search

Arcadia-Science / 2023-amblyomma-americanum-txome-assembly

MIT License
0 stars 0 forks source link

removal of samples petx96sgfemale and petx120sgfemale due to transrate failure from too few contigs/mapped reads #8

Open taylorreiter opened 12 months ago

taylorreiter commented 12 months ago

snakemake error message below:

Sat Sep  9 18:23:26 2023]
rule transrate:
    input: outputs/assembly/merged/petx96sgfemale_merged_filtered.fa, outputs/assembly_group_separated_reads/petx96sgfemale_R1.fq.gz, outputs/assembly_group_separated_reads/petx96sgfemale_R2.fq.gz
    output: outputs/orthofuser/transrate_full/petx96sgfemale_merged_filtered/contigs.csv
    jobid: 107
    reason: Missing output files: outputs/orthofuser/transrate_full/petx96sgfemale_merged_filtered/contigs.csv
    wildcards: assembly_group=petx96sgfemale
    threads: 28
    resources: tmpdir=/tmp

Activating singularity image /home/ubuntu/2023-amblyomma-americanum-txome-assembly/sandbox/try_orthofuser/.snakemake/singularity/cbde6d526d9f43471f7e74567b7be376.simg
INFO:    Converting SIF file to temporary sandbox...
[ INFO] 2023-09-09 18:23:50 : Loading assembly: /home/ubuntu/2023-amblyomma-americanum-txome-assembly/sandbox/try_orthofuser/outputs/assembly/merged/petx96sgfemale_merged_filtered.fa
[ INFO] 2023-09-09 18:23:51 : Analysing assembly: /home/ubuntu/2023-amblyomma-americanum-txome-assembly/sandbox/try_orthofuser/outputs/assembly/merged/petx96sgfemale_merged_filtered.fa
[ INFO] 2023-09-09 18:23:51 : Results will be saved in /home/ubuntu/2023-amblyomma-americanum-txome-assembly/sandbox/try_orthofuser/outputs/orthofuser/transrate_full/petx96sgfemale_merged_filtered
[ INFO] 2023-09-09 18:23:51 : Calculating contig metrics...
[ INFO] 2023-09-09 18:23:51 : Contig metrics:
[ INFO] 2023-09-09 18:23:51 : -----------------------------------
[ INFO] 2023-09-09 18:23:51 : n seqs                          351
[ INFO] 2023-09-09 18:23:51 : smallest                        106
[ INFO] 2023-09-09 18:23:51 : largest                        1505
[ INFO] 2023-09-09 18:23:51 : n bases                       76444
[ INFO] 2023-09-09 18:23:51 : mean len                     126.32
[ INFO] 2023-09-09 18:23:51 : n under 200                     233
[ INFO] 2023-09-09 18:23:51 : n over 1k                         6
[ INFO] 2023-09-09 18:23:51 : n over 10k                        0
[ INFO] 2023-09-09 18:23:51 : n with orf                       17
[ INFO] 2023-09-09 18:23:51 : mean orf percent              84.75
[ INFO] 2023-09-09 18:23:51 : n90                             237
[ INFO] 2023-09-09 18:23:51 : n70                             402
[ INFO] 2023-09-09 18:23:51 : n50                            1048
[ INFO] 2023-09-09 18:23:51 : n30                            1505
[ INFO] 2023-09-09 18:23:51 : n10                            1505
[ INFO] 2023-09-09 18:23:51 : gc                             0.51
[ INFO] 2023-09-09 18:23:51 : bases n                           0
[ INFO] 2023-09-09 18:23:51 : proportion n                    0.0
[ INFO] 2023-09-09 18:23:51 : Contig metrics done in 0 seconds
[ INFO] 2023-09-09 18:23:51 : Calculating read diagnostics...
/home/orp/Oyster_River_Protocol/software/orp-transrate/lib/app/lib/transrate/read_metrics.rb:109:in `get_read_length': undefined method `length' for nil:NilClass (NoMethodError)
        from /home/orp/Oyster_River_Protocol/software/orp-transrate/lib/app/lib/transrate/read_metrics.rb:49:in `run'
        from /home/orp/Oyster_River_Protocol/software/orp-transrate/lib/app/lib/transrate/transrater.rb:98:in `read_metrics'
        from /home/orp/Oyster_River_Protocol/software/orp-transrate/lib/app/lib/transrate/cmdline.rb:508:in `read_metrics'
        from /home/orp/Oyster_River_Protocol/software/orp-transrate/lib/app/lib/transrate/cmdline.rb:404:in `block in analyse_assembly'
        from /home/orp/Oyster_River_Protocol/software/orp-transrate/lib/app/lib/transrate/cmdline.rb:400:in `chdir'
        from /home/orp/Oyster_River_Protocol/software/orp-transrate/lib/app/lib/transrate/cmdline.rb:400:in `analyse_assembly'
        from /home/orp/Oyster_River_Protocol/software/orp-transrate/lib/app/lib/transrate/cmdline.rb:38:in `block (2 levels) in run'
        from /home/orp/Oyster_River_Protocol/software/orp-transrate/lib/app/lib/transrate/cmdline.rb:37:in `zip'
        from /home/orp/Oyster_River_Protocol/software/orp-transrate/lib/app/lib/transrate/cmdline.rb:37:in `block in run'
        from /home/orp/Oyster_River_Protocol/software/orp-transrate/lib/app/lib/transrate/cmdline.rb:32:in `chdir'
        from /home/orp/Oyster_River_Protocol/software/orp-transrate/lib/app/lib/transrate/cmdline.rb:32:in `run'
        from /home/orp/Oyster_River_Protocol/software/orp-transrate/lib/app/bin/transrate:23:in `<main>'
INFO:    Cleaning up image...
[Sat Sep  9 18:23:59 2023]
Error in rule transrate:
    jobid: 107
    input: outputs/assembly/merged/petx96sgfemale_merged_filtered.fa, outputs/assembly_group_separated_reads/petx96sgfemale_R1.fq.gz, outputs/assembly_group_separated_reads/petx96sgfemale_R2.fq.gz
    output: outputs/orthofuser/transrate_full/petx96sgfemale_merged_filtered/contigs.csv
    shell:

    transrate -o outputs/orthofuser/transrate_full -t 28 -a outputs/assembly/merged/petx96sgfemale_merged_filtered.fa --left outputs/assembly_group_separated_reads/petx96sgfemale_R1.fq.gz --right outputs/assembly_group_separated_reads/petx96sgfemale_R2.fq.gz
    mv outputs/orthofuser/transrate_full/assemblies.csv outputs/orthofuser/transrate_full/petx96sgfemale_merged_filtered_assemblies.csv
    # cleanup big output files
    rm outputs/orthofuser/transrate_full/petx96sgfemale_merged_filtered/*bam

        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Select jobs to execute...

[Sat Sep  9 18:23:59 2023]
rule transrate:
    input: outputs/assembly/merged/petx120sgfemale_merged_filtered.fa, outputs/assembly_group_separated_reads/petx120sgfemale_R1.fq.gz, outputs/assembly_group_separated_reads/petx120sgfemale_R2.fq.gz
    output: outputs/orthofuser/transrate_full/petx120sgfemale_merged_filtered/contigs.csv
    jobid: 105
    reason: Missing output files: outputs/orthofuser/transrate_full/petx120sgfemale_merged_filtered/contigs.csv
    wildcards: assembly_group=petx120sgfemale
    threads: 28
    resources: tmpdir=/tmp

Activating singularity image /home/ubuntu/2023-amblyomma-americanum-txome-assembly/sandbox/try_orthofuser/.snakemake/singularity/cbde6d526d9f43471f7e74567b7be376.simg
INFO:    Converting SIF file to temporary sandbox...
[ INFO] 2023-09-09 18:24:23 : Loading assembly: /home/ubuntu/2023-amblyomma-americanum-txome-assembly/sandbox/try_orthofuser/outputs/assembly/merged/petx120sgfemale_merged_filtered.fa
[ INFO] 2023-09-09 18:24:23 : Analysing assembly: /home/ubuntu/2023-amblyomma-americanum-txome-assembly/sandbox/try_orthofuser/outputs/assembly/merged/petx120sgfemale_merged_filtered.fa
[ INFO] 2023-09-09 18:24:23 : Results will be saved in /home/ubuntu/2023-amblyomma-americanum-txome-assembly/sandbox/try_orthofuser/outputs/orthofuser/transrate_full/petx120sgfemale_merged_filtered
[ INFO] 2023-09-09 18:24:23 : Calculating contig metrics...
[ INFO] 2023-09-09 18:24:24 : Contig metrics:
[ INFO] 2023-09-09 18:24:24 : -----------------------------------
[ INFO] 2023-09-09 18:24:24 : n seqs                          338
[ INFO] 2023-09-09 18:24:24 : smallest                        106
[ INFO] 2023-09-09 18:24:24 : largest                        1524
[ INFO] 2023-09-09 18:24:24 : n bases                       69764
[ INFO] 2023-09-09 18:24:24 : mean len                     112.05
[ INFO] 2023-09-09 18:24:24 : n under 200                     232
[ INFO] 2023-09-09 18:24:24 : n over 1k                         3
[ INFO] 2023-09-09 18:24:24 : n over 10k                        0
[ INFO] 2023-09-09 18:24:24 : n with orf                       14
[ INFO] 2023-09-09 18:24:24 : mean orf percent              82.58
[ INFO] 2023-09-09 18:24:24 : n90                             236
[ INFO] 2023-09-09 18:24:24 : n70                             399
[ INFO] 2023-09-09 18:24:24 : n50                            1011
[ INFO] 2023-09-09 18:24:24 : n30                            1524
[ INFO] 2023-09-09 18:24:24 : n10                            1524
[ INFO] 2023-09-09 18:24:24 : gc                              0.5
[ INFO] 2023-09-09 18:24:24 : bases n                           0
[ INFO] 2023-09-09 18:24:24 : proportion n                    0.0
[ INFO] 2023-09-09 18:24:24 : Contig metrics done in 0 seconds
[ INFO] 2023-09-09 18:24:24 : Calculating read diagnostics...
/home/orp/Oyster_River_Protocol/software/orp-transrate/lib/app/lib/transrate/read_metrics.rb:109:in `get_read_length': undefined method `length' for nil:NilClass (NoMethodError)
        from /home/orp/Oyster_River_Protocol/software/orp-transrate/lib/app/lib/transrate/read_metrics.rb:49:in `run'
        from /home/orp/Oyster_River_Protocol/software/orp-transrate/lib/app/lib/transrate/transrater.rb:98:in `read_metrics'
        from /home/orp/Oyster_River_Protocol/software/orp-transrate/lib/app/lib/transrate/cmdline.rb:508:in `read_metrics'
        from /home/orp/Oyster_River_Protocol/software/orp-transrate/lib/app/lib/transrate/cmdline.rb:404:in `block in analyse_assembly'
        from /home/orp/Oyster_River_Protocol/software/orp-transrate/lib/app/lib/transrate/cmdline.rb:400:in `chdir'
        from /home/orp/Oyster_River_Protocol/software/orp-transrate/lib/app/lib/transrate/cmdline.rb:400:in `analyse_assembly'
        from /home/orp/Oyster_River_Protocol/software/orp-transrate/lib/app/lib/transrate/cmdline.rb:38:in `block (2 levels) in run'
        from /home/orp/Oyster_River_Protocol/software/orp-transrate/lib/app/lib/transrate/cmdline.rb:37:in `zip'
        from /home/orp/Oyster_River_Protocol/software/orp-transrate/lib/app/lib/transrate/cmdline.rb:37:in `block in run'
        from /home/orp/Oyster_River_Protocol/software/orp-transrate/lib/app/lib/transrate/cmdline.rb:32:in `chdir'
        from /home/orp/Oyster_River_Protocol/software/orp-transrate/lib/app/lib/transrate/cmdline.rb:32:in `run'
        from /home/orp/Oyster_River_Protocol/software/orp-transrate/lib/app/bin/transrate:23:in `<main>'
INFO:    Cleaning up image...
[Sat Sep  9 18:24:33 2023]
Error in rule transrate:
    jobid: 105
    input: outputs/assembly/merged/petx120sgfemale_merged_filtered.fa, outputs/assembly_group_separated_reads/petx120sgfemale_R1.fq.gz, outputs/assembly_group_separated_reads/petx120sgfemale_R2.fq.gz
    output: outputs/orthofuser/transrate_full/petx120sgfemale_merged_filtered/contigs.csv
    shell:

    transrate -o outputs/orthofuser/transrate_full -t 28 -a outputs/assembly/merged/petx120sgfemale_merged_filtered.fa --left outputs/assembly_group_separated_reads/petx120sgfemale_R1.fq.gz --right outputs/assembly_group_separated_reads/petx120sgfemale_R2.fq.gz
    mv outputs/orthofuser/transrate_full/assemblies.csv outputs/orthofuser/transrate_full/petx120sgfemale_merged_filtered_assemblies.csv
    # cleanup big output files
    rm outputs/orthofuser/transrate_full/petx120sgfemale_merged_filtered/*bam

        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)