http://qa.lifesciencedb.jp/questions/872/tophat%E3%81%AE%E3%82%A8%E3%83%A9%E3%83%BC%E3%81%AB%E3%81%A4%E3%81%84%E3%81%A6<p>dry解析教本という本で自習中の初心者です。大学のMacでは出来たのに家のMacMiniだとエラーが出て、理由が分かりません。</p> <p>SKMac-mini:expression SK$ tophat -p 1 -G Homo_sapiens/NCBI/build37.2/Annotation/Archives/archive-2014-06-02-13-47-29/Genes/genes.gtf -o tophat_results/ERR266337_P5 Homo_sapiens/NCBI/build37.2/Sequence/Bowtie2Index/genome ERR266337_trim.fastq</p> <h2>[2017-10-31 21:32:10] Beginning TopHat run (v2.1.1)</h2> <p>[2017-10-31 21:32:10] Checking for Bowtie Bowtie version: 2.3.3.1 [2017-10-31 21:32:10] Checking for Bowtie index files (genome).. [2017-10-31 21:32:10] Checking for reference FASTA file [2017-10-31 21:32:10] Generating SAM header for Homo_sapiens/NCBI/build37.2/Sequence/Bowtie2Index/genome Traceback (most recent call last): File "/usr/local/bin/tophat", line 4107, in &lt;module&gt; sys.exit(main()) File "/usr/local/bin/tophat", line 3961, in main params.read_params = check_reads_format(params, reads_list) File "/usr/local/bin/tophat", line 1856, in check_reads_format zf = ZReader(f_name, params) File "/usr/local/bin/tophat", line 1809, in <strong>init</strong> self.file=open(filename) IOError: [Errno 2] No such file or directory: 'ERR266337_trim.fastq'</p> <p>ところが今いるexpressionというディレクトリには確かにERR266337_trim.fastqが存在するはずだと思います。</p> <p>SKMac-mini:expression SK$ ls ERR266335.fastq ERR266347.fastq ERR266351_trim.fastq　 ERR266335_trim.fastq　 ERR266347.fastq.gz FastQC ERR266337.fastq ERR266347_trim.fastq　 Homo_sapiens ERR266337_trim.fastq　 ERR266349.fastq Homo_sapiens_NCBI_build37.2.tar.gz ERR266338.fastq ERR266349_trim.fastq　 tophat_results ERR266338_trim.fastq　 ERR266351.fastq</p> <p>このエラーはどうして出てきたのでしょう？ご助言がいただければ幸いです。</p>jaMon, 06 Nov 2017 21:39:14 +0900http://qa.lifesciencedb.jp/questions/872/tophat%E3%81%AE%E3%82%A8%E3%83%A9%E3%83%BC%E3%81%AB%E3%81%A4%E3%81%84%E3%81%A6/873<p>解決はしていませんが、１つわかったことがあります。１番目のサンプルは無事に解析できているようです。２番目のサンプルを解析しようとすると同じエラーがでました。２番目を諦めて３番目を解析しようとしても同じでした。前回の質問の後でディレクトリを変えて(expression-&gt;expression2)別のサンプルセットを解析しようとして気づきました。実は前回のサンプルセットでも１番目は解析できていたのです。２番目以降を解析しようとするとエラーが出ます。エラーメッセージはBiostarsのQuestion: Weird Tophat2 Error Message　https://www.biostars.org/p/78628/　に似ている気はしています。</p> <p>[SKMac-mini:expression2 SK$ tophat -p 2 -G ~/expression/Homo_sapiens/NCBI/build37.2/Annotation/Archives/archive-2014-06-02-13-47-29/Genes/genes.gtf -o tophat_results/ERR030890 ~/expression/Homo_sapiens/NCBI/build37.2/Sequence/Bowtie2Index/genome ERR030890_trim.fastq</p> <h2>[2017-11-06 07:14:27] Beginning TopHat run (v2.1.1)</h2> <p>[2017-11-06 07:14:27] Checking for Bowtie Bowtie version: 2.3.3.1 [2017-11-06 07:14:27] Checking for Bowtie index files (genome).. [2017-11-06 07:14:27] Checking for reference FASTA file [2017-11-06 07:14:27] Generating SAM header for /Users/SK/expression/Homo_sapiens/NCBI/build37.2/Sequence/Bowtie2Index/genome [2017-11-06 07:14:30] Reading known junctions from GTF file [2017-11-06 07:14:36] Preparing reads left reads: min. length=30, max. length=75, 57662957 kept reads (7063 discarded) [2017-11-06 07:33:28] Building transcriptome data files tophat_results/ERR030890/tmp/genes [2017-11-06 07:34:28] Building Bowtie index from genes.fa [2017-11-06 07:42:51] Mapping left_kept_reads to transcriptome genes with Bowtie2 [2017-11-06 08:59:18] Resuming TopHat pipeline with unmapped reads [2017-11-06 08:59:19] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 [2017-11-06 10:08:11] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3) [2017-11-06 10:11:14] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3) [2017-11-06 10:16:20] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3) [2017-11-06 10:19:14] Searching for junctions via segment mapping [2017-11-06 10:27:59] Retrieving sequences for splices [2017-11-06 10:29:30] Indexing splices Building a SMALL index [2017-11-06 10:29:53] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3) [2017-11-06 10:30:35] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3) [2017-11-06 10:31:25] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3) [2017-11-06 10:32:00] Joining segment hits [2017-11-06 10:35:49] Reporting output tracks</p> <hr> <p>[2017-11-06 11:24:13] A summary of the alignment counts can be found in tophat_results/ERR030890/align_summary.txt [2017-11-06 11:24:13] Run complete: 04:09:46 elapsed SKMac-mini:expression2 SK$ tophat -p 2 -G ~/expression/Homo_sapiens/NCBI/build37.2/Annotation/Archives/archive-2014-06-02-13-47-29/Genes/genes.gtf -o tophat_results/ERR030894 ~/expression/Homo_sapiens/NCBI/build37.2/Sequence/Bowtie2Index/genome ERR030894_trim.fastq &amp; [1] 6005 SKMac-mini:expression2 SK$ [2017-11-06 20:40:52] Beginning TopHat run (v2.1.1)</p> <hr> <p>[2017-11-06 20:40:52] Checking for Bowtie Bowtie version: 2.3.3.1 [2017-11-06 20:40:52] Checking for Bowtie index files (genome).. [2017-11-06 20:40:52] Checking for reference FASTA file [2017-11-06 20:40:52] Generating SAM header for /Users/SK/expression/Homo_sapiens/NCBI/build37.2/Sequence/Bowtie2Index/genome Traceback (most recent call last): File "/usr/local/bin/tophat", line 4107, in &lt;module&gt; sys.exit(main()) File "/usr/local/bin/tophat", line 3961, in main params.read_params = check_reads_format(params, reads_list) File "/usr/local/bin/tophat", line 1856, in check_reads_format zf = ZReader(f_name, params) File "/usr/local/bin/tophat", line 1809, in <strong>init</strong> self.file=open(filename) IOError: [Errno 2] No such file or directory: 'ERR030894_trim.fastq'</p>SKMon, 06 Nov 2017 21:39:14 +0900http://qa.lifesciencedb.jp/questions/872/tophat%E3%81%AE%E3%82%A8%E3%83%A9%E3%83%BC%E3%81%AB%E3%81%A4%E3%81%84%E3%81%A6/873