{"action":"created","issue":{"url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/104","repository_url":"https://api.github.com/repos/COMBINE-lab/salmon","labels_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/104/labels{/name}","comments_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/104/comments","events_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/104/events","html_url":"https://github.com/COMBINE-lab/salmon/issues/104","id":188412945,"number":104,"title":"salmon quant fails when the input is a bam file and the --seqBias or --gcBias arguments is included","user":{"login":"tomsing1","id":10490984,"avatar_url":"https://avatars.githubusercontent.com/u/10490984?v=3","gravatar_id":"","url":"https://api.github.com/users/tomsing1","html_url":"https://github.com/tomsing1","followers_url":"https://api.github.com/users/tomsing1/followers","following_url":"https://api.github.com/users/tomsing1/following{/other_user}","gists_url":"https://api.github.com/users/tomsing1/gists{/gist_id}","starred_url":"https://api.github.com/users/tomsing1/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tomsing1/subscriptions","organizations_url":"https://api.github.com/users/tomsing1/orgs","repos_url":"https://api.github.com/users/tomsing1/repos","events_url":"https://api.github.com/users/tomsing1/events{/privacy}","received_events_url":"https://api.github.com/users/tomsing1/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2016-11-10T03:37:54Z","updated_at":"2016-12-15T21:39:15Z","closed_at":null,"body":"The documentation states\r\n\r\n>If your alignments for the sample you want to quantify appear in multiple .bam/.sam files, then you can simply provide the Salmon -a parameter with a (space-separated) list of these files.\r\n\r\nBut I somehow can't get that to work. I have two bam files, each of them with (different) STAR alignments to the same reference. When I pass either one of them, salmon works just fine, e.g. with the following commands:\r\n\r\n```\r\nsalmon quant -t transcripts.fasta  -l IU  -p 2 -o quantitation/quant.sf  -a run1/Aligned.toTranscriptome.out.bam\r\n# or\r\nsalmon quant -t transcripts.fasta  -l IU  -p 2 -o quantitation/quant.sf  -a run2/Aligned.toTranscriptome.out.bam\r\n```\r\nBut when I try to pass both of them, I get the following error:\r\n\r\n```\r\nsalmon quant -t transcripts.fasta  -l IU  -p 2 -o quantitation/quant.sf)  -a run1/Aligned.toTranscriptome.out.bam run2/Aligned.toTranscriptome.out.bam\r\n\r\nVersion Info: This is the most recent version of Salmon.\r\n# salmon (alignment-based) v0.7.2\r\n# [ program ] => salmon\r\n# [ command ] => quant\r\n# [ targets ] => { transcripts.fasta }\r\n# [ libType ] => { IU }\r\n# [ threads ] => { 2 }\r\n# [ output ] => { sample1/quantitation }\r\n# [ alignments ] => { run1/Aligned.toTranscriptome.out.bam run2/Aligned.toTranscriptome.out.bam }\r\nLibrary format { type:paired end, relative orientation:inward, strandedness:unstranded }\r\nLogs will be written to quantitation/logs\r\nnumQuantThreads = 2\r\nparseThreads = 2\r\nChecking that provided alignment files have consistent headers . . . done\r\nPopulating targets from aln = \"run1/Aligned.toTranscriptome.out.bam\", fasta = \"transcripts.fasta\" . . .replaced 0 non-ACGT nucleotides with random nucleotides\r\ndone\r\n\r\nprocessed 0 reads in current roundSegmentation fault (core dumped)\r\n```\r\n\r\nThe `Checking that provided alignment files have consistent headers . . . done` line seems to indicate that both bam files were recognized and that the headers matched. \r\n\r\nAny hints on what might be going on?"},"comment":{"url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/comments/267451963","html_url":"https://github.com/COMBINE-lab/salmon/issues/104#issuecomment-267451963","issue_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/104","id":267451963,"user":{"login":"mikelove","id":69203,"avatar_url":"https://avatars.githubusercontent.com/u/69203?v=3","gravatar_id":"","url":"https://api.github.com/users/mikelove","html_url":"https://github.com/mikelove","followers_url":"https://api.github.com/users/mikelove/followers","following_url":"https://api.github.com/users/mikelove/following{/other_user}","gists_url":"https://api.github.com/users/mikelove/gists{/gist_id}","starred_url":"https://api.github.com/users/mikelove/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mikelove/subscriptions","organizations_url":"https://api.github.com/users/mikelove/orgs","repos_url":"https://api.github.com/users/mikelove/repos","events_url":"https://api.github.com/users/mikelove/events{/privacy}","received_events_url":"https://api.github.com/users/mikelove/received_events","type":"User","site_admin":false},"created_at":"2016-12-15T21:39:15Z","updated_at":"2016-12-15T21:39:15Z","body":"If it's useful, I made an example where you can run beginning to end to reproduce (didn't see this thread beforehand)\r\n\r\nDownload these:\r\n\r\n```\r\nftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz\r\nftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz\r\nftp://ftp.ensembl.org/pub/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh38.87.gtf.gz\r\n\r\nftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR188/ERR188297/ERR188297_1.fastq.gz\r\nftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR188/ERR188297/ERR188297_2.fastq.gz\r\n```\r\n\r\nUsing STAR 2.5.2b\r\n\r\n```\r\nstar --runThreadN 6 \\\r\n     --runMode genomeGenerate \\\r\n     --genomeDir ensembl87 \\\r\n     --genomeFastaFiles Homo_sapiens.GRCh38.dna.primary_assembly.fa \\\r\n     --sjdbGTFfile Homo_sapiens.GRCh38.87.gtf \\\r\n     --sjdbOverhang 100\r\n\r\nstar --runThreadN 6 \\\r\n     --genomeDir ensembl87 \\\r\n     --readFilesIn ERR188297_1.fastq ERR188297_2.fastq \\\r\n     --outFileNamePrefix star/ \\\r\n     --outSAMtype BAM Unsorted \\\r\n     --quantMode TranscriptomeSAM\r\n```\r\n\r\nThen, following Thomas, I chop the version numbers from the FASTA\r\n\r\n```\r\ncut -f1 -d \".\" Homo_sapiens.GRCh38.cdna.all.fa > transcripts_unversioned.fa\r\n```\r\n\r\nNow Salmon v0.7.2\r\n\r\n```\r\nSalmon-0.7.2_linux_x86_64/bin/salmon quant -t transcripts_unversioned.fa -l IU -p 6 -a star/Aligned.toTranscriptome.out.bam -o align_test\r\n```\r\n\r\n**Note**: nothing in `libParams` dir...\r\n\r\n```\r\nSalmon-0.7.2_linux_x86_64/bin/salmon quant --gcBias -t transcripts_unversioned.fa -l IU -p 6 -a star/Aligned.toTranscriptome.out.bam -o align_testGC\r\n```\r\n\r\nThis produces segfault:\r\n\r\n```\r\n^M^MESC[0;32mprocessedESC[0;31m 0 ESC[0;32mreads in current roundESC[0;0m/nas02/home/m/i/milove/.lsbatch/1481837415.333618.shell: line 9: 29198 Segmentation fault      (core dumped)\r\n```"}}
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