Open taylorreiter opened 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!)
snakemake error message below: