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GATB / gatb-minia-pipeline

GATB Minia assembly pipeline
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Error with `make test` #22

Closed nylander closed 4 years ago

nylander commented 4 years ago

Hi,

Following the installation instructions, make test fails with an Error (from runBESST). Is the test correctly designed?

To reproduce:

$ make test
...
Processing is finished.
(2019-12-16 08:32:42) Execution of 'python BESST/runBESST'. Command line: 
     gatb-minia-pipeline/tools/memused python gatb-minia-pipeline/BESST/runBESST -c assembly_k61.contigs.fa -f assembly.lib_0.bam -o assembly_besst -orientation fr --iter 10000
Number of initial contigs: 1
Estimating insert size from 10001 mappings with quality over --min_mapq 11.
Choosing mode: 495
mu_adjusted:499.4076, sigma_adjusted:49.8135148553, skewness_adjusted:-0.0259150237889
Creating contig graph with library:  assembly.lib_0.bam
Too few contigs to calculate coverage on. Got: 1 contigs. If you have specified  -z_min or --min_mapq, consider lower them. If not, check the BAM file for proper alignments. Exiting here before scaffolding...
maximal memory used: 84 MB
(2019-12-16 08:32:44) Execution of 'python BESST/runBESST' failed. Command line: 
     gatb-minia-pipeline/tools/memused python gatb-minia-pipeline/BESST/runBESST -c assembly_k61.contigs.fa -f assembly.lib_0.bam -o assembly_besst -orientation fr --iter 10000
Makefile:14: recipe for target 'test' failed
make: *** [test] Error 1
Processing is finished.
(2019-12-16 08:32:42) Execution of 'python BESST/runBESST'. Command line: 
     gatb-minia-pipeline/tools/memused python gatb-minia-pipeline/BESST/runBESST -c assembly_k61.contigs.fa -f assembly.lib_0.bam -o assembly_besst -orientation fr --iter 10000
Number of initial contigs: 1
Estimating insert size from 10001 mappings with quality over --min_mapq 11.
Choosing mode: 495
mu_adjusted:499.4076, sigma_adjusted:49.8135148553, skewness_adjusted:-0.0259150237889
Creating contig graph with library:  assembly.lib_0.bam
Too few contigs to calculate coverage on. Got: 1 contigs. If you have specified  -z_min or --min_mapq, consider lower them. If not, check the BAM file for proper alignments. Exiting here before scaffolding...
maximal memory used: 84 MB
(2019-12-16 08:32:44) Execution of 'python BESST/runBESST' failed. Command line: 
     gatb-minia-pipeline/tools/memused python gatb-minia-pipeline/BESST/runBESST -c assembly_k61.contigs.fa -f assembly.lib_0.bam -o assembly_besst -orientation fr --iter 10000
Makefile:14: recipe for target 'test' failed
make: *** [test] Error 1

File assembly_k61.contigs.fa:

Nseqs Min.len Max.len Avg.len
1         9985     9985     9985

File assembly.lib_0.bam:

$ samtools flagstat assembly.lib_0.bam
20000 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
20000 + 0 mapped (100.00% : N/A)
20000 + 0 paired in sequencing
10000 + 0 read1
10000 + 0 read2
20000 + 0 properly paired (100.00% : N/A)
20000 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
osowiecki commented 4 years ago

Aligning with bwa mem. Temp directory: /media/2/CORN/gatb-minia-pipeline/test/BESST_tmp Output path: assembly.lib_0 Stderr file: assembly.lib_0.bwa.1 Make bwa index... Done. Align with bwa mem... Done. Time elapsed for bwa index and mem: 0:00:00.572580

Convert SAM to BAM... Done. Time elapsed for SAM to BAM conversion: 0:00:00.166237

Sort BAM... Done. Time elapsed for BAM sorting: 0:00:00.136098

Index BAM... Done. Time elapsed for BAM indexing: 0:00:00.012084

Remove temp files... Done. Time elapsed for temp files removing: 0:00:00.000678

Processing is finished. (2019-12-24 18:19:17) Execution of 'python BESST/runBESST'. Command line: /media/2/CORN/gatb-minia-pipeline/tools/memused python /media/2/CORN/gatb-minia-pipeline/BESST/runBESST -c assembly_k61.contigs.fa -f assembly.lib_0.bam -o assembly_besst -orientation fr --iter 10000 Number of initial contigs: 1 Estimating insert size from 10001 mappings with quality over --min_mapq 11. Choosing mode: 495 mu_adjusted:499.4076, sigma_adjusted:49.8135148553, skewness_adjusted:-0.0259150237889 Creating contig graph with library: assembly.lib_0.bam Too few contigs to calculate coverage on. Got: 1 contigs. If you have specified -z_min or --min_mapq, consider lower them. If not, check the BAM file for proper alignments. Exiting here before scaffolding... maximal memory used: 61 MB (2019-12-24 18:19:18) Execution of 'python BESST/runBESST' failed. Command line: /media/2/CORN/gatb-minia-pipeline/tools/memused python /media/2/CORN/gatb-minia-pipeline/BESST/runBESST -c assembly_k61.contigs.fa -f assembly.lib_0.bam -o assembly_besst -orientation fr --iter 10000 Makefile:14: recipe for target 'test' failed make: *** [test] Error 1

sebschmi commented 4 years ago

I am getting the same error for the k61 test case, also just one contig generated.

rchikhi commented 4 years ago

thanks for reporting it. Fixed by removing BESST from the test.