{"action":"created","issue":{"url":"https://api.github.com/repos/isovic/racon/issues/68","repository_url":"https://api.github.com/repos/isovic/racon","labels_url":"https://api.github.com/repos/isovic/racon/issues/68/labels{/name}","comments_url":"https://api.github.com/repos/isovic/racon/issues/68/comments","events_url":"https://api.github.com/repos/isovic/racon/issues/68/events","html_url":"https://github.com/isovic/racon/issues/68","id":314528883,"number":68,"title":"Further explanation of 'error: unequal lengths in sequence and overlap file for sequence'","user":{"login":"Benji3841","id":13872884,"avatar_url":"https://avatars0.githubusercontent.com/u/13872884?v=4","gravatar_id":"","url":"https://api.github.com/users/Benji3841","html_url":"https://github.com/Benji3841","followers_url":"https://api.github.com/users/Benji3841/followers","following_url":"https://api.github.com/users/Benji3841/following{/other_user}","gists_url":"https://api.github.com/users/Benji3841/gists{/gist_id}","starred_url":"https://api.github.com/users/Benji3841/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Benji3841/subscriptions","organizations_url":"https://api.github.com/users/Benji3841/orgs","repos_url":"https://api.github.com/users/Benji3841/repos","events_url":"https://api.github.com/users/Benji3841/events{/privacy}","received_events_url":"https://api.github.com/users/Benji3841/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2018-04-16T07:21:05Z","updated_at":"2018-05-02T21:12:24Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\n\r\nAttempting to implement racon in nanopore polishing pipeline.\r\n\r\nUsing bowtie2 for alignment of concatenated fastq illumina read files, passing this and the  concatenated read file to racon.\r\n\r\nI get the following error code during execution:\r\n\r\nBegining racon polish iteration: 1...\r\n[racon::Polisher::initialize] loaded target sequences\r\n[racon::Polisher::initialize] loaded sequences\r\n[racon::overlap::find_breaking_points] error: unequal lengths in sequence and overlap file for sequence M03542:170:000000000-BL6WR:1:1101:22727:1756!\r\n\r\nCould you elaborate on the error message so I can troubleshoot?\r\n\r\nGreatly appreciate you time!\r\n\r\nCheers,\r\nBen\r\n\r\nP.S. Here is code from pipeline:\r\n\r\n\tRACONBASEDIR=racoon0\"$I\"\r\n\tmkdir $RACONBASEDIR\r\n\tINDX=\"$RACONBASEDIR\"/\"$GENOMEBASE\"\"$I\"\r\n\tprintf \"Building bowtie2 index: $INDX\\n\"\r\n\tprintf \"Buidling...\\n\"\r\n\tsleep 1\r\n\tbowtie2-build $ITERGENOME $INDX\r\n\tprintf \"Completed buidling bowtie2 index.\\n\\n\"\r\n\r\n\t#\tAlign Illmuina fastq reads\r\n\tprintf \"Concatenating Illumina reads for alignment...\\n\"\r\n\tCATREADS=\"$RACONBASEDIR\"/temp.fastq.gz\r\n\tzcat $ILLREAD1 $ILLREAD2 | gzip -c > $CATREADS\r\n\tprintf \"Completed concatenation.\\n\\n\"\r\n\r\n\tALIGNDREADS=\"$RACONBASEDIR\"/\"$GENOMEBASE\".\"$I\".sam\r\n\tprintf \"Aligning $CATREADS to $INDX with bowtie2...\\n\"\r\n\r\n\tbowtie2 -p 12 --fast -x $INDX -U $CATREADS -S $ALIGNDREADS\r\n\tprintf\t\"Completer bowtie2 alignment.\\n\"\r\n\tprintf \"Aligned reads ouput file: $ALIGNDREADS\\n\\n\"\r\n\r\n\t#\tPass genome.iteration, illumina.reads, and iteration.alignment to racon\r\n\tprintf \"Begining racon polish iteration: $I...\\n\"\r\n\tPOLISHEDGENOME=\"$RACONBASEDIR\"/\"$GENOMEBASE\".polish.\"$I\".fasta\r\n\tracon $CATREADS $ALIGNDREADS $ITERGENOME > $POLISHEDGENOME"},"comment":{"url":"https://api.github.com/repos/isovic/racon/issues/comments/386122981","html_url":"https://github.com/isovic/racon/issues/68#issuecomment-386122981","issue_url":"https://api.github.com/repos/isovic/racon/issues/68","id":386122981,"user":{"login":"sarah872","id":29072882,"avatar_url":"https://avatars0.githubusercontent.com/u/29072882?v=4","gravatar_id":"","url":"https://api.github.com/users/sarah872","html_url":"https://github.com/sarah872","followers_url":"https://api.github.com/users/sarah872/followers","following_url":"https://api.github.com/users/sarah872/following{/other_user}","gists_url":"https://api.github.com/users/sarah872/gists{/gist_id}","starred_url":"https://api.github.com/users/sarah872/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sarah872/subscriptions","organizations_url":"https://api.github.com/users/sarah872/orgs","repos_url":"https://api.github.com/users/sarah872/repos","events_url":"https://api.github.com/users/sarah872/events{/privacy}","received_events_url":"https://api.github.com/users/sarah872/received_events","type":"User","site_admin":false},"created_at":"2018-05-02T21:12:24Z","updated_at":"2018-05-02T21:12:24Z","author_association":"NONE","body":"For instance the read 'HWI-ST863:386:C5Y8UACXX:3:1107:14282:8547'\r\n\r\nthis one is twice in the read fastq because they are paired end:\r\n\r\n    $ zgrep -A 3 \"HWI-ST863:386:C5Y8UACXX:3:1107:14282:8547\" reads.fastq.gz \r\n    @HWI-ST863:386:C5Y8UACXX:3:1107:14282:8547 \r\n    CCGCTGATCACCGCGCAAACACACAGCAGCAAAATTTCCTCCAGATCATAAAGCTTGTTCTTGTCCGAGCGGGGATCTTTGATCGTCGAAAAATGCGAGA\r\n    +\r\n    CCCFFFFFHHFHHJJJIJJJGIJJJJJJJJIJIGIJJJJIJIJJIIIIIJHIJJHGHEHFFFFFFEDDBDDDDDDBDDDDDDCDD<89>BBB<ACDDDD#\r\n    --\r\n    @HWI-ST863:386:C5Y8UACXX:3:1107:14282:8547\r\n    TCGATATGATAGTCGTGGCCCGCCTTCTTGTTGAGCGCGATGGTAGCGCCGCCGTGCTTGGGTTGTTTGGTCTTTGCCATCGTGGAAGTGTAACCCAAGA\r\n    +\r\n    CCCFFFFFHHHHHJJJJJJJJJIJIJJIIIJJIFGIIIJGIJJGIJJHGFACDDBDDDDDDD?@DBBDCDACDDD@CCDCDDBBD?CDCCDDEDDDDDDB\r\n\r\n\r\nand they are therefore 4 times in the alignment file:\r\n\r\n    $ grep HWI-ST863:386:C5Y8UACXX:3:1107:14282:8547 mapped_ill-pe_hybr-genome.bwamem.sam \r\n    HWI-ST863:386:C5Y8UACXX:3:1107:14282:8547\t0\tNODE_1_length_96688_cov_60.6554\t1\t60\t5S95M\t*\t0\t0\t    CCGCTGATCACCGCGCAAACACACAGCAGCAAAATTTCCTCCAGATCATAAAGCTTGTTCTTGTCCGAGCGGGGATCTTTGATCGTCGAAAAATGCGAGCCCFFFFFHHFHHJJJIJJJGIJJJJJJJJIJIGIJJJJIJIJJIIIIIJHIJJHGHEHFFFFFFEDDBDDDDDDBDDDDDDCDD<89>BBB<ACDDDD#\tNM:i:0\tMD:Z:95\tAS:i:95\tXS:i:60\r\n    HWI-ST863:386:C5Y8UACXX:3:1107:14282:8547\t0\tNODE_15_length_49256_cov_64.9048\t49063\t60\t100M\t*\t0\t0\tTCGATATGATAGTCGTGGCCCGCCTTCTTGTTGAGCGCGATGGTAGCGCCGCCGTGCTTGGGTTGTTTGGTCTTTGCCATCGTGGAAGTGTAACCCAAGA\tCCCFFFFFHHHHHJJJJJJJJJIJIJJIIIJJIFGIIIJGIJJGIJJHGFACDDBDDDDDDD?@DBBDCDACDDD@CCDCDDBBD?CDCCDDEDDDDDDB\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\r\n\r\n"}}
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