jeffreybarrick
commented
1 year ago There's something up with with the part of your command that is specifying the FASTQ files:
"/users/user/library/cloudstorage/onedrive/year 2/WGS/Illumina\ reads/.fastq"
Is that actually what you typed? It's processing the same file "Illumina reads" file (or maybe folder) three times and finding that these are empty files with no reads.
Maybe it should be this?
"/users/user/library/cloudstorage/onedrive/year 2/WGS/Illumina reads/*.fastq"
I would try running it with providing the full path to one FASTQ file and see if that works
Hiya,
I'm totally new to breseq :') and I very much want to learn it. I'm facing this error whenever I run the reference alignment, my sequences are good, so I don't think they are causing the issue because my PI was able to get a nice table for the SNPs and mutations using them. Breseq and bowtie2 are both in the bin file of miniconda 3, so I don't think its a PATH problem either, what do you think is causing this error :( I would very much appreciate your help.
this is my run (or pipeline? totally new to these terms xD : breseq -n analyses6 -r DSM639_reference.gbff -j 3 "/users/user/library/cloudstorage/onedrive/year 2/WGS/Illumina\ reads/.fastq" &> analyses6.out &
below is the output I get whenever I run cat nohup.out command:
breseq 0.37.1 http://barricklab.org/breseq
Active Developers: Barrick JE, Deatherage DE Contact: jeffrey.e.barrick@gmail.com
breseq is free software; you can redistribute it and/or modify it under the terms the GNU General Public License as published by the Free Software Foundation; either version 2, or (at your option) any later version.
Copyright (c) 2008-2010 Michigan State University Copyright (c) 2011-2022 The University of Texas at Austin
If you use breseq in your research, please cite:
Deatherage, D.E., Barrick, J.E. (2014) Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol. Biol. 1151: 165–188.
If you use structural variation (junction) predictions, please cite:
Barrick, J.E., Colburn, G., Deatherage D.E., Traverse, C.C., Strand, M.D., Borges, J.J., Knoester, D.B., Reba, A., Meyer, A.G. (2014) Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq. BMC Genomics 15:1039.
---> bowtie2 :: version 2.5.1 [/Users/user/miniconda3/envs/file/bin/bowtie2] ---> bowtie2 :: NOTE :: breseq output may vary slightly depending on your bowtie2 version ---> bowtie2 :: NOTE :: and occasionally bowtie2 versions may have bugs that cause crashes. ---> bowtie2 :: NOTE :: bowtie2 version 2.4.5 is recommended with this breseq version. ---> R :: version 4.2.2 [/Users/user/miniconda3/envs/file/bin/R] +++ NOW PROCESSING Read and reference sequence file input READ FILE::Illumina reads Converting/filtering FASTQ file... Original base quality format: ILLUMINA_1.3+ New format: SANGER Original reads: 0 bases: 0 Filtered reads: none Analyzed reads: 0 bases: 0 READ FILE::Iluumina reads Converting/filtering FASTQ file... Original base quality format: ILLUMINA_1.3+ New format: SANGER Original reads: 0 bases: 0 Filtered reads: none Analyzed reads: 0 bases: 0 READ FILE::illumina reads Converting/filtering FASTQ file... Original base quality format: ILLUMINA_1.3+ New format: SANGER Original reads: 0 bases: 0 Filtered reads: none Analyzed reads: 0 bases: 0 ::TOTAL:: Original reads: 0 bases: 0 Analyzed reads: 0 bases: 0 [samtools] faidx ./data/reference.fasta REFERENCE: NZ_CP046615 LENGTH: 2225130 libc++abi: terminating with uncaught exception of type std::domain_error: type must be number, but is null