yusugihara / mutmap Goto Github PK

Dear Yu,

I use the mutmap v2.3.3 with snpeff. The mutmap_plot were showed in the attached file. The the "red cross (❌)" made me confused. I didn't find any information from the readme. I thought it should be from the snpeff analysis. The plot will have no red cross if I run mutmap without the snpeff. But I could not link the snpeff analysis data with the red cross. Please update more explanation for the plot.

This pipeline helps me a lot. Many thanks to the developers.

All best,
Xizhe

Hi!

Say for example that I have parental lines- 2 samples and a bulk sequenced the progenies, 2 datasets that I know are phenotypically different (based on observations). Is there a way that I can apply MutMap to this situation?

Any suggestions would be really great!

Thanks!

Dear developers,
I'm using Mutmap to perform some analysis on a set of 4 F2 bulk (2 mutant and 2 wild type) and 2 parentals (1 mutant and 1 wild type).
I was running the MutMap command with bam files:

mutmap -r genome.fasta -c Wild_type/alignment.bam -b Pool_1_Mut/alignment.bam -n 11 -o Pool_1_Mut

but what is not clear to me is the role of the cultivar (parental) in the final results. How does it affect the alignment and the variant calling of the bulk?
Moreover, I've tried to run each bulk with the opposite parental as cultivar, but I'm not sure if it was correct.

Thanks,
Leonardo

I use mutmap to mapping gene from begining.

when calling variants, the following error was generated :
bcftools concat -a -o z mutmap.vcf.gz mutmap.*.vcf.gz >> log/bcftools.log 2>&1
Please check below ：
Failed to open 30_vcf/mutmap.AAAA02040040.1.vcf.gz : could not load index .

Any ideas what I might be missing or overlooking?

Dear Yu,
Thank you for MutMap. I bumped into a weird mistake. My guess is that it is due to the split of the genome reference into chromosomes. Don't really know.

This is my OS Linux x86_64 GNU/Linux and my conda environment:

name: bsaseq
channels:
  - bioconda
  - conda-forge
  - defaults
dependencies:
  - mutmap = 2.3.2
  - snakemake = 5.20.0
  - fastp = 0.19.5
  - multiqc = 1.9
  - yaml = 0.2.5
  - snpeff = 5.0
  - parallel-fastq-dump = 0.6.7 
  - samtools = 1.14
  - bcftools = 1.14

Finally, here is the error message I got:

(bsaseq) bash-4.2$ mutmap --ref Oy-0DeNovo.fa -c D_Oy_0.final.sorted.bam  -b trimmed/bulk_R1_trimmed.fq.gz,trimmed/bulk_R2_trimmed.fq.gz        -n 51        --out run1/ -t 30
[MutMap:2021-11-22 17:20:16] start to run MutMap.
[MutMap:2021-11-22 17:20:16] maximum number of threads which you can use is up to 64.
[MutMap:2021-11-22 17:20:16] start to index reference fasta.
[MutMap:2021-11-22 17:21:39] indexing of reference successfully finished.
[MutMap:2021-11-22 17:21:39] start to align reads of bulk.0000 by BWA.
[MutMap:2021-11-22 17:41:24] alignment bulk.0000 successfully finished.
[MutMap:2021-11-22 17:41:24] start to merge BAMs.
[MutMap:2021-11-22 17:42:44] merging process successfully finished.
[MutMap:2021-11-22 17:42:44] start to call variants.
[MutMap:2021-11-22 17:42:45] !!ERROR!! bcftools mpileup -a AD,ADF,ADR -B -q 40 -Q 18 -C 50 -O u -r Chr5 -f run1//10_ref/Oy-0DeNovo.fa run1//20_bam/cultivar.bam run1//20_bam/bulk.bam | bcftools call -vm -f GQ,GP -O u | bcftools filter -i "INFO/MQ>=40" -O z -o run1//30_vcf/mutmap.Chr5.vcf.gz >> run1//log/bcftools.Chr5.log 2>&1

please check below:

[MutMap:2021-11-22 17:42:45] !!ERROR!! bcftools mpileup -a AD,ADF,ADR -B -q 40 -Q 18 -C 50 -O u -r Chr2 -f run1//10_ref/Oy-0DeNovo.fa run1//20_bam/cultivar.bam run1//20_bam/bulk.bam | bcftools call -vm -f GQ,GP -O u | bcftools filter -i "INFO/MQ>=40" -O z -o run1//30_vcf/mutmap.Chr2.vcf.gz >> run1//log/bcftools.Chr2.log 2>&1

please check below:

[MutMap:2021-11-22 17:42:45] !!ERROR!! bcftools mpileup -a AD,ADF,ADR -B -q 40 -Q 18 -C 50 -O u -r Chr4 -f run1//10_ref/Oy-0DeNovo.fa run1//20_bam/cultivar.bam run1//20_bam/bulk.bam | bcftools call -vm -f GQ,GP -O u | bcftools filter -i "INFO/MQ>=40" -O z -o run1//30_vcf/mutmap.Chr4.vcf.gz >> run1//log/bcftools.Chr4.log 2>&1

please check below:

[MutMap:2021-11-22 17:42:45] !!ERROR!! bcftools mpileup -a AD,ADF,ADR -B -q 40 -Q 18 -C 50 -O u -r Chr3 -f run1//10_ref/Oy-0DeNovo.fa run1//20_bam/cultivar.bam run1//20_bam/bulk.bam | bcftools call -vm -f GQ,GP -O u | bcftools filter -i "INFO/MQ>=40" -O z -o run1//30_vcf/mutmap.Chr3.vcf.gz >> run1//log/bcftools.Chr3.log 2>&1

please check below:

[MutMap:2021-11-22 17:42:45] !!ERROR!! bcftools mpileup -a AD,ADF,ADR -B -q 40 -Q 18 -C 50 -O u -r Chr1 -f run1//10_ref/Oy-0DeNovo.fa run1//20_bam/cultivar.bam run1//20_bam/bulk.bam | bcftools call -vm -f GQ,GP -O u | bcftools filter -i "INFO/MQ>=40" -O z -o run1//30_vcf/mutmap.Chr1.vcf.gz >> run1//log/bcftools.Chr1.log 2>&1

please check below:

multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/home/mgallan1/miniconda3/envs/bsaseq/lib/python3.10/site-packages/mutmap/mpileup.py", line 139, in mpileup
    sbp.run(cmd1,
  File "/home/mgallan1/miniconda3/envs/bsaseq/lib/python3.10/subprocess.py", line 524, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'bcftools mpileup -a AD,ADF,ADR -B -q 40 -Q 18 -C 50 -O u -r Chr5 -f run1//10_ref/Oy-0DeNovo.fa run1//20_bam/cultivar.bam run1//20_bam/bulk.bam | bcftools call -vm -f GQ,GP -O u | bcftools filter -i "INFO/MQ>=40" -O z -o run1//30_vcf/mutmap.Chr5.vcf.gz >> run1//log/bcftools.Chr5.log 2>&1' returned non-zero exit status 255.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/mgallan1/miniconda3/envs/bsaseq/lib/python3.10/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/home/mgallan1/miniconda3/envs/bsaseq/lib/python3.10/multiprocessing/pool.py", line 48, in mapstar
    return list(map(*args))
  File "/home/mgallan1/miniconda3/envs/bsaseq/lib/python3.10/site-packages/mutmap/mpileup.py", line 145, in mpileup
    call_log(self.out, 'bcftools', cmd1)
  File "/home/mgallan1/miniconda3/envs/bsaseq/lib/python3.10/site-packages/mutmap/utils.py", line 19, in call_log
    with open('{}/log/{}.log'.format(out_dir, name)) as log:
FileNotFoundError: [Errno 2] No such file or directory: 'run1//log/bcftools.log'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/mgallan1/miniconda3/envs/bsaseq/bin/mutmap", line 10, in <module>
    sys.exit(main())
  File "/home/mgallan1/miniconda3/envs/bsaseq/lib/python3.10/site-packages/mutmap/mutmap.py", line 146, in main
    MutMap(args).run()
  File "/home/mgallan1/miniconda3/envs/bsaseq/lib/python3.10/site-packages/mutmap/mutmap.py", line 141, in run
    self.mpileup()
  File "/home/mgallan1/miniconda3/envs/bsaseq/lib/python3.10/site-packages/mutmap/mutmap.py", line 102, in mpileup
    mp.run()
  File "/home/mgallan1/miniconda3/envs/bsaseq/lib/python3.10/site-packages/mutmap/mpileup.py", line 227, in run
    p.map(self.mpileup, chr_names)
  File "/home/mgallan1/miniconda3/envs/bsaseq/lib/python3.10/multiprocessing/pool.py", line 364, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
  File "/home/mgallan1/miniconda3/envs/bsaseq/lib/python3.10/multiprocessing/pool.py", line 771, in get
    raise self._value
FileNotFoundError: [Errno 2] No such file or directory: 'run1//log/bcftools.log'

Any clue why?
Thank you in advance,
Marc

Please add a license file so that people can understand whether they can redistribute the tool

i experienced this error when i am running Mutmap as well as Mutplot also

Traceback (most recent call last):
File "/home/priyanka/miniconda3/bin/mutplot", line 11, in
load_entry_point('mutmap', 'console_scripts', 'mutplot')()
File "/home/priyanka/miniconda3/lib/python3.6/site-packages/pkg_resources/init.py", line 490, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/home/priyanka/miniconda3/lib/python3.6/site-packages/pkg_resources/init.py", line 2853, in load_entry_point
return ep.load()
File "/home/priyanka/miniconda3/lib/python3.6/site-packages/pkg_resources/init.py", line 2453, in load
return self.resolve()
File "/home/priyanka/miniconda3/lib/python3.6/site-packages/pkg_resources/init.py", line 2459, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/home/priyanka/MutMap/mutmap/mutplot.py", line 12, in
from mutmap.plot import Plot
File "/home/priyanka/MutMap/mutmap/plot.py", line 8, in
from qtlseq.utils import time_stamp
ModuleNotFoundError: No module named 'qtlseq'

Dear Yu,
Thank you for MutMap. I've had some problems with it. When I use mutmap with BAM file, I found I can obtain the file of mutmap.vcf.gz, but I can not obtain the result files in 40_mutmap. I guess the problem is mutplot. Could you help me see how to solve this problem. The details of error are as follows:
(mutmap) root@ecs-75cc:~/snp2# mutmap -r /root/snp/genome/Fragaria_vesca_v4.0.a1.fasta -c /root/snp/mapping/wt.MarkDup.bam -b /root/snp/mapping/mut.sorted.bam -n 33 -o example_dir
[MutMap:2021-12-12 17:26:17] start to run MutMap.
[MutMap:2021-12-12 17:26:17] maximum number of threads which you can use is up to 8.
[MutMap:2021-12-12 17:26:17] start to index reference fasta.
[MutMap:2021-12-12 17:29:19] indexing of reference successfully finished.
[MutMap:2021-12-12 17:29:19] start to merge BAMs.
[MutMap:2021-12-12 17:41:48] merging process successfully finished.
[MutMap:2021-12-12 17:41:48] start to call variants.
[MutMap:2021-12-12 17:52:56] variant calling successfully finished.
[MutMap:2021-12-12 17:52:56] start to index VCF.
[MutMap:2021-12-12 17:52:56] indexing VCF successfully finished.
[MutMap:2021-12-12 17:52:57] start to run MutPlot.
[MutMap:2021-12-12 17:52:57] start to calculate SNP-index.
[MutMap:2021-12-12 17:52:58] SNP-index successfully finished.
[MutMap:2021-12-12 17:52:58] start to smooth SNP-index.
[MutMap:2021-12-12 17:52:58] smoothing process successfully finished.
[MutMap:2021-12-12 17:52:58] plotting now...
Traceback (most recent call last):
File "/root/BSA/enter/envs/mutmap/lib/python3.10/site-packages/PIL/ImageFile.py", line 504, in _save
fh = fp.fileno()
AttributeError: '_idat' object has no attribute 'fileno'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/root/BSA/enter/envs/mutmap/bin/mutplot", line 10, in
sys.exit(main())
File "/root/BSA/enter/envs/mutmap/lib/python3.10/site-packages/mutmap/mutplot.py", line 189, in main
mp.run()
File "/root/BSA/enter/envs/mutmap/lib/python3.10/site-packages/mutmap/mutplot.py", line 178, in run
pt.run()
File "/root/BSA/enter/envs/mutmap/lib/python3.10/site-packages/mutmap/plot.py", line 143, in run
plt.savefig('{}/mutmap_plot.{}'.format(self.out, self.args.format))
File "/root/BSA/enter/envs/mutmap/lib/python3.10/site-packages/matplotlib/pyplot.py", line 958, in savefig
res = fig.savefig(*args, **kwargs)
File "/root/BSA/enter/envs/mutmap/lib/python3.10/site-packages/matplotlib/figure.py", line 3012, in savefig
self.canvas.print_figure(fname, **kwargs)
File "/root/BSA/enter/envs/mutmap/lib/python3.10/site-packages/matplotlib/backend_bases.py", line 2314, in print_figure
result = print_method(
File "/root/BSA/enter/envs/mutmap/lib/python3.10/site-packages/matplotlib/backend_bases.py", line 1643, in wrapper
return func(*args, **kwargs)
File "/root/BSA/enter/envs/mutmap/lib/python3.10/site-packages/matplotlib/_api/deprecation.py", line 412, in wrapper
return func(*inner_args, **inner_kwargs)
File "/root/BSA/enter/envs/mutmap/lib/python3.10/site-packages/matplotlib/backends/backend_agg.py", line 541, in print_png
mpl.image.imsave(
File "/root/BSA/enter/envs/mutmap/lib/python3.10/site-packages/matplotlib/image.py", line 1675, in imsave
image.save(fname, **pil_kwargs)
File "/root/BSA/enter/envs/mutmap/lib/python3.10/site-packages/PIL/Image.py", line 2240, in save
save_handler(self, fp, filename)
File "/root/BSA/enter/envs/mutmap/lib/python3.10/site-packages/PIL/PngImagePlugin.py", line 1348, in _save
ImageFile._save(im, _idat(fp, chunk), [("zip", (0, 0) + im.size, 0, rawmode)])
File "/root/BSA/enter/envs/mutmap/lib/python3.10/site-packages/PIL/ImageFile.py", line 512, in _save
e.setimage(im.im, b)
SystemError: tile cannot extend outside image
[MutMap:2021-12-12 17:52:59] MutMap successfully finished.

Best wishes.

Pengbo Xu

Is there a license? Is this open source, unrestricted?

mutmap -r mutmap_ref.fasta -c mutmap_cultivar.1.fastq,mutmap_cultivar.2.fastq -b mutmap_bulk.1.fastq,mutmap_bulk.2.fastq -n 20 -o output
[MutMap:2020-08-18 01:26:01] start to run MutMap.
[MutMap:2020-08-18 01:26:01] maximum number of threads which you can use is up to 8.
[MutMap:2020-08-18 01:26:01] start to index reference fasta.
[MutMap:2020-08-18 01:26:03] indexing of reference successfully finished.
[MutMap:2020-08-18 01:26:03] start to align reads of cultivar.0000 by BWA.
[MutMap:2020-08-18 01:26:17] alignment cultivar.0000 successfully finished.
[MutMap:2020-08-18 01:26:17] start to align reads of bulk.0000 by BWA.
[MutMap:2020-08-18 01:26:30] alignment bulk.0000 successfully finished.
[MutMap:2020-08-18 01:26:30] start to filter reads.
[MutMap:2020-08-18 01:26:49] filtering process successfully finished.
[MutMap:2020-08-18 01:26:49] start to merge BAMs.
[MutMap:2020-08-18 01:27:01] merging process successfully finished.
[MutMap:2020-08-18 01:27:01] start to call variants.
[MutMap:2020-08-18 01:27:23] variant calling successfully finished.
[MutMap:2020-08-18 01:27:23] start to index VCF.
[MutMap:2020-08-18 01:27:23] indexing VCF successfully finished.
Traceback (most recent call last):
File "/home/priyanka/miniconda3/bin/mutplot", line 11, in
load_entry_point('mutmap', 'console_scripts', 'mutplot')()
File "/home/priyanka/miniconda3/lib/python3.6/site-packages/pkg_resources/init.py", line 488, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/home/priyanka/miniconda3/lib/python3.6/site-packages/pkg_resources/init.py", line 2872, in load_entry_point
return ep.load()
File "/home/priyanka/miniconda3/lib/python3.6/site-packages/pkg_resources/init.py", line 2472, in load
return self.resolve()
File "/home/priyanka/miniconda3/lib/python3.6/site-packages/pkg_resources/init.py", line 2478, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/home/priyanka/MutMap/mutmap/mutplot.py", line 12, in
from mutmap.plot import Plot
File "/home/priyanka/MutMap/mutmap/plot.py", line 8, in
from qtlseq.utils import time_stamp
ModuleNotFoundError: No module named 'qtlseq'
[MutMap:2020-08-18 01:27:24] MutMap successfully finished.

after starting to call variants, I found this error even through using fastq or bam files

-r IRGSP-1.0_genome.fasta
-c cultivar.bam
-b bulk.bam
-n 24
-o result

[MutMap:2020-08-08 21:10:53] start to run MutMap.
[MutMap:2020-08-08 21:10:53] maximum number of threads which you can use is up to 12.
[MutMap:2020-08-08 21:10:53] start to index reference fasta.
[MutMap:2020-08-08 21:14:41] indexing of reference successfully finished.
[MutMap:2020-08-08 21:14:41] start to filter reads.
[MutMap:2020-08-08 21:34:36] filtering process successfully finished.
[MutMap:2020-08-08 21:34:36] start to merge BAMs.
[MutMap:2020-08-08 21:46:14] merging process successfully finished.
[MutMap:2020-08-08 21:46:14] start to call variants.
[MutMap:2020-08-08 21:46:16] !!ERROR!! bcftools mpileup -a AD,ADF,ADR -B -q 40 -Q 18 -C 50 -O u -r chr03 -f result/10_ref/IRGSP-1.0_genome.fasta result/20_bam/cultivar.filt.bam result/20_bam/bulk.filt.bam | bcftools call -vm -f GQ,GP -O u | bcftools filter -i "INFO/MQ>=40" -O z -o result/30_vcf/mutmap.chr03.vcf.gz >> result/log/bcftools.chr03.log 2>&1
[MutMap:2020-08-08 21:46:16] !!ERROR!! bcftools mpileup -a AD,ADF,ADR -B -q 40 -Q 18 -C 50 -O u -r chr01 -f result/10_ref/IRGSP-1.0_genome.fasta result/20_bam/cultivar.filt.bam result/20_bam/bulk.filt.bam | bcftools call -vm -f GQ,GP -O u | bcftools filter -i "INFO/MQ>=40" -O z -o result/30_vcf/mutmap.chr01.vcf.gz >> result/log/bcftools.chr01.log 2>&1

please check below:

[MutMap:2020-08-08 21:46:16] !!ERROR!! bcftools mpileup -a AD,ADF,ADR -B -q 40 -Q 18 -C 50 -O u -r chr05 -f result/10_ref/IRGSP-1.0_genome.fasta result/20_bam/cultivar.filt.bam result/20_bam/bulk.filt.bam | bcftools call -vm -f GQ,GP -O u | bcftools filter -i "INFO/MQ>=40" -O z -o result/30_vcf/mutmap.chr05.vcf.gz >> result/log/bcftools.chr05.log 2>&1
During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/Users/...../opt/anaconda3/lib/python3.7/multiprocessing/pool.py", line 121, in worker
result = (True, func(*args, **kwds))

Hello，
I found MutMap+ while doing research, and I really found it useful. But I only find the latest version (2.3.3) of MutMap on GitHub. Would it be possible for you to tell me where to download Mutmap+ ?

Hi there,

A subprocess.CalledProcessError occurred when starting to call variants. Python version 3.8 and 3.7 did not make any difference. The jobs were submitted with LSF to a cluster (see blow script). I also forced the CPU number to 1, still the same error.

Any solutions fort that?

Thank you in advance,
Shawn

By the way, "conda install -c bioconda mutmap" doesn't work, as 'samtools' and/or 'bcftools' keep giving the following error
samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory

So I installed mutmap and dependencies manually. Version info as below:

(python3.7) [qtclab1@loginview03 MutMap-master]$ bcftools --version
bcftools 1.3.1
Using htslib 1.3.1
Copyright (C) 2016 Genome Research Ltd.
License Expat: The MIT/Expat license
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

(python3.7) [qtclab1@loginview03 MutMap-master]$ samtools --version
samtools 1.3.1
Using htslib 1.3.1
Copyright (C) 2016 Genome Research Ltd.

The stout was like:

[MutMap:2020-09-21 09:45:08] start to run MutMap.
[MutMap:2020-09-21 09:45:08] maximum number of threads which you can use is up to 16.
[MutMap:2020-09-21 09:45:08] start to index reference fasta.
[MutMap:2020-09-21 09:47:07] indexing of reference successfully finished.
[MutMap:2020-09-21 09:47:07] start to filter reads.
[MutMap:2020-09-21 10:06:36] filtering process successfully finished.
[MutMap:2020-09-21 10:06:36] start to merge BAMs.
[MutMap:2020-09-21 10:18:37] merging process successfully finished.
[MutMap:2020-09-21 10:18:37] start to call variants.
[MutMap:2020-09-21 10:18:38] !!ERROR!! bcftools mpileup -a AD,ADF,ADR -B -q 40 -Q 18 -C 50 -O u -r 4 -f /
Share2/home/qtclab1/00.users/shang_gao/01.SongSS/01.mutmap/CNUsongA11C3G337_new_python3.7/10_ref/Arabidop
sis_thaliana.TAIR10.dna.toplevel.fa /Share2/home/qtclab1/00.users/shang_gao/01.SongSS/01.mutmap/CNUsongA1
1C3G337_new_python3.7/20_bam/cultivar.filt.bam /Share2/home/qtclab1/00.users/shang_gao/01.SongSS/01.mutma
p/CNUsongA11C3G337_new_python3.7/20_bam/bulk.filt.bam | bcftools call -vm -f GQ,GP -O u | bcftools filter
-i "INFO/MQ>=40" -O z -o /Share2/home/qtclab1/00.users/shang_gao/01.SongSS/01.mutmap/CNUsongA11C3G337_ne
w_python3.7/30_vcf/mutmap.4.vcf.gz >> /Share2/home/qtclab1/00.users/shang_gao/01.SongSS/01.mutmap/CNUsong
A11C3G337_new_python3.7/log/bcftools.4.log 2>&1

The sterr was like:

multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/Share2/home/qtclab1/apps/MutMap-master/mutmap/mpileup.py", line 143, in mpileup
check=True)
File "/Share2/home/qtclab1/anaconda3/envs/python3.7/lib/python3.7/subprocess.py", line 512, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command 'bcftools mpileup -a AD,ADF,ADR -B -q 40 -Q 18 -C 50 -O u -r 1 -f /Share2/home/qtclab1/00.users/shang_gao/01.SongSS/01.mutmap/CNUsongA11C3G337_new_python3.7/10_ref/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa /Share2/home/qtclab1/00.users/shang_gao/01.SongSS/01.mutmap/CNUsongA11C3G337_new_python3.7/20_bam/cultivar.filt.bam /Share2/home/qtclab1/00.users/shang_gao/01.SongSS/01.mutmap/CNUsongA11C3G337_new_python3.7/20_bam/bulk.filt.bam | bcftools call -vm -f GQ,GP -O u | bcftools filter -i "INFO/MQ>=40" -O z -o /Share2/home/qtclab1/00.users/shang_gao/01.SongSS/01.mutmap/CNUsongA11C3G337_new_python3.7/30_vcf/mutmap.1.vcf.gz >> /Share2/home/qtclab1/00.users/shang_gao/01.SongSS/01.mutmap/CNUsongA11C3G337_new_python3.7/log/bcftools.1.log 2>&1' returned non-zero exit status 255.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/Share2/home/qtclab1/anaconda3/envs/python3.7/lib/python3.7/multiprocessing/pool.py", line 121, in worker
result = (True, func(*args, **kwds))
File "/Share2/home/qtclab1/anaconda3/envs/python3.7/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar
return list(map(*args))
File "/Share2/home/qtclab1/apps/MutMap-master/mutmap/mpileup.py", line 145, in mpileup
call_log(self.out, 'bcftools', cmd1)
File "/Share2/home/qtclab1/apps/MutMap-master/mutmap/utils.py", line 19, in call_log
with open('{}/log/{}.log'.format(out_dir, name)) as log:
FileNotFoundError: [Errno 2] No such file or directory: '/Share2/home/qtclab1/00.users/shang_gao/01.SongSS/01.mutmap/CNUsongA11C3G337_new_python3.7/log/bcftools.log'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/Share2/home/qtclab1/anaconda3/envs/python3.7/bin/mutmap", line 33, in
sys.exit(load_entry_point('mutmap', 'console_scripts', 'mutmap')())
File "/Share2/home/qtclab1/apps/MutMap-master/mutmap/mutmap.py", line 152, in main
MutMap(args).run()
File "/Share2/home/qtclab1/apps/MutMap-master/mutmap/mutmap.py", line 147, in run
self.mpileup()
File "/Share2/home/qtclab1/apps/MutMap-master/mutmap/mutmap.py", line 107, in mpileup
mp.run()
File "/Share2/home/qtclab1/apps/MutMap-master/mutmap/mpileup.py", line 228, in run
p.map(self.mpileup, chr_names)
File "/Share2/home/qtclab1/anaconda3/envs/python3.7/lib/python3.7/multiprocessing/pool.py", line 268, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/Share2/home/qtclab1/anaconda3/envs/python3.7/lib/python3.7/multiprocessing/pool.py", line 657, in get
raise self._value
FileNotFoundError: [Errno 2] No such file or directory: '/Share2/home/qtclab1/00.users/shang_gao/01.SongSS/01.mutmap/CNUsongA11C3G337_new_python3.7/log/bcftools.log'

The job submission script:

 15 #BSUB -J Mutmap
 16 #BSUB -q TEST-A
 17 #BSUB -e /Share2/home/qtclab1/00.users/shang_gao/01.SongSS/01.mutmap/00.log/%J.err
 18 #BSUB -o /Share2/home/qtclab1/00.users/shang_gao/01.SongSS/01.mutmap/00.log/%J.out
 19 #BSUB -n 4
 20 #BSUB -R "span[hosts=1]"
 21
 22 source /Share2/home/qtclab1/.bashrc
 23 conda deactivate
 24 conda activate python3.7
 25 conda env list
 26
 27
 28 REF="/Share2/home/qtclab1/00.users/shang_gao/00.reference"
 29 INPUT="/Share2/home/qtclab1/00.users/shang_gao/01.SongSS/01.mutmap"
 30 OUTPUT="/Share2/home/qtclab1/00.users/shang_gao/01.SongSS/01.mutmap"
 31
 32 mutmap \
 33 -t 4 \
 34 -r $REF/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa \
 35 -c $INPUT/CNUsongA11C3G337/20_bam/cultivar.filt.bam \
 36 -b $INPUT/CNUsongA11C3G337/20_bam/bulk.filt.bam \
 37 -n 20 \
 38 -o $OUTPUT/CNUsongA11C3G337_new_python3.7

Hi,
Many thanks to the developers.
I used use the mutmap v2.3.3 and showed "MutMap successfully finished". But the message "SystemError: tile cannot extend outside image" showed in the last line. I don't know how to deal with it.

Could you help me?

Best wishes!