processors available on this system. Please enter the maximum number of processors to use for this analysis.
Do you want to quality trim your reads? Type yes or no and press [ENTER]? (base) [alnus@n000 ddocent_teak2]$ view dDocent_main.LOG
/usr/bin/bash: line 1: 20108 Illegal instruction freebayes -b cat-RRG.bam -t mapped.$1.bed -v raw.$1.vcf -f reference.fasta -m 5 -q 5 -E 3 --min-repeat-entropy 1 -V --populations popmap -n 10 -F 0.1 &>fb.$1.error.log parallel: This job failed: call_genos 22010
ERROR: freebayes instance DID NOT COMPLETE
See below: /usr/bin/bash: line 1: 20111 Illegal instruction freebayes -b cat-RRG.bam -t mapped.$1.bed -v raw.$1.vcf -f reference.fasta -m 5 -q 5 -E 3 --min-repeat-entropy 1 -V --populations popmap -n 10 -F 0.1 &>fb.$1.error.log parallel: This job failed: call_genos 22862
ERROR: freebayes instance DID NOT COMPLETE
See below: /usr/bin/bash: line 1: 20113 Illegal instruction freebayes -b cat-RRG.bam -t mapped.$1.bed -v raw.$1.vcf -f reference.fasta -m 5 -q 5 -E 3 --min-repeat-entropy 1 -V --populations popmap -n 10 -F 0.1 &>fb.$1.error.log parallel: This job failed: call_genos 31577
ERROR: freebayes instance DID NOT COMPLETE
See below: /usr/bin/bash: line 1: 20115 Illegal instruction freebayes -b cat-RRG.bam -t mapped.$1.bed -v raw.$1.vcf -f reference.fasta -m 5 -q 5 -E 3 --min-repeat-entropy 1 -V --populations popmap -n 10 -F 0.1 &>fb.$1.error.log parallel: This job failed: call_genos 22510
FreeBayes has now failed a third time, likely because of memory issues. More resources must be allocated to finish this analysis. vcfcombine: symbol lookup error: /home/alnus/miniconda3/envs/ddocent_env/bin/../lib/libvcflib.so.1: undefined symbol: wavefront_align
Using VCFtools to parse TotalRawSNPS.vcf for SNPs that are called in at least 90% of individuals
dDocent has finished with errors in /home/alnus/ddocent_teak2
dDocent started Tue Mar 26 16:27:46 JST 2024
dDocent finished Wed Mar 27 18:38:28 JST 2024
Please check log files
After filtering, kept 0 out of a possible 0 Sites
dDocent 2.9.4 The 'd' is silent, hillbilly.