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Dear Anton,

I am trying to use your tool to solve some repeatitive regions on my data, however there is something wrong with the option -t. As yo can see I have requested and use -t 48, however the program is just using 1 core.

$ nqstat_anu 10868520
%CPU WallTime Time Lim RSS mem memlim cpus
10868520 R ew6230 xc17 mosaic_N 2 00:14:47 48:00:00 24.6GB 24.6GB 1500GB 48

and the option --threads not recognized.

Could you may help me to understating what is happen?

Thank you,

Emiliana.

some errors in current code

Dear Anton,

Hope you are well. I am trying the current mosaic code to solve a pretty complex region that Flye alone has not been able to solve correctly. However I can see a few errors when testing it with the toyset. BTW, I am running on a 24 core, 256GB RAM server with Centos 7.0.

  1. GLIBC_2.27
    The default GLIBC version for Centos 7.0 is 2.17. I am asking the system admin to upgrade it to 2.27, but it appears to be more troublesome than iniatially tought. Is there any way it can be made compatible wit older GLIBC versions, or at least if it could be compilable from source?
$ ./mosaic --reads test_dataset/reads.fasta -o tmp --contigs test_dataset/axbctbdy.fasta
20.07.28 00:37:39  INFO: Command line: ./mosaic --reads test_dataset/reads.fasta -o tmp --contigs test_dataset/axbctbdy.fasta
20.07.28 00:37:39  INFO: Started
20.07.28 00:37:39  INFO: Preparing initial state
20.07.28 00:37:39  INFO: Creating read collection
/home/Bioinformatics/tools/mosaic/bin/flye-modules: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by /home/Bioinformatics/tools/mosaic/bin/flye-modules)
Traceback (most recent call last):
  File "./mosaic", line 26, in <module>
    mosaic_main.assemble(sys.argv, bin_path)
  File "/home/Bioinformatics/tools/mosaic/py/disjointig_resolve/mosaic_main.py", line 99, in assemble
    disjointigs_file = constructDisjointigs(reads, params.expected_size, assembly_dir)
  File "/home/Bioinformatics/tools/mosaic/py/disjointig_resolve/initialization.py", line 316, in constructDisjointigs
    "--config", "flye/config/bin_cfg/asm_raw_reads.cfg", "--min-ovlp", "1500", "--threads", str(params.threads), "--log", log_file])
  File "/home/Bioinformatics/tools/SMRTLink/smrtlink/install/smrtlink-release_8.0.0.80529/bundles/smrttools/install/smrttools-release_8.0.0.80502/private/thirdparty/python/python_2.7.16/lib/python2.7/subprocess.py", line 190, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/home/Bioinformatics/tools/mosaic/bin/flye-modules', 'assemble', '--reads', 'tmp/assembly_initial/reads.fasta', '--out-asm', 'tmp/assembly_initial/disjointigs.fasta', '--genome-size', '5000000', '--config', 'flye/config/bin_cfg/asm_raw_reads.cfg', '--min-ovlp', '1500', '--threads', '16', '--log', 'tmp/assembly_initial/log.txt']' returned non-zero exit status 1
  1. some options not recognized
    The current help gives several running options:
    usage: mosaic --reads <file> -o <dir> (--genome-size <int> | --flye-dir <dir> | --contigs <contigs>) [--threads <int>]
    However, neither "--genome-size" nor "--threads" are currently available and throw an error:
option --genome_size not recognized
option --threads not recognized

Do you have any other recommended way of testing the current version. If you could give me some advice on how best to test it, I would be grateful.

Kind regards,

Juan D. Montenegro

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