broken pipeline

[WRui]

I use the same bashrc setting in three servers, the code can be run successfully, but showed a broken pipeline in one server. The samtools(samtools-1.14), python(python3.9) and bwameth all the same. I have no idea what is happening, looking for your help, Thank you.

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Found BWA MEM2 index
running: /drive3/ruiwr/Software/Anaconda3/bin/python /drive3/ruiwr/Software/bwa-meth-master/bwameth_mem2.py c2t /drive3/ruiwr/Project/cfDNA_Meth/01.clean_data/LDCT159-N1_Normal_R1.good.fq.gz /drive3/ruiwr/Project/cfDNA_Meth/01.clean_data/LDCT159-N1_Normal_R2.good.fq.gz |bwa-mem2 mem -T 40 -B 2 -L 10 -CM -U 100 -p -R '@RG\tID:LDCT159-N1_Normal_R.good\tSM:LDCT159-N1_Normal_R.good' -t 4  /drive3/ruiwr/Database/hg19/hg19_lambda_puc19_bwameth_mem2/hg19_lambda_puc19.fa.bwameth.c2t /dev/stdin
--------------------
converting reads in /drive3/ruiwr/Project/cfDNA_Meth/01.clean_data/LDCT159-N1_Normal_R1.good.fq.gz,/drive3/ruiwr/Project/cfDNA_Meth/01.clean_data/LDCT159-N1_Normal_R2.good.fq.gz

Please verify that both the operating system and the processor support Intel(R) X87, CMOV, MMX, FXSAVE, SSE, SSE2, SSE3, SSSE3, SSE4_1, SSE4_2, MOVBE, POPCNT, F16C, AVX, FMA, BMI, LZCNT and AVX2 instructions.

Traceback (most recent call last):
  File "/drive3/ruiwr/Software/bwa-meth-master/bwameth_mem2.py", line 560, in <module>
    main(sys.argv[1:])
  File "/drive3/ruiwr/Software/bwa-meth-master/bwameth_mem2.py", line 518, in main
    sys.exit(convert_reads(args[1], args[2]))
  File "/drive3/ruiwr/Software/bwa-meth-master/bwameth_mem2.py", line 144, in convert_reads
    convert_and_write_read(name,seq,qual,read_i%2,out)
  File "/drive3/ruiwr/Software/bwa-meth-master/bwameth_mem2.py", line 177, in convert_and_write_read
    out.write("".join((name, seq, "\n+\n", qual)))
BrokenPipeError: [Errno 32] Broken pipe
cmd was:/drive3/ruiwr/Software/Anaconda3/bin/python /drive3/ruiwr/Software/bwa-meth-master/bwameth_mem2.py c2t /drive3/ruiwr/Project/cfDNA_Meth/01.clean_data/LDCT159-N1_Normal_R1.good.fq.gz /drive3/ruiwr/Project/cfDNA_Meth/01.clean_data/LDCT159-N1_Normal_R2.good.fq.gz |bwa-mem2 mem -T 40 -B 2 -L 10 -CM -U 100 -p -R '@RG\tID:LDCT159-N1_Normal_R.good\tSM:LDCT159-N1_Normal_R.good' -t 4  /drive3/ruiwr/Database/hg19/hg19_lambda_puc19_bwameth_mem2/hg19_lambda_puc19.fa.bwameth.c2t /dev/stdin
return code was:1
Traceback (most recent call last):
  File "/drive3/ruiwr/Software/bwa-meth-master/bwameth_mem2.py", line 560, in <module>
    main(sys.argv[1:])
  File "/drive3/ruiwr/Software/bwa-meth-master/bwameth_mem2.py", line 551, in main
    bwa_mem(args.reference, conv_fqs_cmd, ' '.join(map(str, pass_through_args)),
  File "/drive3/ruiwr/Software/bwa-meth-master/bwameth_mem2.py", line 371, in bwa_mem
    as_bam(cmd, fa, set_as_failed, do_not_penalize_chimeras)
  File "/drive3/ruiwr/Software/bwa-meth-master/bwameth_mem2.py", line 383, in as_bam
    for line in sam_iter:
  File "/drive3/ruiwr/Software/Anaconda3/lib/python3.9/site-packages/toolshed/files.py", line 61, in process_iter
    raise ProcessException(cmd)
toolshed.files.ProcessException: /drive3/ruiwr/Software/Anaconda3/bin/python /drive3/ruiwr/Software/bwa-meth-master/bwameth_mem2.py c2t /drive3/ruiwr/Project/cfDNA_Meth/01.clean_data/LDCT159-N1_Normal_R1.good.fq.gz /drive3/ruiwr/Project/cfDNA_Meth/01.clean_data/LDCT159-N1_Normal_R2.good.fq.gz |bwa-mem2 mem -T 40 -B 2 -L 10 -CM -U 100 -p -R '@RG\tID:LDCT159-N1_Normal_R.good\tSM:LDCT159-N1_Normal_R.good' -t 4  /drive3/ruiwr/Database/hg19/hg19_lambda_puc19_bwameth_mem2/hg19_lambda_puc19.fa.bwameth.c2t /dev/stdin
[main_samview] fail to read the header from "-".
samtools sort: failed to read header from "-"

[brentp]

Hi, here is the relevant error:

Please verify that both the operating system and the processor support Intel(R) X87, CMOV, MMX, FXSAVE, SSE, SSE2, SSE3, SSSE3, SSE4_1, SSE4_2, MOVBE, POPCNT, F16C, AVX, FMA, BMI, LZCNT and AVX2 instructions.

this means that server does not support those instructions so you cant use bwa-mem2

[WRui]

Thank you for you reply, do you have some recommendations to run the bwa-meth mem2 with an AMD EPYC(Milan 7763) processor. Here are the flags of the processor:

fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm art rep_good nopl extd_apicid eagerfpu pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm cmp_legacy cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw topoext perfctr_core invpcid_single retpoline_amd ssbd ibrs ibpb stibp vmmcall fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid rdseed adx smap clflushopt clwb sha_ni xsaveopt xsavec xgetbv1 clzero xsaveerptr arat umip pku ospke vaes vpclmulqdq spec_ctrl intel_stibp arch_capabilities

[brentp]

Hi, I'm not sure what the problem is except it seems that your bwa mem2 does not work on your processor. You could verify this by trying to run bwa-mem2 directly, outside of bwa-meth. Either way, you could also run bwa-meth.py with the normal bwa mem.