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ERROR MESSAGE #371

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tuelomogashoa opened this issue Jun 24, 2024 · 19 comments
Open

ERROR MESSAGE #371

tuelomogashoa opened this issue Jun 24, 2024 · 19 comments

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@tuelomogashoa
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BTB001_S140.errlog.txt

Please help resolve this error. I have attached one f the errlog.txt files
@jodyphelan
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jodyphelan commented Jun 24, 2024 •
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Did you install with conda?
Can you try run the command delly on your commandline and paste the output here?

@tuelomogashoa
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tuelomogashoa commented Jun 24, 2024 via email

@tuelomogashoa
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Did you install with conda? Can you try run the command delly on your commandline and paste the output here?

tb-profiler error report

  • OS: linux
  • Program version: 6.2.1
  • Database version: {'name': 'tbdb', 'commit': '82777ea', 'Author': 'Jody Phelan [email protected]', 'Date': 'Sun Mar 17 01:14:00 2024 +0000'}
  • Program call:
{'logging': 'INFO', 'read1': '/home/tuelomogashoa/Final_TBP_run/BTB001_S140_R1.fastq.gz', 'read2': '/home/tuelomogashoa/Final_TBP_run/BTB001_S140_R2.fastq.gz', 'bam': '/home/tuelomogashoa/Final_TBP_run/672044f1-b990-4474-9219-bdb7bba82116.bam', 'fasta': None, 'vcf': None, 'platform': 'illumina', 'db': 'tbdb', 'external_db': None, 'prefix': 'BTB001_S140', 'csv': False, 'txt': True, 'text_template': None, 'docx': False, 'docx_template': None, 'add_columns': 'true', 'add_mutation_metadata': False, 'dir': '/home/tuelomogashoa/Final_TBP_run', 'depth': '0,10', 'af': '0,0.01', 'strand': '0,3', 'sv_depth': '0,10', 'sv_af': '0.5,0.9', 'sv_len': '100000,50000', 'mapper': 'bwa', 'caller': 'lofreq', 'calling_params': None, 'kmer_counter': 'kmc', 'coverage_tool': 'samtools', 'suspect': True, 'spoligotype': False, 'update_phylo': False, 'call_whole_genome': True, 'snp_dist': 200, 'snp_diff_db': None, 'snp_diff_no_store': False, 'no_trim': False, 'no_coverage_qc': False, 'no_samclip': False, 'no_delly': False, 'no_lineage': False, 'add_variant_annotations': False, 'threads': 1, 'ram': 30, 'delly_vcf': None, 'supplementary_bam': None, 'no_clean': False, 'temp': '.', 'func': <function main_profile at 0x7fe853ff6b60>, 'software_name': 'tbprofiler', 'version': '6.2.1', 'tmp_prefix': '672044f1-b990-4474-9219-bdb7bba82116', 'files_prefix': '/home/tuelomogashoa/Final_TBP_run/672044f1-b990-4474-9219-bdb7bba82116', 'conf': {'snpEff_db': 'Mycobacterium_tuberculosis_h37rv', 'drugs': ['rifampicin', 'isoniazid', 'ethambutol', 'pyrazinamide', 'moxifloxacin', 'levofloxacin', 'bedaquiline', 'delamanid', 'pretomanid', 'linezolid', 'streptomycin', 'amikacin', 'kanamycin', 'capreomycin', 'clofazimine', 'ethionamide', 'para-aminosalicylic_acid', 'cycloserine'], 'tb-profiler-version': '>=6.0.0,<7.0.0', 'version': {'name': 'tbdb', 'commit': '82777ea', 'Author': 'Jody Phelan <[email protected]>', 'Date': 'Sun Mar 17 01:14:00 2024 +0000'}, 'amplicon': False, 'files': {'ref': 'tbdb.fasta', 'gff': 'tbdb.gff', 'bed': 'tbdb.bed', 'json_db': 'tbdb.dr.json', 'variables': 'tbdb.variables.json', 'spoligotype_spacers': 'tbdb.spoligotype_spacers.txt', 'spoligotype_annotations': 'tbdb.spoligotype_list.csv', 'bedmask': 'tbdb.mask.bed', 'barcode': 'tbdb.barcode.bed', 'rules': 'tbdb.rules.txt'}, 'ref': '/home/tuelomogashoa/miniforge3/envs/tbp621/share/tbprofiler//tbdb.fasta', 'gff': '/home/tuelomogashoa/miniforge3/envs/tbp621/share/tbprofiler//tbdb.gff', 'bed': '/home/tuelomogashoa/miniforge3/envs/tbp621/share/tbprofiler//tbdb.bed', 'variables': {'snpEff_db': 'Mycobacterium_tuberculosis_h37rv', 'drugs': ['rifampicin', 'isoniazid', 'ethambutol', 'pyrazinamide', 'moxifloxacin', 'levofloxacin', 'bedaquiline', 'delamanid', 'pretomanid', 'linezolid', 'streptomycin', 'amikacin', 'kanamycin', 'capreomycin', 'clofazimine', 'ethionamide', 'para-aminosalicylic_acid', 'cycloserine'], 'tb-profiler-version': '>=6.0.0,<7.0.0', 'version': {'name': 'tbdb', 'commit': '82777ea', 'Author': 'Jody Phelan <[email protected]>', 'Date': 'Sun Mar 17 01:14:00 2024 +0000'}, 'amplicon': False, 'files': {'ref': 'tbdb.fasta', 'gff': 'tbdb.gff', 'bed': 'tbdb.bed', 'json_db': 'tbdb.dr.json', 'variables': 'tbdb.variables.json', 'spoligotype_spacers': 'tbdb.spoligotype_spacers.txt', 'spoligotype_annotations': 'tbdb.spoligotype_list.csv', 'bedmask': 'tbdb.mask.bed', 'barcode': 'tbdb.barcode.bed', 'rules': 'tbdb.rules.txt'}}, 'spoligotype_spacers': '/home/tuelomogashoa/miniforge3/envs/tbp621/share/tbprofiler//tbdb.spoligotype_spacers.txt', 'spoligotype_annotations': '/home/tuelomogashoa/miniforge3/envs/tbp621/share/tbprofiler//tbdb.spoligotype_list.csv', 'bedmask': '/home/tuelomogashoa/miniforge3/envs/tbp621/share/tbprofiler//tbdb.mask.bed', 'barcode': '/home/tuelomogashoa/miniforge3/envs/tbp621/share/tbprofiler//tbdb.barcode.bed', 'rules': ['Variant(gene_name=mmpL5,type=lof) inactivates_resistance Variant(gene_name=mmpR5)', 'Variant(gene_name=eis,type=lof) inactivates_resistance Variant(gene_name=eis)'], 'variant_filters': {'depth_hard': 0, 'depth_soft': 10, 'af_hard': 0, 'af_soft': 0.01, 'strand_hard': 0, 'strand_soft': 3, 'sv_depth_hard': 0, 'sv_depth_soft': 10, 'sv_af_hard': 0.5, 'sv_af_soft': 0.9, 'sv_len_hard': 100000, 'sv_len_soft': 50000}}, 'run_delly': True, 'samclip': True, 'coverage_qc': True, 'data_source': 'fastq', 'call_lineage': True}

Traceback:

  File "/home/tuelomogashoa/miniforge3/envs/tbp621/bin/tb-profiler", line 587, in <module>
    args.func(args)
  File "/home/tuelomogashoa/miniforge3/envs/tbp621/bin/tb-profiler", line 101, in main_profile
    variants_profile = pp.run_profiler(args)
                       ^^^^^^^^^^^^^^^^^^^^^
  File "/home/tuelomogashoa/miniforge3/envs/tbp621/lib/python3.12/site-packages/pathogenprofiler/cli.py", line 192, in run_profiler
    get_vcf_file(args)
  File "/home/tuelomogashoa/miniforge3/envs/tbp621/lib/python3.12/site-packages/pathogenprofiler/cli.py", line 174, in get_vcf_file
    args.vcf = get_vcf_from_bam(args)
               ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/tuelomogashoa/miniforge3/envs/tbp621/lib/python3.12/site-packages/pathogenprofiler/cli.py", line 154, in get_vcf_from_bam
    delly_vcf_obj = bam.run_delly(conf['bed'])
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/tuelomogashoa/miniforge3/envs/tbp621/lib/python3.12/site-packages/pathogenprofiler/bam.py", line 91, in run_delly
    run_cmd("delly call -t DEL -g %(ref_file)s %(bam_file)s -o %(prefix)s.delly.bcf" % vars(self))
  File "/home/tuelomogashoa/miniforge3/envs/tbp621/lib/python3.12/site-packages/pathogenprofiler/utils.py", line 486, in run_cmd
    raise ValueError("Command Failed:\n%s\nstderr:\n%s" % (cmd,result.stderr.decode()))

Value:

Command Failed:
/bin/bash -c set -o pipefail; delly call -t DEL -g /home/tuelomogashoa/miniforge3/envs/tbp621/share/tbprofiler//tbdb.fasta /home/tuelomogashoa/Final_TBP_run/672044f1-b990-4474-9219-bdb7bba82116.bam -o /home/tuelomogashoa/Final_TBP_run/672044f1-b990-4474-9219-bdb7bba82116.delly.bcf
stderr:
delly: error while loading shared libraries: libboost_iostreams.so.1.85.0: cannot open shared object file: No such file or directory

@jodyphelan
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If you open up your terminal, type in delly and then hit enter.

Did you install with conda? I think delly is not working.

@tuelomogashoa
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tuelomogashoa commented Jun 24, 2024 via email

@tuelomogashoa
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tuelomogashoa commented Jun 24, 2024 via email

@jodyphelan
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I suspect the conda environment has not correctly been solved. You could download the conda environment file from here: https://raw.githubusercontent.com/jodyphelan/TBProfiler/dev/conda/linux-latest.txt to rebuild your environment.
After downloading just run the following command to create a new environment with all the correct dependancies:

wget https://raw.githubusercontent.com/jodyphelan/TBProfiler/dev/conda/linux-latest.txt
conda create --name tb-profiler --file linux-latest.txt
conda activate tb-profiler
tb-profiler

@jloubser
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I apologise for chipping in here....getting some strange errors here @jodyphelan. Please see below. I just removed the openjdk line from the txt file but I don't think this is why we are getting these errors.

(base) [tuelomogashoa@khaos Final_TBP_run]$ mamba create --name tb-profiler --file linux-latest.txt

Downloading and Extracting Packages:
pillow-10.0.1 | #########################5 | 19%
/home/tuelomogashoa/miniforge3/lib/python3.10/site-packages/tqdm/std.py:636: TqdmWarning: clamping frac to range [0, 1]####################################3 | 98%

Error with archive /home/tuelomogashoa/miniforge3/pkgs/mash-2.3-ha9a2dd8_3.tar.bz2. You probably need to delete and re-download or re-create this file. Message was:

failed with error: Invalid data stream
HTTP 404 NOT FOUND for url https://conda.anaconda.org/t/no-15126f85-4dce-4462-b41b1e2_0.conda
Elapsed: 00:01.005817
CF-RAY: 898e4289d8690718-CPT

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

HTTP 404 NOT FOUND for url https://conda.anaconda.org/t/no-15126f85-4dce-4462-b41b1e2_0.conda
Elapsed: 00:01.005817
CF-RAY: 898e4289d8690718-CPT

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

InvalidArchiveError('Error with archive /home/tuelomogashoa/miniforge3/pkgs/mash-2.3-ha9a2dd8_3.tar.bz2. You probably need to delete and re-download or re-create this file. Message was:\n\nfailed with error: Invalid data stream')
CondaHTTPError: HTTP 404 NOT FOUND for url https://conda.anaconda.org/t/no-15126f85-4dce-4462-b41b1e2_0.conda
Elapsed: 00:01.005817
CF-RAY: 898e4289d8690718-CPT

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

CondaHTTPError: HTTP 404 NOT FOUND for url https://conda.anaconda.org/t/no-15126f85-4dce-4462-b41b1e2_0.conda
Elapsed: 00:01.005817
CF-RAY: 898e4289d8690718-CPT

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

@jloubser
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Some context for removing the openjdk line... We have seen that it installed a 'strange' internal Java build that has given me issues in the past. Would this openjdk version be suitable for the latest version of TB Profiler: (base) [tuelomogashoa@khaos Final_TBP_run]$ java -version
openjdk version "11.0.23" 2024-04-16 LTS
OpenJDK Runtime Environment (Red_Hat-11.0.23.0.9-2.el7_9) (build 11.0.23+9-LTS)
OpenJDK 64-Bit Server VM (Red_Hat-11.0.23.0.9-2.el7_9) (build 11.0.23+9-LTS, mixed mode, sharing)

@jloubser
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I've restarted it all. Used micromamba. Got an error line for each of the package: warning libmamba Could not validate package '/home/tuelomogashoa/micromamba/pkgs/xorg-recordproto-1.14.2-h7f98852_1002/info/repodata_record.json': md5 and sha256 sum unknown.
Final line:
Set safety_checks to disabled to override this warning.

But, delly seems to be working...

@jodyphelan
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Some context for removing the openjdk line... We have seen that it installed a 'strange' internal Java build that has given me issues in the past. Would this openjdk version be suitable for the latest version of TB Profiler: (base) [tuelomogashoa@khaos Final_TBP_run]$ java -version
openjdk version "11.0.23" 2024-04-16 LTS
OpenJDK Runtime Environment (Red_Hat-11.0.23.0.9-2.el7_9) (build 11.0.23+9-LTS)
OpenJDK 64-Bit Server VM (Red_Hat-11.0.23.0.9-2.el7_9) (build 11.0.23+9-LTS, mixed mode, sharing)

Yes I think that should be fine - as long as trimmomatic works then that should be ok.

I've restarted it all. Used micromamba. Got an error line for each of the package: warning libmamba Could not validate package '/home/tuelomogashoa/micromamba/pkgs/xorg-recordproto-1.14.2-h7f98852_1002/info/repodata_record.json': md5 and sha256 sum unknown.
Final line:
Set safety_checks to disabled to override this warning.

I'm not sure why this is happening but seems to be an error specific to the system rather than the environment file?

Now that delly works ok, does tb-profiler run ok also?

@taranewman
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Hi @jodyphelan

Just a note that we've encountered the same delly issue relating to libboost_iostreams.so.1.85.0 and know a few others that have as well for v6.2.0 and 6.2.1 : bioconda/bioconda-recipes#48755

I did not experience this issue when I updated tbprofliler within an existing conda environment using the pypi channel.

@dfornika has worked to pin boost-cpp to v1.85.0 on the delly recipe, however we are still experiencing this issue.

This may get updated, but we are currently seeing this error in our pipeline checks here: https://github.com/BCCDC-PHL/tbprofiler-nf/pull/38/checks

@dfornika
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dfornika commented Jun 28, 2024 •
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I hope this is helpful, I'm still a bit confused about what is going on with all of this dependency resolution. But at this point, if I try to create a conda env for TBProfiler:

conda create -n tb-profiler-6.2.1-test tb-profiler=6.2.1

...I'm still getting these builds of boost-cpp and delly:

image

that is:

boost-cpp          conda-forge/linux-64::boost-cpp-1.78.0-h2c5509c_4
delly              bioconda/linux-64::delly-1.2.6-h6dccd9a_2

...and if I try to specify the new build of delly that requires boost-cpp v1.85.0 as follows:

conda create -n tb-profiler-6.2.1-test tb-profiler=6.2.1 delly=1.2.6=hdcf5f25_3

...then I get this:

image

...saying that usher wants an older version of boost-cpp.

But I'm confused because the usher recipe doesn't pin to any specific version of boost-cpp:

https://github.com/bioconda/bioconda-recipes/blob/4b4544a052e8fa802a19d793e7cdcdef88cc55b8/recipes/usher/meta.yaml#L32

...so I don't understand why conda thinks it needs those version ranges. I'll try to ask around on the bioconda gitter to see if anyone there understands what's going wrong.

@jodyphelan
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Interesting, not too sure what's going on here either. For now I could pin a lower version of delly to the tb-profiler recipe as it seems to work ok when delly=v1.1.6 is used?

@apetkau
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apetkau commented Jun 28, 2024 •
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Installation seems to work for me for delly 1.2.6 build hb7e2ac5_1, but not for build h6dccd9a_2, which is currently the default that is installed.

Installation that doesn't work

That is, if I install tb-profiler using the below:

conda create --name tb-profiler 'tb-profiler=6.2.1' -y

I will get:

conda list --name tb-profiler 'delly|boost-cpp'

# Name                    Version                   Build  Channel
boost-cpp                 1.78.0               h2c5509c_4    conda-forge
delly                     1.2.6                h6dccd9a_2    bioconda

This installation doesn't work, since delly is linked to libboost 1.85.0 libraries:

ldd envs/tb-profiler/bin/delly

...
        libboost_iostreams.so.1.85.0 => not found
        libboost_filesystem.so.1.85.0 => not found
        libboost_program_options.so.1.85.0 => not found

Installation that is working

But, if I instead install tb-profiler and specify an older build of delly:

conda create --name tb-profiler 'tb-profiler=6.2.1' 'delly=1.2.6=hb7e2ac5_1' -y

I get:

conda list --name tb-profiler 'delly|boost-cpp'

# Name                    Version                   Build  Channel
boost-cpp                 1.78.0               h2c5509c_4    conda-forge
delly                     1.2.6                hb7e2ac5_1    bioconda

This installation does work, since the older build of delly seems linked to the boost 1.78.0 libraries:

ldd tb-profiler/bin/delly

...
        libboost_iostreams.so.1.78.0 => [...]/envs/tb-profiler/bin/../lib/libboost_iostreams.so.1.78.0 (0x00007ff211d8d000)
        libboost_filesystem.so.1.78.0 => [...]/envs/tb-profiler/bin/../lib/libboost_filesystem.so.1.78.0 (0x00007ff211d6d000)
        libboost_program_options.so.1.78.0 => [...]/envs/tb-profiler/bin/../lib/libboost_program_options.so.1.78.0 (0x00007ff211d1b000)

So the difference between delly 1.2.6 build hb7e2ac5_1 and h6dccd9a_2 must have been building against different versions of boost.

@dfornika
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Thanks for doing those tests @apetkau, I hadn't found a way to get a successful dependency resolution and installation.

Based on what I'm seeing, I do think targeting an earlier version of delly (one that uses boost v1.78.0) would make sense. It looks like we need a way to get usher and delly aligned on which version of boost they want when they come together in the tb-profiler environment. I think technically the place to do that is probably the pathogen-profiler recipe because that's where delly is listed as a dependency.

I really hope I haven't made things worse by pinning the delly recipe against boost v1.85.0 or later. Please let me know if you think that was a bad move. I don't have much experience with C++ or the details of how linking is done with .so files. So it's not entirely clear to me how flexible delly is with which versions of boost that it's compatible with. But my error logs were saying that delly wanted boost v1.85.0, and my conda environment had boost v1.78.0, so it seemed sensible to me to pin boost to v1.85.0 or later on the delly recipe.

@jodyphelan
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Thanks for all the help debugging this. I think for now I'll specify delly <=1.1.6 in the pathogen-profiler recipe.

@jodyphelan jodyphelan mentioned this issue Jul 2, 2024
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@jloubser
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jloubser commented Jul 3, 2024

@jodyphelan all seems to working now, yes. Thank you!

@jodyphelan
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I might have to review this again as I came across what looks like a bug in delly v1.1.6 which seems to be fixed in v.1.2.6. There is a large deletion in SRR8651614 which is has different end coordinates based on which version you use. I looked more closely and it looks like v1.2.6 produces the right coordinates.

(pp) jody@s10:~/temp$ bcftools view 116.bcf | snpEff ann Mycobacterium_tuberculosis_h37rv | grep 2288545
Chromosome	2288545	DEL00000208	G	<DEL>	1200.0	PASS	PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.6;END=2288732;PE=0;MAPQ=0;CT=3to5;CIPOS=-3,3;CIEND=-3,3;SRMAPQ=60;INSLEN=0;HOMLEN=4;SR=20;SRQ=1;CONSENSUS=AGTTCGAGATCGCGCAGCACCACCGTGCCGGAGACGATATCCAGATCGCGATGGAACGTGATATCCCGCGGCCCGATGAAGGTGTCGTAGAAGCGGCCGATGGCCTCATGCCCCACCTGCGGGCGACGGTGGTATCGGCCGACACACCCGCTGTCAGGTCCACCAGCACCCTGG;CE=1.92873;ANN=<DEL>|gene_fusion|HIGH|Rv2042c&pncA|Rv2042c&Rv2043c|gene_variant|Rv2042c|||n.2288732_2288546del||||||,<DEL>|frameshift_variant&start_lost|HIGH|Rv2042c|Rv2042c|transcript|CCP44815|protein_coding|1/1|c.-51_136del|p.Met1fs|136/798|1/798|1/265||,<DEL>|frameshift_variant&stop_lost&splice_region_variant|HIGH|pncA|Rv2043c|transcript|CCP44816|protein_coding|1/1|c.510_*135del|p.Ala170fs||510/561|170/186||,<DEL>|upstream_gene_variant|MODIFIER|Rv2037c|Rv2037c|transcript|CCP44810|protein_coding||c.-5011_-4825del|||||4825|WARNING_TRANSCRIPT_NO_START_CODON,<DEL>|upstream_gene_variant|MODIFIER|Rv2038c|Rv2038c|transcript|CCP44811|protein_coding||c.-3936_-3750del|||||3750|,<DEL>|upstream_gene_variant|MODIFIER|Rv2039c|Rv2039c|transcript|CCP44812|protein_coding||c.-3091_-2905del|||||2905|WARNING_TRANSCRIPT_NO_START_CODON,<DEL>|upstream_gene_variant|MODIFIER|Rv2040c|Rv2040c|transcript|CCP44813|protein_coding||c.-2202_-2016del|||||2016|,<DEL>|upstream_gene_variant|MODIFIER|Rv2041c|Rv2041c|transcript|CCP44814|protein_coding||c.-886_-700del|||||700|,<DEL>|upstream_gene_variant|MODIFIER|Rv2042c|Rv2042c|transcript|CCP44815|protein_coding|1/1|c.-51_136del|||||0|,<DEL>|upstream_gene_variant|MODIFIER|lppI|Rv2046|transcript|CCP44819|protein_coding||c.-2723_-2537del|||||2723|,<DEL>|downstream_gene_variant|MODIFIER|pncA|Rv2043c|transcript|CCP44816|protein_coding|1/1|c.510_*135del|||||135|,<DEL>|downstream_gene_variant|MODIFIER|Rv2044c|Rv2044c|transcript|CCP44817|protein_coding||c.*550_*736del|||||736|,<DEL>|downstream_gene_variant|MODIFIER|lipT|Rv2045c|transcript|CCP44818|protein_coding||c.*953_*1139del|||||1139|WARNING_TRANSCRIPT_NO_START_CODON,<DEL>|downstream_gene_variant|MODIFIER|Rv2047c|Rv2047c|transcript|CCP44820|protein_coding||c.*3230_*3416del|||||3416|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(Rv2042c|Rv2042c|1|1.00),(pncA|Rv2043c|1|1.00)	GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV	1/1:-851.565,-64.5226,0:10000:PASS:30696:1224:26835:0:0:0:3:247
(pp) jody@s10:~/temp$ bcftools view 126.bcf | snpEff ann Mycobacterium_tuberculosis_h37rv | grep 2288545
Chromosome	2288545	DEL00000422	GGCTGCGAACCCACCGGGTCTTCGACCCGCGCGTCACCGGTGAACAACCCGACCCAGCCGGCGCGGTCGTGCGCGGCGGCCGCTTGCGGCGAGCGCTCCACCGCCGCCAACAGTTCATCCCGGTTCGGCGGTGCCATCAGGAGCTGCAAACCAACTCGACGCTGGCGGTGCGCATCTCCTCCAGCGC	G	1200.0	PASS	PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.2.6;END=2288731;PE=0;MAPQ=0;CT=3to5;CIPOS=-3,3;CIEND=-3,3;SRMAPQ=60;INSLEN=0;HOMLEN=4;SR=20;SRQ=1;CONSENSUS=TCGAGATCGCGCAGCACCACCGTGCCGGAGACGATATCCAGATCGCGATGGAACGTGATATCCCGCGGCCCGATGAAGGTGTCGTAGAAGCGGCCGATGGCCTCATGCCCCACCTGCGGGCGACGGTGGTATCGGCCGACACACCCGCTGTCAGGTCCACCAGCACCCTGG;CE=1.92313;CONSBP=118;ANN=G|gene_fusion|HIGH|Rv2042c&pncA|Rv2042c&Rv2043c|gene_variant|Rv2042c|||n.2288731_2288546del||||||,G|frameshift_variant&start_lost|HIGH|Rv2042c|Rv2042c|transcript|CCP44815|protein_coding|1/1|c.-50_136del|p.Met1fs|136/798|1/798|1/265||,G|stop_lost&conservative_inframe_deletion&splice_region_variant|HIGH|pncA|Rv2043c|transcript|CCP44816|protein_coding|1/1|c.511_*135del|p.Ala171_Ter187del||511/561|171/186||,G|upstream_gene_variant|MODIFIER|Rv2037c|Rv2037c|transcript|CCP44810|protein_coding||c.-5010_-4825del|||||4825|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|Rv2038c|Rv2038c|transcript|CCP44811|protein_coding||c.-3935_-3750del|||||3750|,G|upstream_gene_variant|MODIFIER|Rv2039c|Rv2039c|transcript|CCP44812|protein_coding||c.-3090_-2905del|||||2905|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|Rv2040c|Rv2040c|transcript|CCP44813|protein_coding||c.-2201_-2016del|||||2016|,G|upstream_gene_variant|MODIFIER|Rv2041c|Rv2041c|transcript|CCP44814|protein_coding||c.-885_-700del|||||700|,G|upstream_gene_variant|MODIFIER|Rv2042c|Rv2042c|transcript|CCP44815|protein_coding|1/1|c.-50_136del|||||0|,G|upstream_gene_variant|MODIFIER|lppI|Rv2046|transcript|CCP44819|protein_coding||c.-2723_-2538del|||||2723|,G|downstream_gene_variant|MODIFIER|pncA|Rv2043c|transcript|CCP44816|protein_coding|1/1|c.511_*135del|||||135|,G|downstream_gene_variant|MODIFIER|Rv2044c|Rv2044c|transcript|CCP44817|protein_coding||c.*551_*736del|||||736|,G|downstream_gene_variant|MODIFIER|lipT|Rv2045c|transcript|CCP44818|protein_coding||c.*954_*1139del|||||1139|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|Rv2047c|Rv2047c|transcript|CCP44820|protein_coding||c.*3231_*3416del|||||3416|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(Rv2042c|Rv2042c|1|1.00)	GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV	1/1:-851.565,-64.5226,0:10000:PASS:30696:1224:26835:0:0:0:3:247

It looks like v1.1.6 ends one nucleotide after the actual deletion end and this has a knock on effect on the snpEff annotation - frameshift vs inframe mutation, which will lead to a different drug resistance prediction to pyrazinamide. Though rare I don't think we should be compromising the resistance predictions just so we can have usher there.

Not really sure how to proceed, in the short term I could remove usher?

@emarinier emarinier mentioned this issue Nov 12, 2024
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@dfornika @apetkau @jodyphelan @jloubser @taranewman @tuelomogashoa