{"action":"created","issue":{"url":"https://api.github.com/repos/maximilianh/crisporWebsite/issues/13","repository_url":"https://api.github.com/repos/maximilianh/crisporWebsite","labels_url":"https://api.github.com/repos/maximilianh/crisporWebsite/issues/13/labels{/name}","comments_url":"https://api.github.com/repos/maximilianh/crisporWebsite/issues/13/comments","events_url":"https://api.github.com/repos/maximilianh/crisporWebsite/issues/13/events","html_url":"https://github.com/maximilianh/crisporWebsite/issues/13","id":342301456,"node_id":"MDU6SXNzdWUzNDIzMDE0NTY=","number":13,"title":"Errors while trying to run command-line CRISPOR","user":{"login":"ceejaylee","id":27700341,"node_id":"MDQ6VXNlcjI3NzAwMzQx","avatar_url":"https://avatars2.githubusercontent.com/u/27700341?v=4","gravatar_id":"","url":"https://api.github.com/users/ceejaylee","html_url":"https://github.com/ceejaylee","followers_url":"https://api.github.com/users/ceejaylee/followers","following_url":"https://api.github.com/users/ceejaylee/following{/other_user}","gists_url":"https://api.github.com/users/ceejaylee/gists{/gist_id}","starred_url":"https://api.github.com/users/ceejaylee/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ceejaylee/subscriptions","organizations_url":"https://api.github.com/users/ceejaylee/orgs","repos_url":"https://api.github.com/users/ceejaylee/repos","events_url":"https://api.github.com/users/ceejaylee/events{/privacy}","received_events_url":"https://api.github.com/users/ceejaylee/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-07-18T12:11:55Z","updated_at":"2018-07-18T12:29:39Z","closed_at":null,"author_association":"NONE","body":"Hi there! I have been trying to run command-line CRISPOR. Unfortunately it keeps throwing root errors and I haven't been able to generate any guides. This is the code I have been running:\r\n`singularity run docker://pinellolab/crispor_crispresso_nat_prot crispor.py hg19 /net/rcstorenfs02/ifs/rc_labs/liau_lab/ceejay/crispor_input.fasta /net/rcstorenfs02/ifs/rc_labs/liau_lab/ceejay/crispor_output.tsv`\r\n\r\nAnd this is the output I have been receiving:\r\n```\r\nCreating container runtime...\r\nExploding layer: sha256:8ad8b3f87b378cfae583fef34e47a3c9203847d779961b7351cbf786af0bc09f.tar.gz\r\nExploding layer: sha256:9ceb84f9e6d343cce995c6e223ae3418a87b25a167aba922953341e94f535cf1.tar.gz\r\nExploding layer: sha256:c675caf21052d23973c95d259dbac97430d796da3fab2fc09802eb69ae48486c.tar.gz\r\nExploding layer: sha256:0c972402cfac710d09baba50faace437a49e067d834ff71aba43b20c825c3428.tar.gz\r\nExploding layer: sha256:e90d10a215c5bef2f758bcad29fd62d4c3aa63c9390b98c7ca43595ffc0bef1c.tar.gz\r\nExploding layer: sha256:c26de10464117fe619c0d37e215d13f73329c23274248911bf2926b1e75f0880.tar.gz\r\nExploding layer: sha256:44cac1c509e7f6fe4352f8aa3e45e7b8c5c0888c5f14821d433380e84b0e42a6.tar.gz\r\nExploding layer: sha256:ac83b0b490e58aecd2a2605f0551cd1b52d9e894ad44f7c0d69511703f99ecae.tar.gz\r\nExploding layer: sha256:0922aaa6836662bd082286e2a09e9e7eea13f8f56b77a5593e748109ad291b03.tar.gz\r\nExploding layer: sha256:70d872d8f6465e89f63f7ed47604f2b83a33a1c22fc873709d3756b3c0b72e5c.tar.gz\r\nExploding layer: sha256:d630f1c18b4996fbe11e0df6981e75b0e659ddcd095a059b0deff70fbad54d51.tar.gz\r\nExploding layer: sha256:2960bc1f6572ea3c80c3f67dff1cfa917619571d95f5bec2843d5b3076adf967.tar.gz\r\nExploding layer: sha256:226437feb6f94b5e2e4f2f4b4b7a1c445b6d3f06ead88f2dd0c5f62640ecf7f9.tar.gz\r\nExploding layer: sha256:0dc4a9118e98c8a685a71f616fc21d2fac1b0ed3425bc87c6c87949903b45d93.tar.gz\r\nExploding layer: sha256:18b5faa6fdbc67e5090848e782cc2fb65b39a01b34d1ad080ac4f4af8b506e22.tar.gz\r\nExploding layer: sha256:f578d6a95786009d26fc050c4d46af5592023f6f11a12cd5a30e74f088b46255.tar.gz\r\nExploding layer: sha256:155353c8b2c0d1a6182763bd818f06c42513f52af0f437097f6e20e05acf5497.tar.gz\r\nExploding layer: sha256:978aea45006018bc20f94cd5404a9f3349b9c7a2c28157f6ccaec1cf1080d32e.tar.gz\r\nExploding layer: sha256:ef7844c5f02d1915239aa4abac3ed3728d81c2c231a6a1a3f4a8f544dc7562a5.tar.gz\r\n[WARN  tini (103249)] Tini is not running as PID 1 and isn't registered as a child subreaper.\r\nZombie processes will not be re-parented to Tini, so zombie reaping won't work.\r\nTo fix the problem, use the -s option or set the environment variable TINI_SUBREAPER to register Tini as a child subreaper, or run Tini as PID 1.\r\nINFO:root:running on sequence ID 'hg19_wgEncodeGencodeBasicV19_ENST00000413440.1_1 range=chr1:14104913-14109326 5'pad=0 3'pad=0 strand=+ repeatMasking=none'\r\nERROR:root:no match found for sequence /net/rcstorenfs02/ifs/rc_labs/liau_lab/ceejay/crispor_input.fasta in genome hg19\r\nINFO:root:Progress oAybu0NdRWqXk0IOTZ2b - effScores - Calculating guide efficiency scores\r\nINFO:root:Wrote eff scores to /dev/shm/crisporG5dXIS/oAybu0NdRWqXk0IOTZ2b.effScores.tab\r\nINFO:root:Progress oAybu0NdRWqXk0IOTZ2b - bwa - Alignment of potential guides, mismatches <= 4\r\n[bwa_aln] fail to locate the index\r\nERROR:root:Error: could not run command set -o pipefail; /crisporWebsite/bin/Linux/bwa aln -o 0 -m 1980000 -n 4 -k 4 -N -l 20 /crisporWebsite/genomes/hg19/hg19.fa /dev/shm/crisporG5dXIS/oAybu0NdRWqXk0IOTZ2b.fa > /dev/shm/crisporG5dXIS/oAybu0NdRWqXk0IOTZ2b.sa.\r\n```\r\nI have also been running an adapted version of the code on the Nat Prot paper:\r\n```\r\nsingularity run \\\r\n-B /net/rcstorenfs02/ifs/rc_labs/liau_lab/ceejay:/DATA \\\r\n-B /net/rcstorenfs02/ifs/rc_labs/liau_lab/crispor_genomes:/crisporWebsite/genomes \\\r\n-W /DATA \\docker://pinellolab/crispor_crispresso_nat_prot \\\r\ncrispor.py hg19 crispor_input.fasta crispor_output.tsv --satMutDir=./\r\n```\r\nand it gives the same errors.\r\n\r\nDo you have any suggestions why this might be happening? Thank you!"},"comment":{"url":"https://api.github.com/repos/maximilianh/crisporWebsite/issues/comments/405913796","html_url":"https://github.com/maximilianh/crisporWebsite/issues/13#issuecomment-405913796","issue_url":"https://api.github.com/repos/maximilianh/crisporWebsite/issues/13","id":405913796,"node_id":"MDEyOklzc3VlQ29tbWVudDQwNTkxMzc5Ng==","user":{"login":"ceejaylee","id":27700341,"node_id":"MDQ6VXNlcjI3NzAwMzQx","avatar_url":"https://avatars2.githubusercontent.com/u/27700341?v=4","gravatar_id":"","url":"https://api.github.com/users/ceejaylee","html_url":"https://github.com/ceejaylee","followers_url":"https://api.github.com/users/ceejaylee/followers","following_url":"https://api.github.com/users/ceejaylee/following{/other_user}","gists_url":"https://api.github.com/users/ceejaylee/gists{/gist_id}","starred_url":"https://api.github.com/users/ceejaylee/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ceejaylee/subscriptions","organizations_url":"https://api.github.com/users/ceejaylee/orgs","repos_url":"https://api.github.com/users/ceejaylee/repos","events_url":"https://api.github.com/users/ceejaylee/events{/privacy}","received_events_url":"https://api.github.com/users/ceejaylee/received_events","type":"User","site_admin":false},"created_at":"2018-07-18T12:29:39Z","updated_at":"2018-07-18T12:29:39Z","author_association":"NONE","body":"Thank you for your prompt response! I'll try it out of the box and let you know if things still don't work."}}
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