ERROR: fail to open file 'k8'. ERROR: failed to read file 'k8'

[siolybecerra]

Hi, I am trying to run pipeline_Minimap.sh, but I got this warning respect on "k8".

Thanks

 pipeline_Minimap.sh -g /home/sioly/applications/CoreDetector/test_mygenomes/genomes.txt -o /home/sioly/applications/CoreDetector/test_mygenomes/out_test -d 20 -n 16
Number of lines in file /home/sioly/applications/CoreDetector/test_mygenomes/genomes.txt : 3
Genome size gb : 0
/home/sioly/applications/CoreDetector/test_mygenomes/genomes/CGRA01V4.fa
/home/sioly/applications/CoreDetector/test_mygenomes/genomes/CROI41.fa
ERROR: fail to open file 'k8'.
ERROR: failed to read file 'k8'
[M::mm_idx_gen::0.672*1.00] collected minimizers
[M::mm_idx_gen::0.752*1.93] sorted minimizers
[M::main::0.752*1.93] loaded/built the index for 2 target sequence(s)
[M::mm_mapopt_update::0.794*1.88] mid_occ = 74
[M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 1; #seq: 2
[M::mm_idx_stat::0.824*1.85] distinct minimizers: 1697853 (95.20% are singletons); average occurrences: 1.230; average spacing: 7.504; total length: 15668520
/home/sioly/applications/CoreDetector/MFbio.jarProcessing File: /home/sioly/applications/CoreDetector/test_mygenomes/out_test/maf/Genome1_Genome2.maf
Done.
/home/sioly/applications/CoreDetector/test_mygenomes/out_test/temp_fasta/Genome1_Genome2.fa
/home/sioly/applications/CoreDetector/test_mygenomes/genomes/ARG_5133_7.fa
ERROR: fail to open file 'k8'.
ERROR: failed to read file 'k8'
[M::mm_idx_gen::0.670*1.00] collected minimizers
[M::mm_idx_gen::0.747*1.91] sorted minimizers
[M::main::0.747*1.91] loaded/built the index for 2 target sequence(s)
[M::mm_mapopt_update::0.788*1.86] mid_occ = 72
[M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 1; #seq: 2
[M::mm_idx_stat::0.819*1.83] distinct minimizers: 1687413 (95.18% are singletons); average occurrences: 1.226; average spacing: 7.498; total length: 15508171
[M::main] Version: 2.26-r1175
[M::main] CMD: /home/sioly/applications/minimap2/minimap2 -x asm20 -I4g -K1g -H --cs=long -t 16 --secondary=no /home/sioly/applications/CoreDetector/test_mygenomes/genomes/ARG_5133_7.fa /home/sioly/applications/CoreDetector/test_mygenomes/out_test/temp_fasta/Genome1_Genome2.fa
[M::main] Real time: 0.832 sec; CPU: 1.511 sec; Peak RSS: 0.122 GB
/home/sioly/applications/CoreDetector/MFbio.jarProcessing File: /home/sioly/applications/CoreDetector/test_mygenomes/out_test/maf/Genome1_Genome3.maf
Done.
available memory 113.303 gb
/home/sioly/applications/CoreDetector/MFbio.jarProcessing Maf Files at : /home/sioly/applications/CoreDetector/test_mygenomes/out_test/filtered_maf
Start Loading ...
0 was loaded.
Start Loading ...
0 was loaded.
start writing to output file...
Length of Alignment 0
Total Query Length 0
Done!
Done.

[RussellAndrewEdson]

Hi @siolybecerra. It sounds like it's not finding the k8 package. Have you got the k8 javascript package installed and executable on your system path? (from here: https://github.com/attractivechaos/k8)

Apologies for that, k8 is mentioned in the 'Dependencies' section of the readme page for CoreDetector but for some reason it is not mentioned in the 'Quick Start'. Mario's tasked me with cleaning up the readme when I get a spare second, so I plan to reorganise it so that the minimap and k8 dependencies are more explicit.

[siolybecerra]

Hi @RussellAndrewEdson. Now it is working. I copied the "k8-Linux" on my path working and renamed it to "k8".

Number of lines in file genomes.txt : 3
Genome size gb : 0
/home/sioly/applications/CoreDetector/test_mygenomes/genomes/CGRA01V4.fa
/home/sioly/applications/CoreDetector/test_mygenomes/genomes/CROI41.fa
[M::mm_idx_gen::0.664*1.00] collected minimizers
[M::mm_idx_gen::0.762*1.38] sorted minimizers
[M::main::0.762*1.38] loaded/built the index for 2 target sequence(s)
[M::mm_mapopt_update::0.802*1.36] mid_occ = 74
[M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 1; #seq: 2
[M::mm_idx_stat::0.831*1.35] distinct minimizers: 1697853 (95.20% are singletons); average occurrences: 1.230; average spacing: 7.504; total length: 15668520
[M::worker_pipeline::20.084*1.67] mapped 2 sequences
[M::main] Version: 2.26-r1175
[M::main] CMD: /home/sioly/applications/minimap2/minimap2 -x asm20 -I4g -K1g -H --cs=long -t 4 --secondary=no /home/sioly/applications/CoreDetector/test_mygenomes/genomes/CROI41.fa /home/sioly/applications/CoreDetector/test_mygenomes/genomes/CGRA01V4.fa
[M::main] Real time: 20.130 sec; CPU: 33.646 sec; Peak RSS: 1.153 GB
/home/sioly/applications/CoreDetector/MFbio.jarProcessing File: out_test//maf/Genome1_Genome2.maf
Total HSP:80, Total Rejected(bp):0, Total Alignment Length(bp) :14554981, Total ungapped Alignment Length(bp) :13713385 ,Max alignment Length(bp):2083638, Min alignment Length(bp):395, N50:662943
Done.
out_test//temp_fasta/Genome1_Genome2.fa
/home/sioly/applications/CoreDetector/test_mygenomes/genomes/ARG_5133_7.fa
[M::mm_idx_gen::0.684*1.00] collected minimizers
[M::mm_idx_gen::0.786*1.38] sorted minimizers
[M::main::0.786*1.38] loaded/built the index for 2 target sequence(s)
.
.
.
.
processing Query  :contig_02!4043933!4044327:1-395
processing Query  :contig_02!4756098!4758518:85-2199
start writing to output file...
Length of Alignment 14168846
Total Query Length 13146995
Done!
Done.

Thank you so much for following my question.

[RussellAndrewEdson]

No worries @siolybecerra, glad you got it sorted. You reminded me actually that there was some weirdness with the names of the k8 executable that should be sorted out, so I'll update the instructions/script accordingly.