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brentp / bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
https://arxiv.org/abs/1401.1129
MIT License
144 stars 54 forks source link

Meet Error When running bwa meth mem2 #84

Open WRui opened 2 years ago

WRui commented 2 years ago

Found BWA MEM2 index running: /home/users/ruiwr/Software/Anaconda3/bin/python /home/users/ruiwr/Software/bwa-meth-master/bwameth_mem2.py c2t /scratch/users/ruiwr/Project/cfDNA_meth/01.clean_data/LUP1225-T1_Tumor_R1.good.fq.gz /scratch/users/ruiwr/Project/cfDNA_meth/01.clean_data/LUP1225-T1_Tumor_R2.good.fq.gz |bwa-mem2 mem -T 40 -B 2 -L 10 -CM -U 100 -p -R '@RG\tID:LUP1225-T1_Tumor_R.good\tSM:LUP1225-T1_Tumor_R.good' -t 10 /home/groups/arasha/ruiwr/Database/hg19_lambda_puc19_bwameth_mem2/hg19_lambda_puc19.fa.bwameth.c2t /dev/stdin

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.

converting reads in /scratch/users/ruiwr/Project/cfDNA_meth/01.clean_data/LUP1225-T1_Tumor_R1.good.fq.gz,/scratch/users/ruiwr/Project/cfDNA_meth/01.clean_data/LUP1225-T1_Tumor_R2.good.fq.gz Traceback (most recent call last): File "/home/users/ruiwr/Software/bwa-meth-master/bwameth_mem2.py", line 560, in main(sys.argv[1:]) File "/home/users/ruiwr/Software/bwa-meth-master/bwameth_mem2.py", line 518, in main sys.exit(convert_reads(args[1], args[2])) File "/home/users/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 "/home/users/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:/home/users/ruiwr/Software/Anaconda3/bin/python /home/users/ruiwr/Software/bwa-meth-master/bwameth_mem2.py c2t /scratch/users/ruiwr/Project/cfDNA_meth/01.clean_data/LUP1225-T1_Tumor_R1.good.fq.gz /scratch/users/ruiwr/Project/cfDNA_meth/01.clean_data/LUP1225-T1_Tumor_R2.good.fq.gz |bwa-mem2 mem -T 40 -B 2 -L 10 -CM -U 100 -p -R '@RG\tID:LUP1225-T1_Tumor_R.good\tSM:LUP1225-T1_Tumor_R.good' -t 10 /home/groups/arasha/ruiwr/Database/hg19_lambda_puc19_bwameth_mem2/hg19_lambda_puc19.fa.bwameth.c2t /dev/stdin return code was:1 Traceback (most recent call last): File "/home/users/ruiwr/Software/bwa-meth-master/bwameth_mem2.py", line 560, in main(sys.argv[1:]) File "/home/users/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 "/home/users/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 "/home/users/ruiwr/Software/bwa-meth-master/bwameth_mem2.py", line 383, in as_bam for line in sam_iter: File "/home/users/ruiwr/Software/Anaconda3/lib/python3.9/site-packages/toolshed/files.py", line 61, in process_iter raise ProcessException(cmd) toolshed.files.ProcessException: /home/users/ruiwr/Software/Anaconda3/bin/python /home/users/ruiwr/Software/bwa-meth-master/bwameth_mem2.py c2t /scratch/users/ruiwr/Project/cfDNA_meth/01.clean_data/LUP1225-T1_Tumor_R1.good.fq.gz /scratch/users/ruiwr/Project/cfDNA_meth/01.clean_data/LUP1225-T1_Tumor_R2.good.fq.gz |bwa-mem2 mem -T 40 -B 2 -L 10 -CM -U 100 -p -R '@RG\tID:LUP1225-T1_Tumor_R.good\tSM:LUP1225-T1_Tumor_R.good' -t 10 /home/groups/arasha/ruiwr/Database/hg19_lambda_puc19_bwameth_mem2/hg19_lambda_puc19.fa.bwameth.c2t /dev/stdin