Could anyone test and report problems of the tool I've been developing?

[abysslover]

Hi,

I've been developing a sequencing error correction tool for Illumina datasets since 2013 named trowel. I have put statically-linking binaries for 64-bit linux in the repository.
Could anyone let me know any problems while executing the binaries? Obviously, the current codes are working in our cluster setting. I would like to collect any problems in different server configurations and improve the compatibility of the tool. The code is not in public yet since some codes contain unpublished ideas.
Thanks in advance.

Sincerely,
Euncheon Lim
=============================
PhD Student

Max Planck Institute for Developmental Biology
Department of Molecular Biology
Spemannstraße 37-39,
D-72076 Tuebingen, Germany

[Brian Bushnell]

I'm working on error correction at the moment, so I'll try it out tomorrow.

[Richard Finney]

Linux Mint 17 Qiana 3.13.0-24-generic #47-Ubuntu SMP Fri May 2 23:30:00 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

seems to work okay.

Had chmod +x to run.


You should move to github

[abysslover]

Thanks for your times.
I mentioned about chmod command in the README file regarding Mr. Finney's comment.
I am looking forward to seeing more comments.

[Brian Bushnell]

My results:

bushnell@gpint109:/global/scratch2/sd/bushnell/ecoli$ ./trowel
Trowel: An error correction module for genomic FASTQ files(Ver. 0.2.0.0)
=========================================================================
Syntax:    trowel2 -f <file_list> [-k] [-m]
Options:   -f STR  a single list file that contains a list of FASTQ files
           -k INT  size of pre-mer [DEFAULT: 11] (11-15)
           -m      fast less accurate mode [DEFAULT: slow accurate mode]

Example of a file_list file:
           a.thal.chr1.fq a.thal.chr2.fq a.thal.chr3.fq ...
           h.sap.chr1.fq h.sap.chr2.fq h.sap.chr3.fq ...
                        ...

Note:      1. trowel only supports FASTQ files.
           2. For datasets of high coverage or of large genome, you should use k of 13-15.
           3. You have to run the following commands before running trowel
              sudo ulimit -v unlimited
              sudo ulimit -n 8192

Contact:   Euncheon Lim <[email protected]>

bushnell@gpint109:/global/scratch2/sd/bushnell/ecoli$ sudo ulimit -v unlimited
-bash: sudo: command not found
bushnell@gpint109:/global/scratch2/sd/bushnell/ecoli$ sudo ulimit -n 8192
-bash: sudo: command not found
bushnell@gpint109:/global/scratch2/sd/bushnell/ecoli$ memtime ./trowel -f 1snp.fq.gz
Killed [4]
0.00 user, 0.01 system, 1.40 elapsed -- Max VSize = 3724KB, Max RSS = 588KB

Is sudo a default component of Debian?

[abysslover]

Thanks Mr. Bushnell.
Actually, the maximum number of open files should be increased before running trowel. I think that you have specified a root password during installation. Thus, your package configuration does not contain "sudo" command.
Trowel does not support compressed files to enable the parallelism. The -f parameter demands for a fastq-file list containing file names.
e.g.)
echo lsnp.fq > file_list && trowel -f file_list

Thanks for your testing.

[Brian Bushnell]

Oops, my mistake. There's still some problem, though:

bushnell@mc1357:/global/scratch2/sd/bushnell/ecoli$ gunzip 1snp.fq.gz
bushnell@mc1357:/global/scratch2/sd/bushnell/ecoli$ ./trowel -f 1snp.fq
Illegal instruction (core dumped)
bushnell@mc1357:/global/scratch2/sd/bushnell/ecoli$ echo 1snp.fq > file_list && ./trowel -f file_list
Illegal instruction (core dumped)

Note that this is from the binary I downloaded; I did not rebuild it. Should I rebuild it? It works fine for displaying help.

[abysslover]

Thanks, Mr. Bushnell,
I have encountered this problem before. It was a compiler version problem.
Could you try again with "trowel.0.2.0.2.linux.64" binary in the bin folder?

[Brian Bushnell]

Same error still with 0.2.0.2.

[abysslover]

I did overwrite the binary after building it on the debian.
Thanks Mr. Bushnell for testing.

[Brian Bushnell]

OK - the new version completed without crashing, but did not produce any output.

[BlockReader.set_k] K-mer size: 11
[BlockReader.calculate_all_file_sizes] Total: 0 bytes
[BlockReader.calculate_all_file_sizes] Ends at 2015-06-23.10:11:01, Real: 0.016 sec, CPU: 0.006 sec, RSS: 0.645(GB)/447.430(GB), CPU: 32
[BlockReader.create_all_blocks] starts at 2015-06-23.10:11:01
[BlockReader.create_all_blocks] Ends at 2015-06-23.10:11:01, Real: 0.000 sec, CPU: 0.000 sec, RSS: 0.645(GB)/447.430(GB), CPU: 32
[BlockReader.count_all_n_reads] starts at 2015-06-23.10:11:02
[BlockReader.count_all_n_reads] Ends at 2015-06-23.10:11:02, Real: 0.000 sec, CPU: 0.000 sec, RSS: 0.645(GB)/447.430(GB), CPU: 32
[BlockReader.create_all_read_ids] starts at 2015-06-23.10:11:02
[BlockReader.create_all_read_ids] Ends at 2015-06-23.10:11:02, Real: 0.001 sec, CPU: 0.003 sec, RSS: 0.645(GB)/447.430(GB), CPU: 32
[Correction.Main] Ends at 2015-06-23.10:11:02, Real: 58.783 sec, CPU: 57.369 sec, RSS: 0.645(GB)/447.430(GB), CPU: 32
Exit [0]
6.78 user, 54.93 system, 63.26 elapsed -- Max VSize = 744972KB, Max RSS = 675956KB

[abysslover]

I am unsure why the size of total files is zero for your inputs. Have you used regular uncompress fastq files?

[Brian Bushnell]

Yes... I used a 418MB fastq file with 1.2Mx150bp reads. They are synthetic reads, so the headers are not normal Illumina headers, but it's a perfectly valid fastq file. Does the tool need any specific characteristics of the input data?

[abysslover]

I got the problem. Trowel officially does not support fasta files.

[Brian Bushnell]

Sorry, that was a typo on my part - it's actually fastq. Perhaps you could post a very small sample fastq that works correctly on your system?