I am doing rna-seq analyses using tophat. The tophat is mapping against mm9 genome. It is almost 20 hours since I started the execution and it is still running.
Is it normal or I need to tweak any parameter to make it fast?
Is it normal or I need to tweak any parameter to make it fast?
Code:
tophat -p 4 -G genes.gtf -o outputFiles/D13_178_MPP_CKO_tophatOut genome rnaseq/CKO/xxx_1_sequence.fastq rnaseq/CKO/xxx_2_sequence.fastq
Code:
[2013-03-19 15:14:14] Beginning TopHat run (v2.0.8) ----------------------------------------------- [2013-03-19 15:14:14] Checking for Bowtie Bowtie version: 2.1.0.0 [2013-03-19 15:14:14] Checking for Samtools Samtools version: 0.1.18.0 [2013-03-19 15:14:14] Checking for Bowtie index files [2013-03-19 15:14:14] Checking for reference FASTA file [2013-03-19 15:14:14] Generating SAM header for genome format: fastq quality scale: phred33 (default) [2013-03-19 15:14:17] Reading known junctions from GTF file [2013-03-19 15:14:19] Preparing reads left reads: min. length=80, max. length=80, 40008050 kept reads (1239197 discarded) right reads: min. length=80, max. length=80, 40950279 kept reads (296968 discarded) [2013-03-19 15:35:10] Creating transcriptome data files.. [2013-03-19 15:36:00] Building Bowtie index from genes.fa [2013-03-19 15:39:59] Mapping left_kept_reads to transcriptome genes with Bowtie2 [2013-03-19 17:41:34] Mapping right_kept_reads to transcriptome genes with Bowtie2 [2013-03-20 03:43:06] Resuming TopHat pipeline with unmapped reads [2013-03-20 03:43:06] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 [2013-03-20 05:16:00] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3) [2013-03-20 05:20:00] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3) [2013-03-20 05:26:23] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3) [2013-03-20 05:42:15] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2
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