Hello everyone,
I am currently getting an error after computing LCA wand bayesian, when compoting the mismatch.
The error that I get is the following:
`MismatchFileError with get_df_mismatches. See log-file for more information.
Traceback (most recent call last):
File "/opt/miniconda3/envs/metaDMG/lib/python3.9/site-packages/metaDMG/fit/serial.py", line 555, in run_single_c
df_mismatches = get_df_mismatches(config, force=force)
File "/opt/miniconda3/envs/metaDMG/lib/python3.9/site-packages/metaDMG/fit/serial.py", line 393, in get_df_misma
df_mismatches = mismatches.compute(config)
File "/opt/miniconda3/envs/metaDMG/lib/python3.9/site-packages/metaDMG/fit/mismatches.py", line 223, in compute
raise MismatchFileError(f"{filename} only contains a header, no data.")
MismatchFileError: data/lca/Rip527_2.mismatches.txt.gz only contains a header, no data.
`
And the Log file is here reported:
`[2023-02-13 12:47:02] | root:200 | DEBUG | New log started_
[2023-02-13 12:47:02] | root:201 | DEBUG | Log config file: /opt/miniconda3/envs/metaDMG/lib/python3.9/site-packages/metaDMG/loggers/log_config.yaml
[2023-02-13 12:47:02] | root:161 | DEBUG | Logging server started!
[2023-02-13 12:47:02] | metaDMG.loggers.loggers:40 | DEBUG | Running metaDMG version 0.38.0.
[2023-02-13 12:47:02] | metaDMG.loggers.loggers:41 | DEBUG | Using port 51601 for logging.
[2023-02-13 12:47:02] | metaDMG.utils:160 | INFO | Using config.yaml as config file.
[2023-02-13 12:47:02] | metaDMG.fit.workflow:27 | INFO | Running metaDMG on 1 files in total.
[2023-02-13 12:47:02] | metaDMG.fit.workflow:34 | INFO | Running the samples in serial (sequentially), each using 1 core(s).
[2023-02-13 12:47:02] | metaDMG.fit.serial:290 | INFO | Rip527_2 | Getting LCA.
[2023-02-13 12:47:02] | metaDMG.fit.serial:310 | INFO | Rip527_2 | LCA has to be computed. This can take a while, please wait.
[2023-02-13 12:47:02] | metaDMG.fit.serial:317 | DEBUG | Rip527_2 | ../../metaDMG-cpp/metaDMG-cpp lca -bam Rip527_2.sorted.bam -outnames data/tmp/Rip527_2/Rip527_2 -names ../reference/names.dmp -nodes ../reference/nodes.dmp -acc2tax ../reference/combined_taxid_accssionNO_20223103 -simscorelow 0.95 -simscorehigh 1.0 -minmapq 0 -howmany 15 -weighttype 1 -fix_ncbi 0 -tempfolder data/tmp/Rip527_2/
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> metaDMG version: 0.2-46-gedaf069 (htslib: 1.16) build(Jan 25 2023 15:55:35)
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | #../../metaDMG-cpp/metaDMG-cpp lca -bam Rip527_2.sorted.bam -outnames data/tmp/Rip527_2/Rip527_2 -names ../reference/names.dmp -nodes ../reference/nodes.dmp -acc2tax ../reference/combined_taxid_accssionNO_20223103 -simscorelow 0.95 -simscorehigh 1.0 -minmapq 0 -howmany 15 -weighttype 1 -fix_ncbi 0 -tempfolder data/tmp/Rip527_2/
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Will output lca results in file: 'data/tmp/Rip527_2/Rip527_2.lca.gz'
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> [thread1] Will read header
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Will output lca distribution in file: 'data/tmp/Rip527_2/Rip527_2.stat'
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Will output lca weight in file: 'data/tmp/Rip527_2/Rip527_2.wlca'
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Will output log info (problems) in file: 'data/tmp/Rip527_2/Rip527_2.log'
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> [thread1] Done reading header: 0.00 sec, header contains: 494760
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -bam Rip527_2.sorted.bam
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -names ../reference/names.dmp
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -nodes ../reference/nodes.dmp
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -acc2tax ../reference/combined_taxid_accssionNO_20223103
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -simscoreLow 0.950000
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -simscoreHigh 1.000000
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -editdistMin 0
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -editdistMax 10
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -outnames data/tmp/Rip527_2/Rip527_2
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -minmapq 0
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -lca_rank species
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -norank2species 0
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -howmany 15
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -fix_ncbi 0
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -weighttype 1
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -tempfolder -215122080
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -stopIfErrors 1
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Starting to extract (acc->taxid) from binary file: '../reference/combined_taxid_accssionNO_20223103'
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Checking if exits: 'data/tmp/Rip527_2/combined_taxid_accssionNO_20223103Rip527_2.sorted.bam.bin'
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Checking if bimnary file exists. dodump=1
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> opening file: 'data/tmp/Rip527_2/combined_taxid_accssionNO_20223103Rip527_2.sorted.bam.bin' mode: 'wb'
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Setting threads to: 4
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> opening file: '../reference/combined_taxid_accssionNO_20223103' mode: 'rb'
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Setting threads to: 2
[2023-02-13 12:50:44] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Number of entries to use from accesion to taxid: 342949, time taken: 222.00 sec
[2023-02-13 12:50:48] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> [../reference/names.dmp] Number of unique names (column1): 2293592 with third column 'scientific name'
[2023-02-13 12:50:53] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Number of unique names (column1): 2293592 from file: ../reference/nodes.dmp parent.size():2293592 child.size():0
[2023-02-13 12:50:53] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Number of entries with level information: 48
[2023-02-13 12:50:53] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Problem finding level for rank: serotype
[2023-02-13 12:50:53] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Problem finding level for rank: serotype
[2023-02-13 12:50:53] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Problem finding level for rank: serotype
[2023-02-13 12:50:53] | metaDMG.fit.serial:278 | DEBUG | Rip527_2 | ...
[2023-02-13 12:50:53] | metaDMG.fit.serial:279 | DEBUG | Rip527_2 | ...
[2023-02-13 12:50:53] | metaDMG.fit.serial:280 | DEBUG | Rip527_2 | ...
[2023-02-13 12:50:55] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | [hts] -> editMin:0 editmMax:10 scoreLow:0.950000 scoreHigh:1.000000 minlength:-1 discard: 516 prefix: data/tmp/Rip527_2/Rip527_2 howmany: 15 skipnorank: 1 weighttype: 1
[2023-02-13 12:50:55] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Will dump: 'data/tmp/Rip527_2/Rip527_2.bdamage.gz' this contains damage patterns for: 0 items
[2023-02-13 12:50:55] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Setting threads to: 4
[2023-02-13 12:50:55] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Number of species with reads that map uniquely: 0
[2023-02-13 12:50:55] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> [ALL done] walltime used = 233.00 sec
[2023-02-13 12:50:56] | metaDMG.fit.serial:248 | DEBUG | Rip527_2 | Hid the following lines: {'\t-> Problem finding level for rank: serotype': 1216}.
[2023-02-13 12:50:56] | metaDMG.fit.serial:249 | DEBUG | Rip527_2 | Got return code 0 from ../../metaDMG-cpp/metaDMG-cpp lca -bam Rip527_2.sorted.bam -outnames data/tmp/Rip527_2/Rip527_2 -names ../reference/names.dmp -nodes ../reference/nodes.dmp -acc2tax ../reference/combined_taxid_accssionNO_20223103 -simscorelow 0.95 -simscorehigh 1.0 -minmapq 0 -howmany 15 -weighttype 1 -fix_ncbi 0 -tempfolder data/tmp/Rip527_2/.
[2023-02-13 12:50:56] | metaDMG.fit.serial:320 | DEBUG | Rip527_2 | ../../metaDMG-cpp/metaDMG-cpp print_ugly data/tmp/Rip527_2/Rip527_2.bdamage.gz -names ../reference/names.dmp -nodes ../reference/nodes.dmp -lcastat data/tmp/Rip527_2/Rip527_2.stat
[2023-02-13 12:50:56] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> metaDMG version: 0.2-46-gedaf069 (htslib: 1.16) build(Jan 25 2023 15:55:35)
[2023-02-13 12:50:56] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | #../../metaDMG-cpp/metaDMG-cpp print_ugly data/tmp/Rip527_2/Rip527_2.bdamage.gz -names ../reference/names.dmp -nodes ../reference/nodes.dmp -lcastat data/tmp/Rip527_2/Rip527_2.stat
[2023-02-13 12:50:56] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | ./metaDMG-cpp print_ugly file.bdamage.gz -names file.gz -nodes trestructure.gz -lcastat fil.gz
[2023-02-13 12:50:56] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | infile_names: ../reference/names.dmp infile_bdamage: data/tmp/Rip527_2/Rip527_2.bdamage.gz nodes: ../reference/nodes.dmp lca_stat: data/tmp/Rip527_2/Rip527_2.stat infile_bam: (null)#VERSION:0.2-46-gedaf069
[2023-02-13 12:50:56] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Dumping file: 'data/tmp/Rip527_2/Rip527_2.bdamage.gz.uglyprint.mismatch.txt.gz'
[2023-02-13 12:51:01] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Number of unique names (column1): 2293592 from file: ../reference/nodes.dmp parent.size():2293592 child.size():199230
[2023-02-13 12:51:01] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Done loading binary bdamage.gz file. It contains: 0
[2023-02-13 12:51:01] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Number of entries in damage pattern file: 0 printlength(howmany):15
[2023-02-13 12:51:04] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> [../reference/names.dmp] Number of unique names (column1): 2293592 with third column 'scientific name'
[2023-02-13 12:51:16] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> pre: 0.000000 post:2293592.000000 grownbyfactor: inf
[2023-02-13 12:51:16] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Dumping file: 'data/tmp/Rip527_2/Rip527_2.bdamage.gz.uglyprint.stat.txt.gz'
[2023-02-13 12:51:16] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Done loading lcastat file It contains: 0
[2023-02-13 12:51:25] | metaDMG.fit.serial:249 | DEBUG | Rip527_2 | Got return code 0 from ../../metaDMG-cpp/metaDMG-cpp print_ugly data/tmp/Rip527_2/Rip527_2.bdamage.gz -names ../reference/names.dmp -nodes ../reference/nodes.dmp -lcastat data/tmp/Rip527_2/Rip527_2.stat.
[2023-02-13 12:51:25] | metaDMG.fit.serial:176 | DEBUG | Rip527_2 | Moving data/tmp/Rip527_2/Rip527_2.bdamage.gz.uglyprint.mismatch.txt.gz to data/lca/Rip527_2.mismatches.txt.gz.
[2023-02-13 12:51:25] | metaDMG.fit.serial:176 | DEBUG | Rip527_2 | Moving data/tmp/Rip527_2/Rip527_2.bdamage.gz.uglyprint.stat.txt.gz to data/lca/Rip527_2.mismatches.stat.txt.gz.
[2023-02-13 12:51:25] | metaDMG.fit.serial:176 | DEBUG | Rip527_2 | Moving data/tmp/Rip527_2/Rip527_2.lca.gz to data/lca/Rip527_2.lca.txt.gz.
[2023-02-13 12:51:25] | metaDMG.fit.serial:176 | DEBUG | Rip527_2 | Moving data/tmp/Rip527_2/Rip527_2.log to data/lca/Rip527_2.log.txt.
[2023-02-13 12:51:25] | metaDMG.fit.serial:392 | INFO | Rip527_2 | Computing mismatch matrix dataframes.
[2023-02-13 12:51:25] | root:237 | ERROR | Rip527_2 | MismatchFileError with get_df_mismatches. See log-file for more information.
Traceback (most recent call last):
File "/opt/miniconda3/envs/metaDMG/lib/python3.9/site-packages/metaDMG/fit/serial.py", line 555, in run_single_config
df_mismatches = get_df_mismatches(config, force=force)
File "/opt/miniconda3/envs/metaDMG/lib/python3.9/site-packages/metaDMG/fit/serial.py", line 393, in get_df_mismatches
df_mismatches = mismatches.compute(config)
File "/opt/miniconda3/envs/metaDMG/lib/python3.9/site-packages/metaDMG/fit/mismatches.py", line 223, in compute
raise MismatchFileError(f"{filename} only contains a header, no data.")
MismatchFileError: data/lca/Rip527_2.mismatches.txt.gz only contains a header, no data.
[2023-02-13 12:51:25] | metaDMG.fit.workflow:50 | ERROR | 1 error(s) occurred during the computation.`
What does this means? How can I resolve it?
Thank you
Hello everyone,
I am currently getting an error after computing LCA wand bayesian, when compoting the mismatch.
The error that I get is the following:
`MismatchFileError with get_df_mismatches. See log-file for more information.
Traceback (most recent call last):
File "/opt/miniconda3/envs/metaDMG/lib/python3.9/site-packages/metaDMG/fit/serial.py", line 555, in run_single_c
df_mismatches = get_df_mismatches(config, force=force)
`
And the Log file is here reported:
`[2023-02-13 12:47:02] | root:200 | DEBUG | New log started_
[2023-02-13 12:47:02] | root:201 | DEBUG | Log config file: /opt/miniconda3/envs/metaDMG/lib/python3.9/site-packages/metaDMG/loggers/log_config.yaml
[2023-02-13 12:47:02] | root:161 | DEBUG | Logging server started!
[2023-02-13 12:47:02] | metaDMG.loggers.loggers:40 | DEBUG | Running metaDMG version 0.38.0.
[2023-02-13 12:47:02] | metaDMG.loggers.loggers:41 | DEBUG | Using port 51601 for logging.
[2023-02-13 12:47:02] | metaDMG.utils:160 | INFO | Using config.yaml as config file.
[2023-02-13 12:47:02] | metaDMG.fit.workflow:27 | INFO | Running metaDMG on 1 files in total.
[2023-02-13 12:47:02] | metaDMG.fit.workflow:34 | INFO | Running the samples in serial (sequentially), each using 1 core(s).
[2023-02-13 12:47:02] | metaDMG.fit.serial:290 | INFO | Rip527_2 | Getting LCA.
[2023-02-13 12:47:02] | metaDMG.fit.serial:310 | INFO | Rip527_2 | LCA has to be computed. This can take a while, please wait.
[2023-02-13 12:47:02] | metaDMG.fit.serial:317 | DEBUG | Rip527_2 | ../../metaDMG-cpp/metaDMG-cpp lca -bam Rip527_2.sorted.bam -outnames data/tmp/Rip527_2/Rip527_2 -names ../reference/names.dmp -nodes ../reference/nodes.dmp -acc2tax ../reference/combined_taxid_accssionNO_20223103 -simscorelow 0.95 -simscorehigh 1.0 -minmapq 0 -howmany 15 -weighttype 1 -fix_ncbi 0 -tempfolder data/tmp/Rip527_2/
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> metaDMG version: 0.2-46-gedaf069 (htslib: 1.16) build(Jan 25 2023 15:55:35)
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | #../../metaDMG-cpp/metaDMG-cpp lca -bam Rip527_2.sorted.bam -outnames data/tmp/Rip527_2/Rip527_2 -names ../reference/names.dmp -nodes ../reference/nodes.dmp -acc2tax ../reference/combined_taxid_accssionNO_20223103 -simscorelow 0.95 -simscorehigh 1.0 -minmapq 0 -howmany 15 -weighttype 1 -fix_ncbi 0 -tempfolder data/tmp/Rip527_2/
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Will output lca results in file: 'data/tmp/Rip527_2/Rip527_2.lca.gz'
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> [thread1] Will read header
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Will output lca distribution in file: 'data/tmp/Rip527_2/Rip527_2.stat'
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Will output lca weight in file: 'data/tmp/Rip527_2/Rip527_2.wlca'
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Will output log info (problems) in file: 'data/tmp/Rip527_2/Rip527_2.log'
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> [thread1] Done reading header: 0.00 sec, header contains: 494760
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -bam Rip527_2.sorted.bam
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -names ../reference/names.dmp
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -nodes ../reference/nodes.dmp
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -acc2tax ../reference/combined_taxid_accssionNO_20223103
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -simscoreLow 0.950000
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -simscoreHigh 1.000000
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -editdistMin 0
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -editdistMax 10
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -outnames data/tmp/Rip527_2/Rip527_2
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -minmapq 0
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -lca_rank species
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -norank2species 0
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -howmany 15
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -fix_ncbi 0
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -weighttype 1
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -tempfolder -215122080
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> -stopIfErrors 1
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Starting to extract (acc->taxid) from binary file: '../reference/combined_taxid_accssionNO_20223103'
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Checking if exits: 'data/tmp/Rip527_2/combined_taxid_accssionNO_20223103Rip527_2.sorted.bam.bin'
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Checking if bimnary file exists. dodump=1
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> opening file: 'data/tmp/Rip527_2/combined_taxid_accssionNO_20223103Rip527_2.sorted.bam.bin' mode: 'wb'
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Setting threads to: 4
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> opening file: '../reference/combined_taxid_accssionNO_20223103' mode: 'rb'
[2023-02-13 12:47:02] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Setting threads to: 2
[2023-02-13 12:50:44] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Number of entries to use from accesion to taxid: 342949, time taken: 222.00 sec
[2023-02-13 12:50:48] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> [../reference/names.dmp] Number of unique names (column1): 2293592 with third column 'scientific name'
[2023-02-13 12:50:53] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Number of unique names (column1): 2293592 from file: ../reference/nodes.dmp parent.size():2293592 child.size():0
[2023-02-13 12:50:53] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Number of entries with level information: 48
[2023-02-13 12:50:53] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Problem finding level for rank: serotype
[2023-02-13 12:50:53] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Problem finding level for rank: serotype
[2023-02-13 12:50:53] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Problem finding level for rank: serotype
[2023-02-13 12:50:53] | metaDMG.fit.serial:278 | DEBUG | Rip527_2 | ...
[2023-02-13 12:50:53] | metaDMG.fit.serial:279 | DEBUG | Rip527_2 | ...
[2023-02-13 12:50:53] | metaDMG.fit.serial:280 | DEBUG | Rip527_2 | ...
[2023-02-13 12:50:55] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | [hts] -> editMin:0 editmMax:10 scoreLow:0.950000 scoreHigh:1.000000 minlength:-1 discard: 516 prefix: data/tmp/Rip527_2/Rip527_2 howmany: 15 skipnorank: 1 weighttype: 1
[2023-02-13 12:50:55] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Will dump: 'data/tmp/Rip527_2/Rip527_2.bdamage.gz' this contains damage patterns for: 0 items
[2023-02-13 12:50:55] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Setting threads to: 4
[2023-02-13 12:50:55] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Number of species with reads that map uniquely: 0
[2023-02-13 12:50:55] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> [ALL done] walltime used = 233.00 sec
[2023-02-13 12:50:56] | metaDMG.fit.serial:248 | DEBUG | Rip527_2 | Hid the following lines: {'\t-> Problem finding level for rank: serotype': 1216}.
[2023-02-13 12:50:56] | metaDMG.fit.serial:249 | DEBUG | Rip527_2 | Got return code 0 from ../../metaDMG-cpp/metaDMG-cpp lca -bam Rip527_2.sorted.bam -outnames data/tmp/Rip527_2/Rip527_2 -names ../reference/names.dmp -nodes ../reference/nodes.dmp -acc2tax ../reference/combined_taxid_accssionNO_20223103 -simscorelow 0.95 -simscorehigh 1.0 -minmapq 0 -howmany 15 -weighttype 1 -fix_ncbi 0 -tempfolder data/tmp/Rip527_2/.
[2023-02-13 12:50:56] | metaDMG.fit.serial:320 | DEBUG | Rip527_2 | ../../metaDMG-cpp/metaDMG-cpp print_ugly data/tmp/Rip527_2/Rip527_2.bdamage.gz -names ../reference/names.dmp -nodes ../reference/nodes.dmp -lcastat data/tmp/Rip527_2/Rip527_2.stat
[2023-02-13 12:50:56] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> metaDMG version: 0.2-46-gedaf069 (htslib: 1.16) build(Jan 25 2023 15:55:35)
[2023-02-13 12:50:56] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | #../../metaDMG-cpp/metaDMG-cpp print_ugly data/tmp/Rip527_2/Rip527_2.bdamage.gz -names ../reference/names.dmp -nodes ../reference/nodes.dmp -lcastat data/tmp/Rip527_2/Rip527_2.stat
[2023-02-13 12:50:56] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | ./metaDMG-cpp print_ugly file.bdamage.gz -names file.gz -nodes trestructure.gz -lcastat fil.gz
[2023-02-13 12:50:56] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | infile_names: ../reference/names.dmp infile_bdamage: data/tmp/Rip527_2/Rip527_2.bdamage.gz nodes: ../reference/nodes.dmp lca_stat: data/tmp/Rip527_2/Rip527_2.stat infile_bam: (null)#VERSION:0.2-46-gedaf069
[2023-02-13 12:50:56] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Dumping file: 'data/tmp/Rip527_2/Rip527_2.bdamage.gz.uglyprint.mismatch.txt.gz'
[2023-02-13 12:51:01] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Number of unique names (column1): 2293592 from file: ../reference/nodes.dmp parent.size():2293592 child.size():199230
[2023-02-13 12:51:01] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Done loading binary bdamage.gz file. It contains: 0
[2023-02-13 12:51:01] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Number of entries in damage pattern file: 0 printlength(howmany):15
[2023-02-13 12:51:04] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> [../reference/names.dmp] Number of unique names (column1): 2293592 with third column 'scientific name'
[2023-02-13 12:51:16] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> pre: 0.000000 post:2293592.000000 grownbyfactor: inf
[2023-02-13 12:51:16] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Dumping file: 'data/tmp/Rip527_2/Rip527_2.bdamage.gz.uglyprint.stat.txt.gz'
[2023-02-13 12:51:16] | metaDMG.fit.serial:273 | DEBUG | Rip527_2 | -> Done loading lcastat file It contains: 0
[2023-02-13 12:51:25] | metaDMG.fit.serial:249 | DEBUG | Rip527_2 | Got return code 0 from ../../metaDMG-cpp/metaDMG-cpp print_ugly data/tmp/Rip527_2/Rip527_2.bdamage.gz -names ../reference/names.dmp -nodes ../reference/nodes.dmp -lcastat data/tmp/Rip527_2/Rip527_2.stat.
[2023-02-13 12:51:25] | metaDMG.fit.serial:176 | DEBUG | Rip527_2 | Moving data/tmp/Rip527_2/Rip527_2.bdamage.gz.uglyprint.mismatch.txt.gz to data/lca/Rip527_2.mismatches.txt.gz.
[2023-02-13 12:51:25] | metaDMG.fit.serial:176 | DEBUG | Rip527_2 | Moving data/tmp/Rip527_2/Rip527_2.bdamage.gz.uglyprint.stat.txt.gz to data/lca/Rip527_2.mismatches.stat.txt.gz.
[2023-02-13 12:51:25] | metaDMG.fit.serial:176 | DEBUG | Rip527_2 | Moving data/tmp/Rip527_2/Rip527_2.lca.gz to data/lca/Rip527_2.lca.txt.gz.
[2023-02-13 12:51:25] | metaDMG.fit.serial:176 | DEBUG | Rip527_2 | Moving data/tmp/Rip527_2/Rip527_2.log to data/lca/Rip527_2.log.txt.
[2023-02-13 12:51:25] | metaDMG.fit.serial:392 | INFO | Rip527_2 | Computing mismatch matrix dataframes.
[2023-02-13 12:51:25] | root:237 | ERROR | Rip527_2 | MismatchFileError with get_df_mismatches. See log-file for more information.
Traceback (most recent call last):
File "/opt/miniconda3/envs/metaDMG/lib/python3.9/site-packages/metaDMG/fit/serial.py", line 555, in run_single_config
df_mismatches = get_df_mismatches(config, force=force)
File "/opt/miniconda3/envs/metaDMG/lib/python3.9/site-packages/metaDMG/fit/serial.py", line 393, in get_df_mismatches
df_mismatches = mismatches.compute(config)
File "/opt/miniconda3/envs/metaDMG/lib/python3.9/site-packages/metaDMG/fit/mismatches.py", line 223, in compute
raise MismatchFileError(f"{filename} only contains a header, no data.")
MismatchFileError: data/lca/Rip527_2.mismatches.txt.gz only contains a header, no data.
[2023-02-13 12:51:25] | metaDMG.fit.workflow:50 | ERROR | 1 error(s) occurred during the computation.`
What does this means? How can I resolve it?
Thank you