{"action":"created","issue":{"url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/268","repository_url":"https://api.github.com/repos/COMBINE-lab/salmon","labels_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/268/labels{/name}","comments_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/268/comments","events_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/268/events","html_url":"https://github.com/COMBINE-lab/salmon/issues/268","id":350623927,"node_id":"MDU6SXNzdWUzNTA2MjM5Mjc=","number":268,"title":"Segmentation fault in bioconda installation","user":{"login":"NatPRoach","id":5082137,"node_id":"MDQ6VXNlcjUwODIxMzc=","avatar_url":"https://avatars2.githubusercontent.com/u/5082137?v=4","gravatar_id":"","url":"https://api.github.com/users/NatPRoach","html_url":"https://github.com/NatPRoach","followers_url":"https://api.github.com/users/NatPRoach/followers","following_url":"https://api.github.com/users/NatPRoach/following{/other_user}","gists_url":"https://api.github.com/users/NatPRoach/gists{/gist_id}","starred_url":"https://api.github.com/users/NatPRoach/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/NatPRoach/subscriptions","organizations_url":"https://api.github.com/users/NatPRoach/orgs","repos_url":"https://api.github.com/users/NatPRoach/repos","events_url":"https://api.github.com/users/NatPRoach/events{/privacy}","received_events_url":"https://api.github.com/users/NatPRoach/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-08-14T22:46:22Z","updated_at":"2018-08-24T17:32:56Z","closed_at":"2018-08-14T23:12:51Z","author_association":"NONE","body":"Hello,\r\nI'm running in to problems trying to run salmon quant. I've installed the latest version 0.11.2 via bioconda, and successfully constructed an index of the C. elegans Wormbase WS265 transcriptome with the following settings:\r\n\r\n`salmon index -k 21 -p 24 -t ${txome_reference} -i ${index_path}`\r\n\r\nbut upon running quant with the following command:\r\n\r\n`salmon quant -i ${index_path} -o ${out_prefix} -l IU -1 ${mate1_reads} -2 ${mate2_reads}\r\n`\r\n\r\nI get a segmentation fault error midway through running:\r\n\r\n```hits: 122146249, hits per frag:  2.10747\r\nprocessed 58500001 fragments\r\nhits: 123209453, hits per frag:  2.11344\r\nprocessed 59000000 fragments\r\nhits: 124280773, hits per frag:  2.10932\r\n\r\n/cm/local/apps/slurm/var/spool/job28571481/slurm_script: line 39:  1187 Segmentation fault      salmon quant -i ${index_path} -o ${out_prefix} -l IU -1 ${mate1_reads} -2 ${mate2_reads}\r\n```\r\n\r\nIf it helps I'm running this on the following SRA data:\r\n> SRR016679\r\n> SRR016680\r\n> SRR016681\r\n\r\nThis is running on a CentOS release 6.9 cluster. The script in which salmon is being called is being run through SLURM 17.11.7 workload management software.\r\n\r\nI tried installing a older version of salmon ( 0.9.1 )  through conda and ended up with the same error running that version. \r\nI've also tried downloading the source and compiling, but am running in to an error upon calling make:\r\n\r\n```libtool: compile:  /usr/bin/cc -DHAVE_CONFIG_H -I. -I.. -I.. -MT libstaden_read_la-cram_io.lo -MD -MP -MF .deps/libstaden_read_la-cram_io.Tpo -c cram_io.c -o libstaden_read_la-cram_io.o\r\ncram_io.c:66:18: error: lzma.h: No such file or directory\r\ncram_io.c: In function 'lzma_mem_deflate':\r\ncram_io.c:1389: error: 'LZMA_OK' undeclared (first use in this function)\r\ncram_io.c:1389: error: (Each undeclared identifier is reported only once\r\ncram_io.c:1389: error: for each function it appears in.)\r\ncram_io.c:1389: error: 'LZMA_CHECK_CRC32' undeclared (first use in this function)\r\ncram_io.c: In function 'lzma_mem_inflate':\r\ncram_io.c:1399: error: 'lzma_stream' undeclared (first use in this function)\r\ncram_io.c:1399: error: expected ';' before 'strm'\r\ncram_io.c:1405: error: 'LZMA_OK' undeclared (first use in this function)\r\ncram_io.c:1405: error: 'strm' undeclared (first use in this function)\r\ncram_io.c:1420: error: 'LZMA_RUN' undeclared (first use in this function)\r\ncram_io.c:1421: error: 'LZMA_STREAM_END' undeclared (first use in this function)\r\ncram_io.c:1434: error: 'LZMA_FINISH' undeclared (first use in this function)\r\nmake[5]: *** [libstaden_read_la-cram_io.lo] Error 1\r\nmake[4]: *** [all-recursive] Error 1\r\nmake[3]: *** [all] Error 2\r\nmake[2]: *** [libstadenio-prefix/src/libstadenio-stamp/libstadenio-build] Error 2\r\nmake[1]: *** [CMakeFiles/libstadenio.dir/all] Error 2\r\nmake: *** [all] Error 2```\r\n"},"comment":{"url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/comments/415828393","html_url":"https://github.com/COMBINE-lab/salmon/issues/268#issuecomment-415828393","issue_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/268","id":415828393,"node_id":"MDEyOklzc3VlQ29tbWVudDQxNTgyODM5Mw==","user":{"login":"scottx611x","id":5629547,"node_id":"MDQ6VXNlcjU2Mjk1NDc=","avatar_url":"https://avatars2.githubusercontent.com/u/5629547?v=4","gravatar_id":"","url":"https://api.github.com/users/scottx611x","html_url":"https://github.com/scottx611x","followers_url":"https://api.github.com/users/scottx611x/followers","following_url":"https://api.github.com/users/scottx611x/following{/other_user}","gists_url":"https://api.github.com/users/scottx611x/gists{/gist_id}","starred_url":"https://api.github.com/users/scottx611x/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/scottx611x/subscriptions","organizations_url":"https://api.github.com/users/scottx611x/orgs","repos_url":"https://api.github.com/users/scottx611x/repos","events_url":"https://api.github.com/users/scottx611x/events{/privacy}","received_events_url":"https://api.github.com/users/scottx611x/received_events","type":"User","site_admin":false},"created_at":"2018-08-24T17:32:56Z","updated_at":"2018-08-24T17:32:56Z","author_association":"NONE","body":"FWIW I'm experiencing this same behavior (`salmon quant` segfaults with 0.9.1 & 0.11.2 from bioconda) on my SLURM cluster. Ref #271 \r\n\r\n@NatPRoach If you ever end up figuring out a solution for bioconda installs for this please let me know!\r\n\r\n"}}
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