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barricklab / breseq

breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R.
http://barricklab.org/breseq
GNU General Public License v2.0
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Cannot read reference alignment #353

Closed filifed closed 1 year ago

filifed commented 1 year ago

Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Hi everyone,

I was running alignments of 12 packs of read with the same three sequences. For 3 of them, everything went fine. For the other 9 though, I get this error:

Multiseed full-index search: 03:07:40 9154199 reads; of these: 9154199 (100.00%) were unpaired; of these: 352616 (3.85%) aligned 0 times 8566739 (93.58%) aligned exactly 1 time 234844 (2.57%) aligned >1 times 96.15% overall alignment rate Time searching: 03:07:42 Overall time: 03:07:42 [system] bowtie2 -t --no-unal -p 24 -L 20 --ma 1 --mp 3 --np 0 --rdg 2,3 --rfg 2,3 --ignore-quals --local -i S,1,0.25 --score-min L,6,0.2 -k 2000 --reorder -x "PpCCS3/02_reference_alignment/reference" -U "PpCCS3/02_reference_alignment/CCS3_EKDN230023138-1A_HF5T2DSX7_L2_2.fq.stage1.unmatched.fastq" -S "PpCCS3/02_reference_alignment/CCS3_EKDN230023138-1A_HF5T2DSX7_L2_2.fq.stage2.matched.sam" stat: Bad file descriptor Warning: Could not open read file "PpCCS3/02_reference_alignment/CCS3_EKDN230023138-1A_HF5T2DSX7_L2_2.fq.stage1.unmatched.fastq" for reading; skipping... Error: No input read files were valid (ERR): bowtie2-align exited with value 1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> FATAL ERROR <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Error running command: [system] bowtie2 -t --no-unal -p 24 -L 20 --ma 1 --mp 3 --np 0 --rdg 2,3 --rfg 2,3 --ignore-quals --local -i S,1,0.25 --score-min L,6,0.2 -k 2000 --reorder -x "PpCCS3/02_reference_alignment/reference" -U "PpCCS3/02_reference_alignment/CCS3_EKDN230023138-1A_HF5T2DSX7_L2_2.fq.stage1.unmatched.fastq" -S "PpCCS3/02_reference_alignment/CCS3_EKDN230023138-1A_HF5T2DSX7_L2_2.fq.stage2.matched.sam" Result code: 256 FILE: libbreseq/common.h LINE: 1411 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> STACK TRACE <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Backtrace with 7 stack frames. breseq(+0x44cf4) [0x557d8dfa4cf4] breseq(+0x4a4f1) [0x557d8dfaa4f1]

I have very little experience with coding/running scripts but I will still like to get some help

Best, Filippo breseq(+0x6d585) [0x557d8dfcd585] breseq(+0x36cc4) [0x557d8df96cc4] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7fa365c29d90] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7fa365c29e40] breseq(+0x40559) [0x557d8dfa0559] !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

jeffreybarrick commented 1 year ago

My guess is that you are running out of hard drive space during running breseq and it is not able to create the input file for bowtie2. Delete the entire output directory and try rerunning one of the jobs after you free up some space to see if this is the issue.