I'd like to inspector to perform assembly correction of two haplotype-resolved HiFi assemblies of a human individual; So i fristly run the test dataset to validate successful installation of inspector. In the log file, i found a warning :
cat: test_out/ae_merge_workspace/invmerged*: No such file or directory;
However in the directory of test_out/ae_merge_workspace/, there was a file named inv_merged_ctg1. so do I need to worry about this warning? and only 2 structure error and 298 small-scale assembly error were present in the summary_statistics file. Is the difference of result caused by different versions of dependencies for Inspector?
Any help would be greatly appreciated,
Jingwei Yue!
the log file:
import pandas.util.testing as tm
[M::mm_idx_gen::0.0481.05] collected minimizers
[M::mm_idx_gen::0.0793.31] sorted minimizers
[M::main::0.0793.31] loaded/built the index for 2 target sequence(s)
[M::mm_mapopt_update::0.0913.00] mid_occ = 70
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 2
[M::mm_idx_stat::0.1002.83] distinct minimizers: 242594 (96.40% are singletons); average occurrences: 1.138; average spacing: 5.328; total length: 1470648
[M::worker_pipeline::14.6467.00] mapped 6532 sequences
[M::main] Version: 2.26-r1175
[M::main] CMD: minimap2 -a -Q -N 1 -I 10G -t 8 test_out/valid_contig.fa testdata/read_test.fastq.gz
[M::main] Real time: 14.660 sec; CPU: 102.577 sec; Peak RSS: 1.226 GB
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Collect info from ctg2
cat: test_out/ae_merge_workspace/invmerged*: No such file or directory
[mpileup] 1 samples in 1 input files
Set max per-file depth to 8000
[mpileup] 1 samples in 1 input files
Set max per-file depth to 8000
end n100
####files in the directory of test_out/ae_merge_workspace/
deletion-merged
del_merged_ctg1
insertion-merged
ins_merged_ctg1
inversion-merged
#######Dependencies for Inspector:
python 3.7
minimap2 2.2
samtools 1.6
Johnsonzcode
commented
9 months ago
I'd like to inspector to perform assembly correction of two haplotype-resolved HiFi assemblies of a human individual; So i fristly run the test dataset to validate successful installation of inspector. In the log file, i found a warning : cat: test_out/ae_merge_workspace/invmerged*: No such file or directory; However in the directory of test_out/ae_merge_workspace/, there was a file named inv_merged_ctg1. so do I need to worry about this warning? and only 2 structure error and 298 small-scale assembly error were present in the summary_statistics file. Is the difference of result caused by different versions of dependencies for Inspector?
Any help would be greatly appreciated, Jingwei Yue!
the log file:
import pandas.util.testing as tm [M::mm_idx_gen::0.0481.05] collected minimizers [M::mm_idx_gen::0.0793.31] sorted minimizers [M::main::0.0793.31] loaded/built the index for 2 target sequence(s) [M::mm_mapopt_update::0.0913.00] mid_occ = 70 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 2 [M::mm_idx_stat::0.1002.83] distinct minimizers: 242594 (96.40% are singletons); average occurrences: 1.138; average spacing: 5.328; total length: 1470648 [M::worker_pipeline::14.6467.00] mapped 6532 sequences [M::main] Version: 2.26-r1175 [M::main] CMD: minimap2 -a -Q -N 1 -I 10G -t 8 test_out/valid_contig.fa testdata/read_test.fastq.gz [M::main] Real time: 14.660 sec; CPU: 102.577 sec; Peak RSS: 1.226 GB [bam_sort_core] merging from 0 files and 8 in-memory blocks... Collect info from ctg2 cat: test_out/ae_merge_workspace/invmerged*: No such file or directory [mpileup] 1 samples in 1 input files