Smoove not working !!!!!! Failed to read from standard input: unknown file type panic: write |1: broken pipe

[mansi800]

@brentp Smoove is not working even after my bam size is quite good. Command used: smoove call --outdir test_mansi/SRR6745447_output/smoove_output/ --name SRR6745447 --fasta part_II/references/hg38.fa -p 1 --genotype part_II/output/fq2bam_no_indels/SRR6745447_sorted.bam

The size of bam is : 72 GB(WGS bam )

smoove --help output: smoove version: 0.2.8

smoove calls several programs. Those with 'Y' are found on your $PATH. Only those with '*' are required.

*[Y] bgzip [ sort -> (compress) -> index ] *[Y] gsort [(sort) -> compress -> index ] *[Y] tabix [ sort -> compress -> (index)] *[Y] lumpy *[Y] lumpy_filter *[Y] samtools *[Y] svtyper *[Y] mosdepth [extra filtering of split and discordant files for better scaling]

[ ] duphold [(optional) annotate calls with depth changes] [ ] svtools [only needed for large cohorts].

Available sub-commands are below. Each can be run with -h for additional help.

call : call lumpy (and optionally svtyper) merge : merge and sort (using svtools) calls from multiple samples genotype : parallelize svtyper on an input VCF paste : square final calls from multiple samples (each with same number of variants) plot-counts : plot counts of split, discordant reads before, after smoove filtering annotate : annotate a VCF with gene and quality of SV call hipstr : run hipSTR in parallel duphold : run duphold in parallel (this can be done by adding a flag to call or genotype) Error log: [smoove] 2022/07/06 19:24:11 starting with version 0.2.8 [smoove] 2022/07/06 19:24:11 calculating bam stats for 1 bams [smoove] 2022/07/06 19:24:20 done calculating bam stats [smoove] 2022/07/06 19:24:20 removed 0 alignments out of 3232 (0.00%) with low mapq, depth > 1000, or from excluded chroms from sample.disc.bam in 1 seconds [smoove] 2022/07/06 19:24:20 removed 0 alignments out of 3232 (0.00%) that were bad interchromosomals or flanked-splitters from sample.disc.bam [smoove] 2022/07/06 19:24:20 kept 0 putative orphans [smoove] 2022/07/06 19:24:20 removed 0 discordant orphans in 0 seconds [smoove] 2022/07/06 19:24:20 removed 0 singletons and isolated interchromosomals of 3232 reads (0.00%) from sample.disc.bam in 0 seconds [smoove] 2022/07/06 19:24:20 3232 reads (100.00%) of the original 3232 remain from sample.disc.bam [smoove] 2022/07/06 19:24:21 removed 0 alignments out of 6258 (0.00%) with low mapq, depth > 1000, or from excluded chroms from sample.split.bam in 1 seconds [smoove] 2022/07/06 19:24:21 removed 0 alignments out of 6258 (0.00%) that were bad interchromosomals or flanked-splitters from sample.split.bam [smoove] 2022/07/06 19:24:21 kept 555 putative orphans [smoove] 2022/07/06 19:24:21 removed 22 split orphans in 0 seconds [smoove] 2022/07/06 19:24:21 removed 0 singletons of 6258 reads (0.00%) from sample.split.bam in 0 seconds [smoove] 2022/07/06 19:24:21 6258 reads (100.00%) of the original 6258 remain from sample.split.bam [smoove] 2022/07/06 19:24:21 starting lumpy [smoove] 2022/07/06 19:24:21 wrote lumpy command to /mnt/ST160/part_II/test_mansi/SRR6745447_output/smoove_output//SRR6745447-lumpy-cmd.sh [smoove] 2022/07/06 19:24:21 writing sorted, indexed file to /mnt/ST160/part_II/test_mansi/SRR6745447_output/smoove_output/SRR6745447-smoove.genotyped.vcf.gz [smoove] 2022/07/06 19:24:21 excluding variants with all unknown or homozygous reference genotypes [smoove] 2022/07/06 19:24:21 chr22 1000000 chr22 2000000 chr22 4000000 chr22 8000000 chr22 16000000 [smoove] 2022/07/06 19:24:21 Failed to read from standard input: unknown file type panic: write |1: broken pipe

goroutine 20112 [running]: github.com/brentp/smoove/svtyper.check(...) /home/brentp/src/smoove/svtyper/svtyper.go:33 github.com/brentp/smoove/svtyper.Svtyper.func2(0xc0007a8a20, 0xc0002317d0, 0x1, 0x1, 0x7ffc34697ca7, 0x40, 0xc000027830, 0x2c, 0xc001464000, 0xc001464008, ...) /home/brentp/src/smoove/svtyper/svtyper.go:189 +0xa85 created by github.com/brentp/smoove/svtyper.Svtyper /home/brentp/src/smoove/svtyper/svtyper.go:165 +0xb87

please help me out as soon as possible Thanks in Advance

[brentp]

Hi, your entire bam file has only 3232 discordant reads and 6258 split reads. that is far too few. Your bam file will not work with smoove. Either it's low coverage or targetted sequencing or some other problem.