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ruby: No such file or directory -- solid_pairs.rb (LoadError) #1

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etlioglu opened this issue Feb 28, 2024 · 0 comments
Open

ruby: No such file or directory -- solid_pairs.rb (LoadError) #1

etlioglu opened this issue Feb 28, 2024 · 0 comments

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@etlioglu
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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:

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?

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