[jonas76]

I have 8GB of RAM per job/slot I run on our cluster. So when I submit -p 8, I enable 64GB of RAM since I also open 8 slots then.

[chanwu]

Tophat2 error

Hello, everyone,

I am a newer to use Tophat2/bowtie2 to align illumina paired-end RNA-seq, and a error occured as
No such file or directory.
Can someone help out to solve this problem? thanks,

Chanwu
command used:

tophat -o 81MAGABXX_5PE hg19 /media/sf_F_DRIVE/finished/81MAGABXX_5_R1.fastq /media/sf_F_DRIVE/finished/81MAGABXX_5_R2.fastq



[2013-04-23 10:13:59] Beginning TopHat run (v2.0.8)
-----------------------------------------------
[2013-04-23 10:13:59] Checking for Bowtie
Bowtie version: 2.1.0.0
[2013-04-23 10:14:00] Checking for Samtools
Samtools version: 0.1.18.0
[2013-04-23 10:14:00] Checking for Bowtie index files
[2013-04-23 10:14:00] Checking for reference FASTA file
[2013-04-23 10:14:00] Generating SAM header for hg19
format: fastq
quality scale: phred33 (default)
[2013-04-23 10:14:34] Preparing reads
left reads: min. length=100, max. length=100, 87918264 kept reads (261507 discarded)
right reads: min. length=100, max. length=100, 87900059 kept reads (279712 discarded)
[2013-04-23 11:00:31] Mapping left_kept_reads to genome hg19 with Bowtie2
[2013-04-24 01:54:58] Mapping left_kept_reads_seg1 to genome hg19 with Bowtie2 (1/4)
[2013-04-24 03:07:58] Mapping left_kept_reads_seg2 to genome hg19 with Bowtie2 (2/4)
[2013-04-24 04:21:15] Mapping left_kept_reads_seg3 to genome hg19 with Bowtie2 (3/4)
[2013-04-24 05:43:19] Mapping left_kept_reads_seg4 to genome hg19 with Bowtie2 (4/4)
[2013-04-24 07:03:11] Mapping right_kept_reads to genome hg19 with Bowtie2
[2013-04-25 02:02:18] Mapping right_kept_reads_seg1 to genome hg19 with Bowtie2 (1/4)
[2013-04-25 03:12:53] Mapping right_kept_reads_seg2 to genome hg19 with Bowtie2 (2/4)
[2013-04-25 04:21:35] Mapping right_kept_reads_seg3 to genome hg19 with Bowtie2 (3/4)
[2013-04-25 06:20:24] Mapping right_kept_reads_seg4 to genome hg19 with Bowtie2 (4/4)
[2013-04-25 07:37:57] Searching for junctions via segment mapping
[2013-04-25 09:42:00] Retrieving sequences for splices
[2013-04-25 09:43:50] Indexing splices
[2013-04-25 09:46:05] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2013-04-25 10:09:23] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2013-04-25 10:33:07] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2013-04-25 10:57:47] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2013-04-25 11:20:03] Joining segment hits
[2013-04-25 11:58:22] Mapping right_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2013-04-25 12:21:21] Mapping right_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2013-04-25 12:42:55] Mapping right_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2013-04-25 13:10:07] Mapping right_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2013-04-25 13:30:45] Joining segment hits
[2013-04-25 14:17:03] Reporting output tracks
[FAILED]
Error: [Errno 2] No such file or directory
Found 313015 junctions from happy spliced reads