Question: Error for running Tophat in GALAXY
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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 • 861 views
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by whhowhho0
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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
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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
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