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Versions of BWA and Samtools required for MIPgen #33

Closed tobsecret closed 6 years ago

tobsecret commented 6 years ago

What version of BWA does MIPgen depend on? My script is below:

module load bwa/intel/0.5.9
module load samtools/intel/1.2

project_name="./mips/first_try"
bwa_genome_index="path/to/Genome.fasta"
regions_to_scan="path/to/regions.bed"
min_capture_size=140
max_capture_size=180

~/MIPGEN/mipgen -project_name $project_name -bwa_genome_index $bwa_genome_index -regions_to_scan $regions_to_scan  -min_capture_size $min_capture_size -max_capture_size $max_capture_size

When I run that, I get the following output:

Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.5.9-r16
Contact: Heng Li <lh3@sanger.ac.uk>

Usage:   bwa <command> [options]

Command: index         index sequences in the FASTA format
         aln           gapped/ungapped alignment
         samse         generate alignment (single ended)
         sampe         generate alignment (paired ended)
         bwasw         BWA-SW for long queries

         fa2pac        convert FASTA to PAC format
         pac2bwt       generate BWT from PAC
         pac2bwtgen    alternative algorithm for generating BWT
         bwtupdate     update .bwt to the new format
         pac_rev       generate reverse PAC
         bwt2sa        generate SA from BWT and Occ
         pac2cspac     convert PAC to color-space PAC
         stdsw         standard SW/NW alignment

progress file could not be opened
unable to tile sequences due to circumstance 5

Which suggests to me that either I am not feeding in the right files or the syntax has changed between bwa versions.

tobsecret commented 6 years ago

Update on this - I did not know this and it's not mentioned in the docs but before doing any computation, MIPgen calls bwa and samtools without arguments so seeing the usage message of those is intentional.

The versions that ended up working for me with MIPgen are listed here:

More detail below: My trouble was that I was getting only nan values for the logistic score column, as mentioned in #4 but none of the fixes seemed to have any impact. So I tried different versions of BWA and it turns out using an old version (0.5.9) was what caused the errors (marked in bold) in the log of my MIPgen run:

```shell
[user@c35-09 testrun]$ mipgen -project_name testrun -bwa_genome_index ../Genome.fasta -regions_to_scan ../genes.bed -min_capture_size 162 -max_capture_size 162

Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.5.9-r16
Contact: Heng Li 

Usage:   bwa  [options]

Command: index         index sequences in the FASTA format
         aln           gapped/ungapped alignment
         samse         generate alignment (single ended)
         sampe         generate alignment (paired ended)
         bwasw         BWA-SW for long queries

         fa2pac        convert FASTA to PAC format
         pac2bwt       generate BWT from PAC
         pac2bwtgen    alternative algorithm for generating BWT
         bwtupdate     update .bwt to the new format
         pac_rev       generate reverse PAC
         bwt2sa        generate SA from BWT and Occ
         pac2cspac     convert PAC to color-space PAC
         stdsw         standard SW/NW alignment

[mipgen] success on opening region file
[mipgen] features loaded; retrieving chromosomal sequence

Program: samtools (Tools for alignments in the SAM format)
Version: 1.6 (using htslib 1.6)

Usage:   samtools  [options]

Commands:
  -- Indexing
     dict           create a sequence dictionary file
     faidx          index/extract FASTA
     index          index alignment

  -- Editing
     calmd          recalculate MD/NM tags and '=' bases
     fixmate        fix mate information
     reheader       replace BAM header
     rmdup          remove PCR duplicates
     targetcut      cut fosmid regions (for fosmid pool only)
     addreplacerg   adds or replaces RG tags
     markdup        mark duplicates

  -- File operations
     collate        shuffle and group alignments by name
     cat            concatenate BAMs
     merge          merge sorted alignments
     mpileup        multi-way pileup
     sort           sort alignment file
     split          splits a file by read group
     quickcheck     quickly check if SAM/BAM/CRAM file appears intact
     fastq          converts a BAM to a FASTQ
     fasta          converts a BAM to a FASTA

  -- Statistics
     bedcov         read depth per BED region
     depth          compute the depth
     flagstat       simple stats
     idxstats       BAM index stats
     phase          phase heterozygotes
     stats          generate stats (former bamcheck)

  -- Viewing
     flags          explain BAM flags
     tview          text alignment viewer
     view           SAM<->BAM<->CRAM conversion
     depad          convert padded BAM to unpadded BAM

[mipgen] first line of reference fasta reads: >Org_Strn_chr01 | organism=MyOrganism | version=2015-06-18 | length=830522 | SO=chromosome
[mipgen] no masked feature file found
[mipgen] regions ready; accessing snp file
[mipgen] all 0 snps loaded; generating files for bwa
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9

[bwt_restore_bwt] fail to open file '../Genome.fasta.rbwt'. Abort!
sh: line 1: 39781 Aborted                 (core dumped) bwa aln -t 1 ../Genome.fasta testrun.all_sequences.fq > testrun.all_sequences.sai
[bam_header_read] invalid BAM binary header (this is not a BAM file).

[mipgen] sam file opened
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9

[bwt_restore_bwt] fail to open file '../Genome.fasta.rbwt'. Abort!
sh: line 1: 39786 Aborted                 (core dumped) bwa aln -t 1 ../Genome.fasta testrun.oligo_copy_count.fq > testrun.oligo_copy_count.sai
[bam_header_read] invalid BAM binary header (this is not a BAM file).

[mipgen] checking oligo copy
[mipgen] bwa copy number analysis finished
[mipgen] file of all mips ready for write: testrun.all_mips.txt
[mipgen] file of collapsed mips ready for write: testrun.collapsed_mips.txt
[mipgen] feature #1
[mipgen] feature #2
[mipgen] feature #3
[mipgen] feature #4
[mipgen] feature #5
[mipgen] feature #6
[mipgen] mip picking complete:
testrun.picked_mips.txt
 and 
testrun.snp_mips.txt
```

Below the output of the same run with a newer version of bwa (0.7.15)

[schrat01@c35-09 testrun]$ mipgen -project_name testrun -bwa_genome_index ../Genome.fasta -regions_to_scan ../pf_resistance_genes.bed -min_capture_size 162 -max_capture_size 162

Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.15-r1140
Contact: Heng Li <lh3@sanger.ac.uk>

Usage:   bwa <command> [options]

Command: index         index sequences in the FASTA format
         mem           BWA-MEM algorithm
         fastmap       identify super-maximal exact matches
         pemerge       merge overlapping paired ends (EXPERIMENTAL)
         aln           gapped/ungapped alignment
         samse         generate alignment (single ended)
         sampe         generate alignment (paired ended)
         bwasw         BWA-SW for long queries

         shm           manage indices in shared memory
         fa2pac        convert FASTA to PAC format
         pac2bwt       generate BWT from PAC
         pac2bwtgen    alternative algorithm for generating BWT
         bwtupdate     update .bwt to the new format
         bwt2sa        generate SA from BWT and Occ

Note: To use BWA, you need to first index the genome with `bwa index'.
      There are three alignment algorithms in BWA: `mem', `bwasw', and
      `aln/samse/sampe'. If you are not sure which to use, try `bwa mem'
      first. Please `man ./bwa.1' for the manual.

[mipgen] success on opening region file
[mipgen] features loaded; retrieving chromosomal sequence

Program: samtools (Tools for alignments in the SAM format)
Version: 1.6 (using htslib 1.6)

Usage:   samtools <command> [options]

Commands:
  -- Indexing
     dict           create a sequence dictionary file
     faidx          index/extract FASTA
     index          index alignment

  -- Editing
     calmd          recalculate MD/NM tags and '=' bases
     fixmate        fix mate information
     reheader       replace BAM header
     rmdup          remove PCR duplicates
     targetcut      cut fosmid regions (for fosmid pool only)
     addreplacerg   adds or replaces RG tags
     markdup        mark duplicates

  -- File operations
     collate        shuffle and group alignments by name
     cat            concatenate BAMs
     merge          merge sorted alignments
     mpileup        multi-way pileup
     sort           sort alignment file
     split          splits a file by read group
     quickcheck     quickly check if SAM/BAM/CRAM file appears intact
     fastq          converts a BAM to a FASTQ
     fasta          converts a BAM to a FASTA

  -- Statistics
     bedcov         read depth per BED region
     depth          compute the depth
     flagstat       simple stats
     idxstats       BAM index stats
     phase          phase heterozygotes
     stats          generate stats (former bamcheck)

  -- Viewing
     flags          explain BAM flags
     tview          text alignment viewer
     view           SAM<->BAM<->CRAM conversion
     depad          convert padded BAM to unpadded BAM

[mipgen] first line of reference fasta reads:  >Org_Strn_chr01 | organism=MyOrganism | version=2015-06-18 | length=830522 | SO=chromosome
[mipgen] no masked feature file found
[mipgen] regions ready; accessing snp file
[mipgen] all 0 snps loaded; generating files for bwa
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.92 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 21712 sequences have been processed.
[main] Version: 0.7.15-r1140
[main] CMD: bwa aln -t 1 ../Genome.fasta testrun.all_sequences.fq
[main] Real time: 1.030 sec; CPU: 0.977 sec
[bwa_aln_core] convert to sequence coordinate... 0.08 sec
[bwa_aln_core] refine gapped alignments... 0.01 sec
[bwa_aln_core] print alignments... 0.04 sec
[bwa_aln_core] 21712 sequences have been processed.
[main] Version: 0.7.15-r1140
[main] CMD: bwa samse ../Genome.fasta testrun.all_sequences.sai testrun.all_sequences.fq
[main] Real time: 0.196 sec; CPU: 0.168 sec
[mipgen] sam file opened
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 6.04 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 1.27 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 316946 sequences have been processed.
[main] Version: 0.7.15-r1140
[main] CMD: bwa aln -t 1 ../Genome.fasta testrun.oligo_copy_count.fq
[main] Real time: 7.731 sec; CPU: 7.567 sec
[bwa_aln_core] convert to sequence coordinate... 0.52 sec
[bwa_aln_core] refine gapped alignments... 0.08 sec
[bwa_aln_core] print alignments... 0.40 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 0.11 sec
[bwa_aln_core] refine gapped alignments... 0.02 sec
[bwa_aln_core] print alignments... 0.09 sec
[bwa_aln_core] 316946 sequences have been processed.
[main] Version: 0.7.15-r1140
[main] CMD: bwa samse ../Genome.fasta testrun.oligo_copy_count.sai testrun.oligo_copy_count.fq
[main] Real time: 1.585 sec; CPU: 1.473 sec
[mipgen] checking oligo copy
[mipgen] bwa copy number analysis finished
[mipgen] file of all mips ready for write: testrun.all_mips.txt
[mipgen] file of collapsed mips ready for write: testrun.collapsed_mips.txt
[mipgen] feature #1
[mipgen] feature #2
[mipgen] feature #3
[mipgen] feature #4
[mipgen] feature #5
[mipgen] feature #6
[mipgen] mip picking complete:
testrun.picked_mips.txt
 and 
testrun.snp_mips.txt
augustboyle commented 6 years ago

Thanks for the detective work!

Evan

On May 30, 2018 at 9:41:37 AM, tobsecret (notifications@github.com) wrote:

Update on this - I did not know this and it's not mentioned in the docs but before doing any computation, MIPgen calls bwa and samtools without arguments so seeing the usage message of those is intentional.

The versions that ended up working for me with MIPgen are listed here:

  1. bwa/0.7.15 2) zlib/1.2.8 3) perl/5.24.0 4) samtools/1.6 5) intel/17.0.1 6) htslib/1.4.1

More detail below: My trouble was that I was getting only nan values for the logistic score column, as mentioned in #4 https://github.com/shendurelab/MIPGEN/issues/4 but none of the fixes seemed to have any impact. So I tried different versions of BWA and it turns out using an old version (0.5.9) was what caused the errors (marked in bold) in the log of my MIPgen run:

[user@c35-09 testrun]$ mipgen -project_name testrun -bwa_genome_index ../Genome.fasta -regions_to_scan ../genes.bed -min_capture_size 162 -max_capture_size 162

Program: bwa (alignment via Burrows-Wheeler transformation) Version: 0.5.9-r16 Contact: Heng Li lh3@sanger.ac.uk

Usage: bwa [options]

Command: index index sequences in the FASTA format aln gapped/ungapped alignment samse generate alignment (single ended) sampe generate alignment (paired ended) bwasw BWA-SW for long queries

     fa2pac        convert FASTA to PAC format
     pac2bwt       generate BWT from PAC
     pac2bwtgen    alternative algorithm for generating BWT
     bwtupdate     update .bwt to the new format
     pac_rev       generate reverse PAC
     bwt2sa        generate SA from BWT and Occ
     pac2cspac     convert PAC to color-space PAC
     stdsw         standard SW/NW alignment

[mipgen] success on opening region file [mipgen] features loaded; retrieving chromosomal sequence

Program: samtools (Tools for alignments in the SAM format) Version: 1.6 (using htslib 1.6)

Usage: samtools [options]

Commands: -- Indexing dict create a sequence dictionary file faidx index/extract FASTA index index alignment

-- Editing calmd recalculate MD/NM tags and '=' bases fixmate fix mate information reheader replace BAM header rmdup remove PCR duplicates targetcut cut fosmid regions (for fosmid pool only) addreplacerg adds or replaces RG tags markdup mark duplicates

-- File operations collate shuffle and group alignments by name cat concatenate BAMs merge merge sorted alignments mpileup multi-way pileup sort sort alignment file split splits a file by read group quickcheck quickly check if SAM/BAM/CRAM file appears intact fastq converts a BAM to a FASTQ fasta converts a BAM to a FASTA

-- Statistics bedcov read depth per BED region depth compute the depth flagstat simple stats idxstats BAM index stats phase phase heterozygotes stats generate stats (former bamcheck)

-- Viewing flags explain BAM flags tview text alignment viewer view SAM<->BAM<->CRAM conversion depad convert padded BAM to unpadded BAM

[mipgen] first line of reference fasta reads: >Org_Strn_chr01 | organism=MyOrganism | version=2015-06-18 | length=830522 | SO=chromosome [mipgen] no masked feature file found [mipgen] regions ready; accessing snp file [mipgen] all 0 snps loaded; generating files for bwa [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9[bwt_restore_bwt] fail to open file '../Genome.fasta.rbwt'. Abort! sh: line 1: 39781 Aborted (core dumped) bwa aln -t 1 ../Genome.fasta testrun.all_sequences.fq > testrun.all_sequences.sai [bam_header_read] invalid BAM binary header (this is not a BAM file). [mipgen] sam file opened [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9[bwt_restore_bwt] fail to open file '../Genome.fasta.rbwt'. Abort! sh: line 1: 39786 Aborted (core dumped) bwa aln -t 1 ../Genome.fasta testrun.oligo_copy_count.fq > testrun.oligo_copy_count.sai [bam_header_read] invalid BAM binary header (this is not a BAM file). [mipgen] checking oligo copy [mipgen] bwa copy number analysis finished [mipgen] file of all mips ready for write: testrun.all_mips.txt [mipgen] file of collapsed mips ready for write: testrun.collapsed_mips.txt [mipgen] feature #1 [mipgen] feature #2 [mipgen] feature #3 [mipgen] feature #4 [mipgen] feature #5 [mipgen] feature #6 [mipgen] mip picking complete: testrun.picked_mips.txt and testrun.snp_mips.txt

Below the output of the same run with a newer version of bwa (0.7.15)

[schrat01@c35-09 testrun]$ mipgen -project_name testrun -bwa_genome_index ../Genome.fasta -regions_to_scan ../pf_resistance_genes.bed -min_capture_size 162 -max_capture_size 162

Program: bwa (alignment via Burrows-Wheeler transformation) Version: 0.7.15-r1140 Contact: Heng Li lh3@sanger.ac.uk

Usage: bwa [options]

Command: index index sequences in the FASTA format mem BWA-MEM algorithm fastmap identify super-maximal exact matches pemerge merge overlapping paired ends (EXPERIMENTAL) aln gapped/ungapped alignment samse generate alignment (single ended) sampe generate alignment (paired ended) bwasw BWA-SW for long queries

     shm           manage indices in shared memory
     fa2pac        convert FASTA to PAC format
     pac2bwt       generate BWT from PAC
     pac2bwtgen    alternative algorithm for generating BWT
     bwtupdate     update .bwt to the new format
     bwt2sa        generate SA from BWT and Occ

Note: To use BWA, you need to first index the genome with bwa index'. There are three alignment algorithms in BWA:mem', bwasw', and aln/samse/sampe'. If you are not sure which to use, try bwa mem' first. Pleaseman ./bwa.1' for the manual. [mipgen] success on opening region file[mipgen] features loaded; retrieving chromosomal sequence Program: samtools (Tools for alignments in the SAM format)Version: 1.6 (using htslib 1.6) Usage: samtools [options] Commands: -- Indexing dict create a sequence dictionary file faidx index/extract FASTA index index alignment -- Editing calmd recalculate MD/NM tags and '=' bases fixmate fix mate information reheader replace BAM header rmdup remove PCR duplicates targetcut cut fosmid regions (for fosmid pool only) addreplacerg adds or replaces RG tags markdup mark duplicates -- File operations collate shuffle and group alignments by name cat concatenate BAMs merge merge sorted alignments mpileup multi-way pileup sort sort alignment file split splits a file by read group quickcheck quickly check if SAM/BAM/CRAM file appears intact fastq converts a BAM to a FASTQ fasta converts a BAM to a FASTA -- Statistics bedcov read depth per BED region depth compute the depth flagstat simple stats idxstats BAM index stats phase phase heterozygotes stats generate stats (former bamcheck) -- Viewing flags explain BAM flags tview text alignment viewer view SAM<->BAM<->CRAM conversion depad convert padded BAM to unpadded BAM [mipgen] first line of reference fasta reads: >Org_Strn_chr01 | organism=MyOrganism | version=2015-06-18 | length=830522 | SO=chromosome[mipgen] no masked feature file found[mipgen] regions ready; accessing snp file[mipgen] all 0 snps loaded; generating files for bwa[bwa_aln] 17bp reads: max_diff = 2[bwa_aln] 38bp reads: max_diff = 3[bwa_aln] 64bp reads: max_diff = 4[bwa_aln] 93bp reads: max_diff = 5[bwa_aln] 124bp reads: max_diff = 6[bwa_aln] 157bp reads: max_diff = 7[bwa_aln] 190bp reads: max_diff = 8[bwa_aln] 225bp reads: max_diff = 9[bwa_aln_core] calculate SA coordinate... 0.92 sec[bwa_aln_core] write to the disk... 0.00 sec[bwa_aln_core] 21712 sequences have been processed.[main] Version: 0.7.15-r1140[main] CMD: bwa aln -t 1 ../Genome.fasta testrun.all_sequences.fq[main] Real time: 1.030 sec; CPU: 0.977 sec[bwa_aln_core] convert to sequence coordinate... 0.08 sec[bwa_aln_core] refine gapped alignments... 0.01 sec[bwa_aln_core] print alignments... 0.04 sec[bwa_aln_core] 21712 sequences have been processed.[main] Version: 0.7.15-r1140[main] CMD: bwa samse ../Genome.fasta testrun.all_sequences.sai testrun.all_sequences.fq[main] Real time: 0.196 sec; CPU: 0.168 sec[mipgen] sam file opened[bwa_aln] 17bp reads: max_diff = 2[bwa_aln] 38bp reads: max_diff = 3[bwa_aln] 64bp reads: max_diff = 4[bwa_aln] 93bp reads: max_diff = 5[bwa_aln] 124bp reads: max_diff = 6[bwa_aln] 157bp reads: max_diff = 7[bwa_aln] 190bp reads: max_diff = 8[bwa_aln] 225bp reads: max_diff = 9[bwa_aln_core] calculate SA coordinate... 6.04 sec[bwa_aln_core] write to the disk... 0.02 sec[bwa_aln_core] 262144 sequences have been processed.[bwa_aln_core] calculate SA coordinate... 1.27 sec[bwa_aln_core] write to the disk... 0.00 sec[bwa_aln_core] 316946 sequences have been processed.[main] Version: 0.7.15-r1140[main] CMD: bwa aln -t 1 ../Genome.fasta testrun.oligo_copy_count.fq[main] Real time: 7.731 sec; CPU: 7.567 sec[bwa_aln_core] convert to sequence coordinate... 0.52 sec[bwa_aln_core] refine gapped alignments... 0.08 sec[bwa_aln_core] print alignments... 0.40 sec[bwa_aln_core] 262144 sequences have been processed.[bwa_aln_core] convert to sequence coordinate... 0.11 sec[bwa_aln_core] refine gapped alignments... 0.02 sec[bwa_aln_core] print alignments... 0.09 sec[bwa_aln_core] 316946 sequences have been processed.[main] Version: 0.7.15-r1140[main] CMD: bwa samse ../Genome.fasta testrun.oligo_copy_count.sai testrun.oligo_copy_count.fq[main] Real time: 1.585 sec; CPU: 1.473 sec[mipgen] checking oligo copy[mipgen] bwa copy number analysis finished[mipgen] file of all mips ready for write: testrun.all_mips.txt[mipgen] file of collapsed mips ready for write: testrun.collapsed_mips.txt[mipgen] feature #1[mipgen] feature

2[mipgen] feature #3[mipgen] feature #4[mipgen] feature #5[mipgen]

feature #6[mipgen] mip picking complete:testrun.picked_mips.txt and testrun.snp_mips.txt

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tobsecret commented 6 years ago

You got it - Thanks for writing & maintaining the software!

francois-lecoquierre commented 3 years ago

Hello, I had the same BWA issue. Changing the "-project-name" parameter resolved this problem, it seems like MIPgen did not want to generate a new folder. Providing a folder already existing fixed it.