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Hi,
Thank you for making this tool available to the community.
I am running compare-genome-qualities using the following command:
compare-genome-qualities
nohup docker run --volume=`pwd`:/mnt:rw wurmlab/compare-genome-qualities \ --genome-size 7000000 \ --busco-lineage burkholderiales_odb10.2024-01-08.tar.gz \ --illumina-R1 Cmet/NA4_R1.fastq.gz \ --illumina-R2 Cmet/NA4_R2.fastq.gz \ --num-cpus 8 \ Cmet/assemblies/original_files/NA4.unicycler.fasta \ Cmet/assemblies/original_files/NA4.try.polish.fasta \ Cmet/assemblies/original_files/NA4.raven.fasta \ Cmet/assemblies/original_files/NA4.miniasm.fasta \ Cmet/assemblies/original_files/NA4.flye.fasta \ Cmet/assemblies/original_files/NA4.canu.trim.fasta \ > nohup-nextflow.out \ 2> nohup-nextflow.err
And I am getting the following error:
--2024-02-28 12:24:16-- https://busco-data.ezlab.org/v5/data/lineages/burkholderiales_odb10.2024-01-08.tar.gz Resolving busco-data.ezlab.org (busco-data.ezlab.org)... 129.194.190.40 Connecting to busco-data.ezlab.org (busco-data.ezlab.org)|129.194.190.40|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 17750318 (17M) [application/octet-stream] Saving to: ‘compare-genome-qualities-2024-02-28-122415/burkholderiales_odb10.2024-01-08.tar.gz’ 0K .......... .......... .......... .......... .......... 0% 2.94M 6s 50K .......... .......... .......... .......... .......... 0% 3.01M 6s 100K .......... .......... .......... .......... .......... 0% 75.4M 4s ... 17150K .......... .......... .......... .......... .......... 99% 79.6M 0s 17200K .......... .......... .......... .......... .......... 99% 110M 0s 17250K .......... .......... .......... .......... .......... 99% 107M 0s 17300K .......... .......... .......... .... 100% 141M=0.2s 2024-02-28 12:24:17 (68.6 MB/s) - ‘compare-genome-qualities-2024-02-28-122415/burkholderiales_odb10.2024-01-08.tar.gz’ saved [17750318/17750318] /cmg/quast.sh -g 7000000 -o compare-genome-qualities-2024-02-28-122415/$(basename Cmet/assemblies/original_files/NA4.unicycler.fasta)/quast Cmet/assemblies/original_files/NA4.unicycler.fasta /cmg/quast.sh -g 7000000 -o compare-genome-qualities-2024-02-28-122415/$(basename Cmet/assemblies/original_files/NA4.try.polish.fasta)/quast Cmet/assemblies/original_files/NA4.try.polish.fasta /cmg/quast.sh -g 7000000 -o compare-genome-qualities-2024-02-28-122415/$(basename Cmet/assemblies/original_files/NA4.raven.fasta)/quast Cmet/assemblies/original_files/NA4.raven.fasta /cmg/quast.sh -g 7000000 -o compare-genome-qualities-2024-02-28-122415/$(basename Cmet/assemblies/original_files/NA4.miniasm.fasta)/quast Cmet/assemblies/original_files/NA4.miniasm.fasta /cmg/quast.sh -g 7000000 -o compare-genome-qualities-2024-02-28-122415/$(basename Cmet/assemblies/original_files/NA4.flye.fasta)/quast Cmet/assemblies/original_files/NA4.flye.fasta /cmg/quast.sh -g 7000000 -o compare-genome-qualities-2024-02-28-122415/$(basename Cmet/assemblies/original_files/NA4.canu.trim.fasta)/quast Cmet/assemblies/original_files/NA4.canu.trim.fasta /cmg/busco.sh -b compare-genome-qualities-2024-02-28-122415/burkholderiales_odb10 -n 8 -o compare-genome-qualities-2024-02-28-122415/$(basename Cmet/assemblies/original_files/NA4.unicycler.fasta)/busco Cmet/assemblies/original_files/NA4.unicycler.fasta /cmg/busco.sh -b compare-genome-qualities-2024-02-28-122415/burkholderiales_odb10 -n 8 -o compare-genome-qualities-2024-02-28-122415/$(basename Cmet/assemblies/original_files/NA4.try.polish.fasta)/busco Cmet/assemblies/original_files/NA4.try.polish.fasta /cmg/busco.sh -b compare-genome-qualities-2024-02-28-122415/burkholderiales_odb10 -n 8 -o compare-genome-qualities-2024-02-28-122415/$(basename Cmet/assemblies/original_files/NA4.raven.fasta)/busco Cmet/assemblies/original_files/NA4.raven.fasta /cmg/busco.sh -b compare-genome-qualities-2024-02-28-122415/burkholderiales_odb10 -n 8 -o compare-genome-qualities-2024-02-28-122415/$(basename Cmet/assemblies/original_files/NA4.miniasm.fasta)/busco Cmet/assemblies/original_files/NA4.miniasm.fasta /cmg/busco.sh -b compare-genome-qualities-2024-02-28-122415/burkholderiales_odb10 -n 8 -o compare-genome-qualities-2024-02-28-122415/$(basename Cmet/assemblies/original_files/NA4.flye.fasta)/busco Cmet/assemblies/original_files/NA4.flye.fasta /cmg/busco.sh -b compare-genome-qualities-2024-02-28-122415/burkholderiales_odb10 -n 8 -o compare-genome-qualities-2024-02-28-122415/$(basename Cmet/assemblies/original_files/NA4.canu.trim.fasta)/busco Cmet/assemblies/original_files/NA4.canu.trim.fasta /cmg/map_illumina.sh -n 8 -o compare-genome-qualities-2024-02-28-122415/$(basename Cmet/assemblies/original_files/NA4.unicycler.fasta)/illumina Cmet/assemblies/original_files/NA4.unicycler.fasta Cmet/NA4_R1.fastq.gz Cmet/NA4_R2.fastq.gz /cmg/map_illumina.sh -n 8 -o compare-genome-qualities-2024-02-28-122415/$(basename Cmet/assemblies/original_files/NA4.try.polish.fasta)/illumina Cmet/assemblies/original_files/NA4.try.polish.fasta Cmet/NA4_R1.fastq.gz Cmet/NA4_R2.fastq.gz /cmg/map_illumina.sh -n 8 -o compare-genome-qualities-2024-02-28-122415/$(basename Cmet/assemblies/original_files/NA4.raven.fasta)/illumina Cmet/assemblies/original_files/NA4.raven.fasta Cmet/NA4_R1.fastq.gz Cmet/NA4_R2.fastq.gz /cmg/map_illumina.sh -n 8 -o compare-genome-qualities-2024-02-28-122415/$(basename Cmet/assemblies/original_files/NA4.miniasm.fasta)/illumina Cmet/assemblies/original_files/NA4.miniasm.fasta Cmet/NA4_R1.fastq.gz Cmet/NA4_R2.fastq.gz /cmg/map_illumina.sh -n 8 -o compare-genome-qualities-2024-02-28-122415/$(basename Cmet/assemblies/original_files/NA4.flye.fasta)/illumina Cmet/assemblies/original_files/NA4.flye.fasta Cmet/NA4_R1.fastq.gz Cmet/NA4_R2.fastq.gz /cmg/map_illumina.sh -n 8 -o compare-genome-qualities-2024-02-28-122415/$(basename Cmet/assemblies/original_files/NA4.canu.trim.fasta)/illumina Cmet/assemblies/original_files/NA4.canu.trim.fasta Cmet/NA4_R1.fastq.gz Cmet/NA4_R2.fastq.gz [bwa_index] Pack FASTA... 0.09 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 2.91 seconds elapse. [bwa_index] Update BWT... 0.08 sec [bwa_index] Pack forward-only FASTA... 0.05 sec [bwa_index] Construct SA from BWT and Occ... 1.06 sec [main] Version: 0.7.17-r1188 [main] CMD: bwa index compare-genome-qualities-2024-02-28-122415/NA4.raven.fasta/illumina/NA4.raven.fasta [main] Real time: 4.458 sec; CPU: 4.193 sec [bam_sort_core] merging from 0 files and 8 in-memory blocks... [bwa_index] Pack FASTA... 0.09 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 3.13 seconds elapse. [bwa_index] Update BWT... 0.07 sec [bwa_index] Pack forward-only FASTA... 0.06 sec [bwa_index] Construct SA from BWT and Occ... 1.05 sec [main] Version: 0.7.17-r1188 [main] CMD: bwa index compare-genome-qualities-2024-02-28-122415/NA4.try.polish.fasta/illumina/NA4.try.polish.fasta [main] Real time: 4.697 sec; CPU: 4.408 sec [bam_sort_core] merging from 0 files and 8 in-memory blocks... [bwa_index] Pack FASTA... 0.06 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 3.00 seconds elapse. [bwa_index] Update BWT... 0.08 sec [bwa_index] Pack forward-only FASTA... 0.06 sec [bwa_index] Construct SA from BWT and Occ... 1.05 sec [main] Version: 0.7.17-r1188 [main] CMD: bwa index compare-genome-qualities-2024-02-28-122415/NA4.miniasm.fasta/illumina/NA4.miniasm.fasta [main] Real time: 4.709 sec; CPU: 4.262 sec [bam_sort_core] merging from 0 files and 8 in-memory blocks... [bwa_index] Pack FASTA... 0.10 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 2.86 seconds elapse. [bwa_index] Update BWT... 0.08 sec [bwa_index] Pack forward-only FASTA... 0.06 sec [bwa_index] Construct SA from BWT and Occ... 1.06 sec [main] Version: 0.7.17-r1188 [main] CMD: bwa index compare-genome-qualities-2024-02-28-122415/NA4.unicycler.fasta/illumina/NA4.unicycler.fasta [main] Real time: 4.515 sec; CPU: 4.158 sec [bam_sort_core] merging from 0 files and 8 in-memory blocks... [bwa_index] Pack FASTA... 0.06 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 2.89 seconds elapse. [bwa_index] Update BWT... 0.06 sec [bwa_index] Pack forward-only FASTA... 0.06 sec [bwa_index] Construct SA from BWT and Occ... 1.11 sec [main] Version: 0.7.17-r1188 [main] CMD: bwa index compare-genome-qualities-2024-02-28-122415/NA4.canu.trim.fasta/illumina/NA4.canu.trim.fasta [main] Real time: 4.545 sec; CPU: 4.180 sec [bam_sort_core] merging from 0 files and 8 in-memory blocks... [bwa_index] Pack FASTA... 0.09 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 2.46 seconds elapse. [bwa_index] Update BWT... 0.07 sec [bwa_index] Pack forward-only FASTA... 0.06 sec [bwa_index] Construct SA from BWT and Occ... 1.11 sec [main] Version: 0.7.17-r1188 [main] CMD: bwa index compare-genome-qualities-2024-02-28-122415/NA4.flye.fasta/illumina/NA4.flye.fasta [main] Real time: 4.050 sec; CPU: 3.795 sec [bam_sort_core] merging from 0 files and 8 in-memory blocks... /cmg/solid_pairs.sh compare-genome-qualities-2024-02-28-122415/$(basename Cmet/assemblies/original_files/NA4.unicycler.fasta)/illumina/bwa_mem_default.bam /cmg/solid_pairs.sh compare-genome-qualities-2024-02-28-122415/$(basename Cmet/assemblies/original_files/NA4.try.polish.fasta)/illumina/bwa_mem_default.bam /cmg/solid_pairs.sh compare-genome-qualities-2024-02-28-122415/$(basename Cmet/assemblies/original_files/NA4.raven.fasta)/illumina/bwa_mem_default.bam /cmg/solid_pairs.sh compare-genome-qualities-2024-02-28-122415/$(basename Cmet/assemblies/original_files/NA4.miniasm.fasta)/illumina/bwa_mem_default.bam /cmg/solid_pairs.sh compare-genome-qualities-2024-02-28-122415/$(basename Cmet/assemblies/original_files/NA4.flye.fasta)/illumina/bwa_mem_default.bam /cmg/solid_pairs.sh compare-genome-qualities-2024-02-28-122415/$(basename Cmet/assemblies/original_files/NA4.canu.trim.fasta)/illumina/bwa_mem_default.bam ruby: No such file or directory -- solid_pairs.rb (LoadError) ruby: No such file or directory -- solid_pairs.rb (LoadError) ruby: No such file or directory -- solid_pairs.rb (LoadError) ruby: No such file or directory -- solid_pairs.rb (LoadError) ruby: No such file or directory -- solid_pairs.rb (LoadError)
Would you have any suggestions to overcome this?
The text was updated successfully, but these errors were encountered:
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Hi,
Thank you for making this tool available to the community.
I am running
compare-genome-qualities
using the following command:And I am getting the following error:
Would you have any suggestions to overcome this?
The text was updated successfully, but these errors were encountered: