Open lilymaya opened 7 months ago
You file doesn't appear to have any split or discordant reads. Was it aligned with bwa mem? Is it paired end?
Yes and yes! Oops, is this an issue I have missed somewhere?
Hi @brentp, I have looked through the issues and I haven't been able to find a definitive answer, but from what I understand, I can align with BWA MEM but perhaps I shouldn't then filter these reads? Could you please confirm how to prep the input files? Thank you so much!
Align with bwa mem, mark duplicates, sort and index. Then send to smoove without filtering. They should be paired end reads.
Great, thank you so much for your help and quick reply! :)
Hi @brentp,
I am getting a strange error when I try to run smoove call:
[smoove] 2023/11/03 15:37:14 starting with version 0.1.9 [smoove] 2023/11/03 15:37:14 calculating bam stats for 1 bams [smoove] 2023/11/03 15:37:16 done calculating bam stats [smoove]: 2023/11/03 15:48:09 finished process: lumpy-filter (lumpy_filter -f Oed.genome.c) in user-time:1m31.88s system-time:12.34s [smoove] 2023/11/03 15:48:10 removed 0 alignments out of 0 (NaN%) with depth > 800 or from excluded chroms from BZH_04.disc.bam in 0 seconds [smoove] 2023/11/03 15:48:10 removed 0 alignments out of 0 (NaN%) that were bad interchromosomals or flanked-splitters from BZH_04.disc.bam [smoove] 2023/11/03 15:48:10 removed 0 singletons out of 0 reads (NaN%) from BZH_04.disc.bam in 0 seconds [smoove] 2023/11/03 15:48:10 removed 0 alignments out of 0 (NaN%) with depth > 800 or from excluded chroms from BZH_04.split.bam in 0 seconds [smoove] 2023/11/03 15:48:10 removed 0 alignments out of 0 (NaN%) that were bad interchromosomals or flanked-splitters from BZH_04.split.bam [smoove] 2023/11/03 15:48:10 removed 0 singletons out of 0 reads (NaN%) from BZH_04.split.bam in 0 seconds [smoove] 2023/11/03 15:48:10 starting lumpy [smoove] 2023/11/03 15:48:10 wrote lumpy command to /home1/svcalling/lumpy/results-smoove/BZH_04-lumpy-cmd.sh [smoove] 2023/11/03 15:48:10 writing sorted, indexed file to /home1/svcalling/lumpy/results-smoove/BZH_04-smoove.genotyped.vcf.gz [smoove] 2023/11/03 15:48:10 excluding variants with all unknown or homozygous reference genotypes [smoove] 2023/11/03 15:48:10 > gsort version 0.0.6 [smoove] 2023/11/03 15:48:11 Calculating library metrics from /BZH_04_SS.bam... [smoove] 2023/11/03 15:48:15 done [smoove] 2023/11/03 15:48:15 Writing library metrics to /dev/shm/pbs.7263022[3].datarmor0/tempclean-988305349/086946291svtype-lib... [smoove] 2023/11/03 15:48:15 done [smoove] 2023/11/03 15:48:15 2023/11/03 15:48:15 EOF [smoove] 2023/11/03 15:48:15 Failed to open -: unknown file type [smoove] 2023/11/03 15:48:15 wrote sorted, indexed file to /home1/svcalling/lumpy/results-smoove/BZH_04-smoove.genotyped.vcf.gz panic: exit status 255
goroutine 1 [running]: github.com/brentp/smoove/svtyper.check(0x9f3060, 0xc420282920) /home/brentp/go/src/github.com/brentp/smoove/svtyper/svtyper.go:32 +0x4a github.com/brentp/smoove/svtyper.Svtyper(0x9f2b80, 0xc42000c110, 0x7fffffffe017, 0x5c, 0xc4200b5280, 0x1, 0x1, 0x7fffffffdfbe, 0x42, 0x7fffffffe008, ...) /home/brentp/go/src/github.com/brentp/smoove/svtyper/svtyper.go:215 +0xbee github.com/brentp/smoove/lumpy.Main() /home/brentp/go/src/github.com/brentp/smoove/lumpy/lumpy.go:287 +0x3fb main.main() /home/brentp/go/src/github.com/brentp/smoove/cmd/smoove/smoove.go:115 +0x1dd
This error pops up for every individual file that I have. I have been scouring the Issues tab but I haven't found anything that matches this problem.
Do you have any suggestions? Thank you so much in advance!