{"action":"created","issue":{"url":"https://api.github.com/repos/tseemann/snippy/issues/141","repository_url":"https://api.github.com/repos/tseemann/snippy","labels_url":"https://api.github.com/repos/tseemann/snippy/issues/141/labels{/name}","comments_url":"https://api.github.com/repos/tseemann/snippy/issues/141/comments","events_url":"https://api.github.com/repos/tseemann/snippy/issues/141/events","html_url":"https://github.com/tseemann/snippy/issues/141","id":306152033,"number":141,"title":"running error","user":{"login":"yzhzu","id":5411077,"avatar_url":"https://avatars2.githubusercontent.com/u/5411077?v=4","gravatar_id":"","url":"https://api.github.com/users/yzhzu","html_url":"https://github.com/yzhzu","followers_url":"https://api.github.com/users/yzhzu/followers","following_url":"https://api.github.com/users/yzhzu/following{/other_user}","gists_url":"https://api.github.com/users/yzhzu/gists{/gist_id}","starred_url":"https://api.github.com/users/yzhzu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yzhzu/subscriptions","organizations_url":"https://api.github.com/users/yzhzu/orgs","repos_url":"https://api.github.com/users/yzhzu/repos","events_url":"https://api.github.com/users/yzhzu/events{/privacy}","received_events_url":"https://api.github.com/users/yzhzu/received_events","type":"User","site_admin":false},"labels":[{"id":99675791,"url":"https://api.github.com/repos/tseemann/snippy/labels/question","name":"question","color":"cc317c","default":true}],"state":"open","locked":false,"assignee":{"login":"tseemann","id":453972,"avatar_url":"https://avatars2.githubusercontent.com/u/453972?v=4","gravatar_id":"","url":"https://api.github.com/users/tseemann","html_url":"https://github.com/tseemann","followers_url":"https://api.github.com/users/tseemann/followers","following_url":"https://api.github.com/users/tseemann/following{/other_user}","gists_url":"https://api.github.com/users/tseemann/gists{/gist_id}","starred_url":"https://api.github.com/users/tseemann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tseemann/subscriptions","organizations_url":"https://api.github.com/users/tseemann/orgs","repos_url":"https://api.github.com/users/tseemann/repos","events_url":"https://api.github.com/users/tseemann/events{/privacy}","received_events_url":"https://api.github.com/users/tseemann/received_events","type":"User","site_admin":false},"assignees":[{"login":"tseemann","id":453972,"avatar_url":"https://avatars2.githubusercontent.com/u/453972?v=4","gravatar_id":"","url":"https://api.github.com/users/tseemann","html_url":"https://github.com/tseemann","followers_url":"https://api.github.com/users/tseemann/followers","following_url":"https://api.github.com/users/tseemann/following{/other_user}","gists_url":"https://api.github.com/users/tseemann/gists{/gist_id}","starred_url":"https://api.github.com/users/tseemann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tseemann/subscriptions","organizations_url":"https://api.github.com/users/tseemann/orgs","repos_url":"https://api.github.com/users/tseemann/repos","events_url":"https://api.github.com/users/tseemann/events{/privacy}","received_events_url":"https://api.github.com/users/tseemann/received_events","type":"User","site_admin":false}],"milestone":null,"comments":4,"created_at":"2018-03-17T12:17:32Z","updated_at":"2018-03-31T12:42:29Z","closed_at":null,"author_association":"NONE","body":"hello, everyone,  can you help me to deal with the error, when I perform snippy to investigate SNP between two genome, but the error still occurs. I don't know how to do?\r\nthank you very much.\r\n\r\n\r\nthe snps.log as following:\r\n\r\n\r\n### samtools faidx reference/ref.fa\r\n\r\n\r\n### bwa index reference/ref.fa\r\n\r\n[bwa_index] Pack FASTA... 0.04 sec\r\n[bwa_index] Construct BWT for the packed sequence...\r\n[bwa_index] 2.02 seconds elapse.\r\n[bwa_index] Update BWT... 0.06 sec\r\n[bwa_index] Pack forward-only FASTA... 0.02 sec\r\n[bwa_index] Construct SA from BWT and Occ... 0.63 sec\r\n[main] Version: 0.7.17-r1188\r\n[main] CMD: bwa index reference/ref.fa\r\n[main] Real time: 3.316 sec; CPU: 2.760 sec\r\n\r\n### mkdir reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa\r\n\r\n\r\n### mkdir reference/ref && bgzip -c reference/ref.gff > reference/ref/genes.gff.gz\r\n\r\n\r\n### (bwa mem  -v 2 -M -R '@RG\tID:snps\tSM:snps' -t 8 reference/ref.fa fake_reads.fq | samtools view -@ 8 -F 3844 -q 60 -S -b -u -T reference/ref.fa - | samtools sort -O bam -o snps.bam -@ 8 -)\r\n\r\n[E::bwa_set_rg] the read group line contained literal <tab> characters -- replace with escaped tabs: \\t\r\nsort: invalid option -- 'O'\r\nopen: No such file or directory\r\n[bam_sort_core] fail to open file bam\r\n[sam_header_read2] 41 sequences loaded.\r\n[sam_read1] reference '' is recognized as '*'.\r\n[main_samview] truncated file.\r\n\r\n### samtools index snps.bam\r\n\r\nopen: No such file or directory\r\n[bam_index_build2] fail to open the BAM file.\r\n\r\n### samtools depth -q 20 snps.bam | bgzip > snps.depth.gz\r\n\r\n\r\n### tabix -s 1 -b 2 -e 2 snps.depth.gz\r\n\r\n\r\n### fasta_generate_regions.py reference/ref.fa.fai 203073 > reference/ref.txt\r\n\r\n  File \"miniconda3/bin/fasta_generate_regions.py\", line 7\r\n    print \"usage: \", sys.argv[0], \" <fasta file or index file> <region size>\"\r\n                  ^\r\nSyntaxError: Missing parentheses in call to 'print'. Did you mean print(int \"usage: \", sys.argv[0], \" <fasta file or index file> <region size>\")?"},"comment":{"url":"https://api.github.com/repos/tseemann/snippy/issues/comments/377690463","html_url":"https://github.com/tseemann/snippy/issues/141#issuecomment-377690463","issue_url":"https://api.github.com/repos/tseemann/snippy/issues/141","id":377690463,"user":{"login":"yzhzu","id":5411077,"avatar_url":"https://avatars2.githubusercontent.com/u/5411077?v=4","gravatar_id":"","url":"https://api.github.com/users/yzhzu","html_url":"https://github.com/yzhzu","followers_url":"https://api.github.com/users/yzhzu/followers","following_url":"https://api.github.com/users/yzhzu/following{/other_user}","gists_url":"https://api.github.com/users/yzhzu/gists{/gist_id}","starred_url":"https://api.github.com/users/yzhzu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yzhzu/subscriptions","organizations_url":"https://api.github.com/users/yzhzu/orgs","repos_url":"https://api.github.com/users/yzhzu/repos","events_url":"https://api.github.com/users/yzhzu/events{/privacy}","received_events_url":"https://api.github.com/users/yzhzu/received_events","type":"User","site_admin":false},"created_at":"2018-03-31T12:42:29Z","updated_at":"2018-03-31T12:42:29Z","author_association":"NONE","body":"in current bioconda, the snippy version is 3.1"}}
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