{"action":"opened","issue":{"url":"https://api.github.com/repos/tseemann/nullarbor/issues/83","repository_url":"https://api.github.com/repos/tseemann/nullarbor","labels_url":"https://api.github.com/repos/tseemann/nullarbor/issues/83/labels{/name}","comments_url":"https://api.github.com/repos/tseemann/nullarbor/issues/83/comments","events_url":"https://api.github.com/repos/tseemann/nullarbor/issues/83/events","html_url":"https://github.com/tseemann/nullarbor/issues/83","id":162317325,"number":83,"title":"ERROR(freebayes): Could not open input BAM files","user":{"login":"elliot-sawyer","id":354793,"avatar_url":"https://avatars.githubusercontent.com/u/354793?v=3","gravatar_id":"","url":"https://api.github.com/users/elliot-sawyer","html_url":"https://github.com/elliot-sawyer","followers_url":"https://api.github.com/users/elliot-sawyer/followers","following_url":"https://api.github.com/users/elliot-sawyer/following{/other_user}","gists_url":"https://api.github.com/users/elliot-sawyer/gists{/gist_id}","starred_url":"https://api.github.com/users/elliot-sawyer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/elliot-sawyer/subscriptions","organizations_url":"https://api.github.com/users/elliot-sawyer/orgs","repos_url":"https://api.github.com/users/elliot-sawyer/repos","events_url":"https://api.github.com/users/elliot-sawyer/events{/privacy}","received_events_url":"https://api.github.com/users/elliot-sawyer/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-06-26T08:04:30Z","updated_at":"2016-06-26T08:04:30Z","closed_at":null,"body":"Hello Torsten,\r\nI'm running nullarbor on a Macbook Pro with 16GB of memory. It seems to fail once it gets to the `snippy` tool. I see the following following output:\r\n\r\n```\r\n[19:46:07] Running: samtools index snps.bam 2>> snps.log\r\n[19:46:07] Running: samtools depth -q 20 snps.bam | bgzip > snps.depth.gz 2>> snps.log\r\nopen: No such file or directory\r\n[19:46:07] Running: tabix -s 1 -b 2 -e 2 snps.depth.gz 2>> snps.log\r\n[19:46:07] Running: fasta_generate_regions.py reference/ref.fa.fai 358557 > reference/ref.txt 2>> snps.log\r\n[19:46:07] Running: freebayes-parallel reference/ref.txt 2 -p 1 -q 20 -m 60 --min-coverage 10 -V -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log\r\n[19:46:08] Error running command, check Isolate1/Isolate1/snps.log\r\nmake: *** [Isolate1/Isolate1/snps.tab] Error 2\r\n```\r\n\r\nThis was taken from snps.log:\r\n\r\n```\r\n...\r\n### freebayes-parallel reference/ref.txt 2 -p 1 -q 20 -m 60 --min-coverage 10 -V -f reference/ref.fa snps.bam > snps.raw.vcf\r\n\r\nERROR(freebayes): Could not open input BAM files\r\nBamMultiReader::Open: unable to open all files: \t\r\n\tunable to open file: snps.bam\r\n\r\n...(repeats 7 more times)\r\n```\r\n\r\nI've tried Googling for BamMultiReader::Open and \"Could not open input BAM files\" but I'm not having any luck. It doesn't seem to be a cpan module and all other references point to a problem with freebayes. What else can I do to investigate the cause of the problem and resolve it?\r\n\r\nThanks!"}}
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