Question: Error for running Tophat in GALAXY
0
gravatar for whhowhho
2.3 years ago by
whhowhho0
whhowhho0 wrote:

Hello, I was trying to use Tophat of GALAXY (run by my university) to perform mapping of my RNA-Seq reads to a crop genome (the FASTA file is around 4.6GB). The Tophat seems to accept the job with my groomed reads but after around a few hours of wait, a similar error message would appear:

Job was resubmitted due to node failure Settings: Output files: "genome.*.bt2l" Line rate: 7 (line is 128 bytes) Lines per side: 1 (side is 128 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default M

I just wonder whether it could be a problem that can be resolved by the admin side of our Uni by perhaps allocating more resources for me (remark: my Uni has already allocated about 3TB space for me and I also try to divide my reads into smaller batches before I upload to the GALAXY for mapping purpose. But still, similar error message appear). Or could it help if I request the admin to reinstall a newer version of Tophat repository, or would there be something I could work on my dataset as well (either on the genome or the reads)

I am only a beginning on GALAXY and sorry if I have raised something silly... Thanks for your kind reply in advance!

rna-seq • 877 views
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by whhowhho0
0
gravatar for whhowhho
2.3 years ago by
whhowhho0
whhowhho0 wrote:

To provide further info, below please find the details of the error message:

Tool execution generated the following error message:

Fatal error: Tool execution failed Building a LARGE index nlink domain socket: No such file or directory slurmd[w3]: unlink(/tmp/slurm/slurmd_spool/job04182/slurm_script): No such file or directory slurmd[w3]: rmdir(/tmp/slurm/slurmd_spool/job04182): No such file or directory

[2016-08-07 09:54:26] Beginning TopHat run (v2.0.14)

[2016-08-07 09:54:26] Checking for Bowtie Bowtie version: 2.2.5.0 [2016-08-07 09:54:27] Checking for Bowtie index files (genome).. Error: Could not find Bowtie 2 index files (genome.*.bt2) [bam_header_read] bgzf_check_EOF: Invalid argument

ADD COMMENTlink written 2.3 years ago by whhowhho0
0
gravatar for whhowhho
2.3 years ago by
whhowhho0
whhowhho0 wrote:

The tool produced the following additional output:

Settings: Output files: "genome..bt2l" Line rate: 7 (line is 128 bytes) Lines per side: 1 (side is 128 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default Max bucket size, len divisor: 4 Difference-cover sample period: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void:8, int:4, long:8, size_t:8 Input files DNA, FASTA: /mnt/galaxy/files/016/dataset_16547.dat Reading reference sizes Time reading reference sizes: 00:00:51 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:27 bmax according to bmaxDivN setting: 1111624310 Using parameters --bmax 833718233 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 833718233 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:02:33 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:34 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:57 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:02:58 Splitting and merging Splitting and merging time: 00:00:00 Split 2, merged 7; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:02:27 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 0; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:02:19 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 5.55812e+08 (target: 833718232) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (833718233) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:43 Sorting block of length 551628983 (Using difference cover) Sorting block time: 00:07:05 Returning block of 551628984 Getting block 2 of 8 Reserving size (833718233) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:51 Sorting block of length 683448832 (Using difference cover) Sorting block time: 00:09:15

.... (repeating) ......

Returning block of 754851245 Exited Ebwt loop fchr[A]: 0 fchr[C]: 1235077817 fchr[G]: 2223441633 fchr[T]: 3211648164 fchr[$]: 4446497241 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 1521337361 bytes to primary EBWT file: genome.rev.1.bt2l Wrote 2223248628 bytes to secondary EBWT file: genome.rev.2.bt2l Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 4446497241 bwtLen: 4446497242 sz: 1111624311 bwtSz: 1111624311 lineRate: 7 offRate: 4 offMask: 0xfffffffffffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 160 ftabLen: 1048577 ftabSz: 8388616 offsLen: 277906078 offsSz: 2223248624 lineSz: 128 sideSz: 128 sideBwtSz: 96 sideBwtLen: 384 numSides: 11579420 numLines: 11579420 ebwtTotLen: 1482165760 ebwtTotSz: 1482165760 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 01:21:54 [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [bam_index_core] Invalid BAM header.[bam_index_build2] fail to index the BAM file.

ADD COMMENTlink written 2.3 years ago by whhowhho0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 172 users visited in the last hour