Error message produced by bowtie2 (HiC-Pro)

Question

[Gary]

Hi,

Could you help me about the bowtie2 error message below that I don’t understand? I run HiC-Pro (Servant et al., 2015) for our chicken HiChIP data (Mumbach et al., 2016) with 40bp paired-end reads. HiC-Pro is an aligner based on bowtie2. After running, bowtie2 showes error message below. Could you help me? Please let me know if you need any information. Many thanks.

Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192.

Argument "NS500449" isn't numeric in bitwise and (&) at /root/bowtie2-2.3.2-legacy/bowtie2 line 551, <bt> line 645795.

Use of uninitialized value $l in scalar chomp at /root/bowtie2-2.3.2-legacy/bowtie2 line 564, <bt> line 645795.

Use of uninitialized value $l in substitution (s///) at /root/bowtie2-2.3.2-legacy/bowtie2 line 565, <bt> line 645795.

(ERR): bowtie2-align died with signal 9 (KILL)

Best,

Gary

Reference

Mumbach MR, Rubin AJ, Flynn RA, Dai C, Khavari PA, Greenleaf WJ, et al. HiChIP: efficient and sensitive analysis of protein-directed genome architecture. Nat Methods 2016;13(11):919-+.

Servant N, Varoquaux N, Lajoie BR, Viara E, Chen CJ, Vert JP, et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol 2015;16:11.

Answer 1

[ashwinkelkar]

This seems like an issue with your installation of bowtie though I am not exactly sure of this. You could get around this by using any other HiC tool that uses an aligner that is not based on bowtie2 or that can directly use output of bowtie2 run independenly.

Try using HiCexplorer (link) This package is able to use read aligners different from bowtie2 namely hisat2 and bwa. The authors are very helpful if you contact them and bwa and hisat2 are very versatile aligners to use. Hope this helps -Ashwin