bismark bowtie2

[yhj-j]

The code is as follows:
bismark --bowtie2 -p 10 --genome .. /st_8_bow2_idx/ --basename Stem_WGBS_rep1 -o 2.align/ -1 .. /1.cleandata/Stem_WGBS_rep1_R1_clean.fq.gz -2 .. /1.cleandata/Stem_WGBS_rep1_R2_clean.fq.gz 1>2.align/Stem_WGBS_rep1.log 2>&1
How to solve the error as follows:
(ERR): bowtie2-align died with signal 9 (KILL)
Use of uninitialized value $alignment_score_2 in concatenation (.) or string at /home/yanghj/my_data/software/Bismark/Bismark/bismark line 3378, line 19786920.
Use of uninitialized value $MD_tag_2 in concatenation (.) or string at /home/yanghj/my_data/software/Bismark/Bismark/bismark line 3378, line 19786920.
Failed to extract alignment score 2 () and MD tag ()!
last alignment 1: A00783:1256:HN3CHDSX5:2:1121:3441:23046_1:N:0:AGACCAGCTA+GGCTCTAGTT/1 99 Chr12_CT_converted 169612433 0 150M =
169612593 307 GAGTTTGAGTGGTGGTATATTGTTTTTTAAAAAGGATAAATAGATTTTATAATGAATTTAATTTTTGATTTTTATTTTAGAGTTATGTAATTAAGGGATTTTTTTTTTTTAAGATTTTTG TGATATTTTTAATTTTAGAGTATATATTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF FFFFFFFFFFFFFFF:FFFFFFFFFFFFFF AS:i:-12 XS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:81A37A30 YS:i:-14 YT:Z:CP
last alignment 2: A00783:1256:HN3CHDSX5:2:1121:3441:23046_2:N:0:AGACCAGCTA+GGCTCTAGTT/2 147 Chr12_CT_converted 169612593 0 140M3I7M
= 169612433-307 TTTTTTGATTGTTTTAATTGTAATTATAATTTATTTGATAATTTTTTTAGTTGATGAAATTGTAAAGTTATATGATTTGTTAGAAAAGGGTATAATAGTTATTTTTTTTTGTATAATAGG ATTATTAGTTATTTGTTGGATTTTTT
(ERR): bowtie2-align died with signal 13 (PIPE)

[FelixKrueger]

Hmm this is tricky to debug, but my guess would be that you are running out of memory. On what kind of system are you running this on? I would definitely suggest you drop the parameter -p 10, and see if that works?

bismark --genome .. /st_8_bow2_idx/ --basename Stem_WGBS_rep1 -o 2.align/ -1 .. /1.cleandata/Stem_WGBS_rep1_R1_clean.fq.gz -2 .. /1.cleandata/Stem_WGBS_rep1_R2_clean.fq.gz

[yhj-j]

Thank you for your response. I am using Linux version 3.10.0-862.el7.x86_64 ***@***.***) (gcc version 4.8.5 20150623 (Red Hat 4.8.5-28) (GCC)) #1 SMP Fri Apr 20 16:44:24 UTC 2018. I am running the job on a slurm cluster using sbatch. However, when I tried aligning with "--hisat2 -p 10", the alignment rates ranged from 68% to 70%. I will now try removing the "-p 10" option and see if I can successfully run with Bowtie2. Thank you again for your response.

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------------------ 原始邮件 ------------------ 发件人: "FelixKrueger/Bismark" ***@***.***>; 发送时间: 2023年12月27日(星期三) 晚上11:01 ***@***.***>; ***@***.******@***.***>; 主题: Re: [FelixKrueger/Bismark] bismark bowtie2 (Issue #645) Hmm this is tricky to debug, but my guess would be that you are running out of memory. On what kind of system are you running this on? I would definitely suggest you drop the parameter -p 10, and see if that works? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

[FelixKrueger]

Just for your information, there is still an open issue (#638) describing a memory leak specifically with Bowtie 2 v2.5.2. Is there a chance you ran into the same issue?