This is what I am running:
TopHat run (v2.0.9), Bowtie version: 2.1.0.0, Samtools version: 0.1.19.0
This is what I entered:
And finally, here is my tophat.log
The output directory is created, as are the subdirectories. The tmp directory contains plenty of files, including "left_kept_reads.m2g_um.bam"
That file is ~1GB (and it's permissions are me:read and write, staff:read only, everyone:read only)
Help is appreciated
TopHat run (v2.0.9), Bowtie version: 2.1.0.0, Samtools version: 0.1.19.0
This is what I entered:
Code:
tophat2 -p 24 -G /Users/mascano/Sequence_Analyses/Reference/Homo_sapiens_NCBI_build37.2/Homo_sapiens/NCBI/build37.2/Annotation/Genes/genes.gtf -o PMA_0hr_TotalRNA /Users/mascano/Sequence_Analyses/Reference/Homo_sapiens_NCBI_build37.2/Homo_sapiens/NCBI/build37.2/Sequence/Bowtie2index/genome /Users/mascano/Sequence_Analyses/DATA/THP1_timecourse/Act_1_ATCACG_L002_R1_001.fastq
Code:
[2013-08-20 12:28:14] Beginning TopHat run (v2.0.9) ----------------------------------------------- [2013-08-20 12:28:14] Checking for Bowtie Bowtie version: 2.1.0.0 [2013-08-20 12:28:14] Checking for Samtools Samtools version: 0.1.19.0 [2013-08-20 12:28:14] Checking for Bowtie index files (genome).. [2013-08-20 12:28:14] Checking for reference FASTA file [2013-08-20 12:28:14] Generating SAM header for /Users/mascano/Sequence_Analyses/Reference/Homo_sapiens_NCBI_build37.2/Homo_sapiens/NCBI/build37.2/Sequence/Bowtie2index/genome format: fastq quality scale: phred33 (default) [2013-08-20 12:28:47] Reading known junctions from GTF file [2013-08-20 12:28:51] Preparing reads left reads: min. length=101, max. length=101, 26861915 kept reads (78856 discarded) [2013-08-20 12:38:22] Building transcriptome data files.. [2013-08-20 12:39:34] Building Bowtie index from genes.fa [2013-08-20 12:52:18] Mapping left_kept_reads to transcriptome genes with Bowtie2 [2013-08-20 13:03:00] Resuming TopHat pipeline with unmapped reads [2013-08-20 13:03:00] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 [2013-08-20 13:36:56] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4) [2013-08-20 13:43:24] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4) [2013-08-20 13:51:47] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4) [2013-08-20 13:59:15] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4) [2013-08-20 14:10:43] Searching for junctions via segment mapping [2013-08-20 14:15:54] Retrieving sequences for splices [2013-08-20 14:18:21] Indexing splices [2013-08-20 14:19:02] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4) [2013-08-20 14:20:37] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4) [2013-08-20 14:22:42] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4) [2013-08-20 14:24:24] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4) [2013-08-20 14:26:36] Joining segment hits [FAILED] Error running 'long_spanning_reads':Error: cannot open PMA_0hr_TotalRNA/tmp/left_kept_reads.m2g_um.bam for reading
That file is ~1GB (and it's permissions are me:read and write, staff:read only, everyone:read only)
Help is appreciated
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