runtime: failed to create new OS thread

[asylvz]

Hello,

I'm running smoke on docker and get the following error. Do you have any suggestion?

Thank you, Arda

docker run -v /Users/asoylev/genomes:/inp -it brentp/smoove smoove call -name dnm --fasta /inp/hg38.fasta --genotype /inp/hg00733_grch38_realigned.bam WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested [smoove] 2022/10/24 21:36:09 starting with version 0.2.6 [smoove] 2022/10/24 21:36:09 calculating bam stats for 1 bams [smoove] 2022/10/24 21:36:40 done calculating bam stats

[smoove]: ([E]lumpy-filter) 2022/10/24 22:19:14 [lumpy_filter] extracted splits and discordants from 696974278 total aligned reads [smoove]:2022/10/24 22:19:17 finished process: lumpy-filter (set -eu; lumpy_filter -f /inp/hg38.fasta /inp/hg00733_grch38_realigned.bam .//sample.split.bam.tmp.b) in user-time:56m8.612767s system-time:15m5.577029s

[smoove] 2022/10/24 22:24:19 removed 5858450 alignments out of 7295943 (80.30%) with low mapq, depth > 1000, or from excluded chroms from sample.split.bam in 303 seconds [smoove] 2022/10/24 22:24:19 removed 388849 alignments out of 7295943 (5.33%) that were bad interchromosomals or flanked-splitters from sample.split.bam

[smoove] 2022/10/24 22:28:50 removed 10477804 alignments out of 15968796 (65.61%) with low mapq, depth > 1000, or from excluded chroms from sample.disc.bam in 573 seconds [smoove] 2022/10/24 22:28:50 removed 452679 alignments out of 15968796 (2.83%) that were bad interchromosomals or flanked-splitters from sample.disc.bam

[smoove] 2022/10/24 22:36:01 kept 9248 putative orphans [smoove] 2022/10/24 22:36:01 removed 1228327 discordant orphans in 306 seconds [smoove] 2022/10/24 22:36:57 removed 4738501 singletons and isolated interchromosomals of 5038313 reads (94.05%) from sample.disc.bam in 488 seconds [smoove] 2022/10/24 22:36:57 299812 reads (1.88%) of the original 15968796 remain from sample.disc.bam

[smoove] 2022/10/24 22:37:48 kept 100685 putative orphans [smoove] 2022/10/24 22:37:48 removed 172600 split orphans in 704 seconds [smoove] 2022/10/24 22:38:04 removed 661586 singletons of 1048644 reads (63.09%) from sample.split.bam in 824 seconds [smoove] 2022/10/24 22:38:04 387058 reads (5.31%) of the original 7295943 remain from sample.split.bam [smoove] 2022/10/24 22:38:04 starting lumpy [smoove] 2022/10/24 22:38:04 wrote lumpy command to .//dnm-lumpy-cmd.sh [smoove] 2022/10/24 22:38:04 writing sorted, indexed file to dnm-smoove.genotyped.vcf.gz [smoove] 2022/10/24 22:38:04 excluding variants with all unknown or homozygous reference genotypes [smoove] 2022/10/24 22:38:05 runtime: failed to create new OS thread (have 2 [smoove] 2022/10/24 22:38:05 already; errno=22) fatal error: newosproc [smoove] 2022/10/24 22:38:05 runtime stack: [smoove] 2022/10/24 22:38:05 runtime.throw( [smoove] 2022/10/24 22:38:05 0x6cb13d [smoove] 2022/10/24 22:38:05 , [smoove] 2022/10/24 22:38:05 0x9) [smoove] 2022/10/24 22:38:05 /home/brentp/go/go1.8/src/runtime/panic.go:596 +0x95 runtime.newosproc(0xc420024000, 0xc420034000) /home/brentp/go/go1.8/src/runtime/os_linux.go:163 +0x18c runtime.newm(0x6d9d28, 0x0) /home/brentp/go/go1.8/src/runtime/proc.go:1628 +0x137 runtime.main.func1() /home/brentp/go/go1.8/src/runtime/proc.go:126 +0x36 runtime.systemstack(0x815400)

[smoove] 2022/10/24 22:38:05 /home/brentp/go/go1.8/src/runtime/asm_amd64.s:327 +0x79 runtime.mstart() /home/brentp/go/go1.8/src/runtime/proc.go:1132

goroutine 1 [running]: [smoove] 2022/10/24 22:38:05 runtime.systemstack_switch() /home/brentp/go/go1.8/src/runtime/asm_amd64.s:281 fp=0xc420020788 sp= [smoove] 2022/10/24 22:38:05 0xc420020780 runtime.main() /home/brentp/go/go1.8/src/runtime/proc.go:127 +0x6c fp=0xc4200207e0 sp=0xc420020788 [smoove] 2022/10/24 22:38:05 runtime.goexit() /home/brentp/go/go1.8/src/runtime/asm_amd64.s:2197 +0x1 fp=0xc4200207e8 sp=0xc4200207e0 [smoove] 2022/10/24 22:38:05 Failed to read from standard input: unknown file type [smoove] 2022/10/24 22:38:05 chr1 1000000 [smoove] 2022/10/24 22:38:05 [W::hts_idx_load3] [smoove] 2022/10/24 22:38:05 The index file is older than the data file: /inp/hg00733_grch38_realigned.bai [smoove] 2022/10/24 22:38:05 [smoove] 2022/10/24 22:38:37 chr10 1000000 [smoove] 2022/10/24 22:38:55 chr11 1000000 [smoove] 2022/10/24 22:38:59 [W::hts_idx_load3] The index file is older than the data file: /inp/hg00733_grch38_realigned.bai [smoove] 2022/10/24 22:38:59 [smoove] 2022/10/24 22:39:11 chr12 1000000 [smoove] 2022/10/24 22:39:29 chr13 1000000 [smoove] 2022/10/24 22:39:29 chr13 2000000 chr13 4000000 chr13 8000000 chr13 16000000 chr13 32000000 [smoove] 2022/10/24 22:39:41 chr14 1000000 chr14 2000000 chr14 4000000 chr14 8000000 chr14 16000000 [smoove] 2022/10/24 22:39:41 chr14 32000000 [smoove] 2022/10/24 22:39:46 [W::hts_idx_load3] [smoove] 2022/10/24 22:39:46 The index file is older than the data file: /inp/hg00733_grch38_realigned.bai [smoove] 2022/10/24 22:39:46 [smoove] 2022/10/24 22:39:52 chr14_GL000009v2_random 1000000 [smoove] 2022/10/24 22:39:52 chr14_GL000225v1_random 1000000 [smoove] 2022/10/24 22:39:52 chr14_KI270722v1_random 1000000 [smoove] 2022/10/24 22:39:52 chr14_GL000194v1_random 1000000 [smoove] 2022/10/24 22:39:52 chr14_KI270723v1_random 1000000 [smoove] 2022/10/24 22:39:52 chr14_KI270724v1_random 1000000 [smoove] 2022/10/24 22:39:52 chr14_KI270725v1_random 1000000 [smoove] 2022/10/24 22:39:52 chr14_KI270726v1_random 1000000 [smoove] 2022/10/24 22:39:53 chr15 1000000 chr15 2000000 chr15 4000000 [smoove] 2022/10/24 22:39:53 chr15 8000000 chr15 16000000 chr15 32000000 [smoove] 2022/10/24 22:40:03 chr16 1000000 [smoove] 2022/10/24 22:40:17 chr16_KI270728v1_random 1000000 [smoove] 2022/10/24 22:40:17 chr17 1000000 [smoove] 2022/10/24 22:40:30 chr17_GL000205v2_random 1000000 [smoove] 2022/10/24 22:40:30 chr17_KI270729v1_random 1000000 panic: write |1: broken pipe

goroutine 117394 [running]: github.com/brentp/smoove/svtyper.check(...) /home/brentp/go/go/src/github.com/brentp/smoove/svtyper/svtyper.go:33 github.com/brentp/smoove/svtyper.Svtyper.func2(0xc000a826c0, 0xc000148590, 0x1, 0x1, 0x4000800ea8, 0xf, 0xc000a90300, 0x2c, 0xc0044eae18, 0xc0044eae30, ...) /home/brentp/go/go/src/github.com/brentp/smoove/svtyper/svtyper.go:189 +0x8e7 created by github.com/brentp/smoove/svtyper.Svtyper /home/brentp/go/go/src/github.com/brentp/smoove/svtyper/svtyper.go:165 +0xab2

[brentp]

Hi, I think this is likely the problem:

WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested

you're running on arm64?

[asylvz]

yes, it's apple m1. Any way to make it run?

[brentp]

I'm surprised it got this far. You could try export GOMAXPROCS=1 before running. And also run with -p 1 Or can you give it somehow access to more processes as that's what the final error is indicating.

[asylvz]

Thank you, I'll try to check that but it took hours to get to that point. I just tried with a linux machine and it was extremely fast compared to that.