Open spitfiredd opened 1 year ago
Here is the contents of pplacer out
Running pplacer v1.1.alpha19-0-g807f6f3 analysis on checkm_folder/storage/tree/concatenated.fasta...
Didn't find any reference sequences in given alignment file. Using supplied reference alignment.
Pre-masking sequences... sequence length cut from 6988 to 6808.
Warning: pplacer results make the most sense when the given tree is multifurcating at the root. See manual for details.
Determining figs... figs disabled.
Allocating memory for internal nodes... done.
Caching likelihood information on reference tree...
I'm not sure if this is relavent
https://github.com/Ecogenomics/GTDBTk/issues/170#issuecomment-514466145
Update:
I am able to run pplacer
independently of checkm after it fails.
Here are the steps I took:
checkm
until where it failscheckm_folder/storage/tree
concatenated.tre
filepplacer command
docker run -v "$(pwd)":/scratch quay.io/biocontainers/checkm-genome:1.2.1--pyhdfd78af_0 pplacer -j 10 -c /usr/local/checkm_data/genome_tree/genome_tree_reduced.refpkg -o /scratch/concatenated.pplacer.json /scratch/concatenated.fasta
guppy command
docker run -v "$(pwd)":/scratch quay.io/biocontainers/checkm-genome:1.2.1--pyhdfd78af_0 pplacer guppy tog -o /scratch/concatenated.tre /scratch/concatenated.pplacer.json
The commands I got from (lines 72-81) https://github.com/Ecogenomics/CheckM/blob/3eac9581ed81fdeb4a13045b912d08d3326ffdc5/checkm/pplacer.py#L72
I am having the same error with checkM 1.2.2 (in a singularity). The Dockerfile I intended to use (and push here):
FROM ubuntu:latest
ENV DEBIAN_FRONTEND=noninteractive
RUN apt-get update \
&& apt install -y git python3-pip hmmer prodigal pplacer wget \
&& pip3 install numpy matplotlib pysam checkm-genome
RUN wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz && tar -zxvf checkm_data_2015_01_16.tar.gz
RUN rm checkm_data_2015_01_16.tar.gz
ENV CHECKM_DATA_PATH=/
ENV PATH="$HOME/.local/bin:$PATH"
CMD checkm
You can get if with docker pull 007ptar007/checkm:lastest
Command I ran:
singularity run --no-home --bind '/home/user/' checkm.sif checkm test ~/testcheckm/
While trying to look for the file ( if it was misplaced), I noticed that the output is appened to the log file instead of re-writing it, which can be confusing. Also, only the stdout is written and stderr is missing. The first error that happens is actually:
[2023-06-21 15:54:41] INFO: CheckM v1.2.2
[2023-06-21 15:54:41] INFO: checkm test /home/user/testcheckm/
[2023-06-21 15:54:41] INFO: CheckM data: /
[2023-06-21 15:54:41] INFO: [CheckM - Test] Processing E.coli K12-W3310 to verify operation of CheckM.
[2023-06-21 15:54:41] INFO: [Step 1]: Verifying tree command.
[2023-06-21 15:54:41] INFO: [CheckM - tree] Placing bins in reference genome tree.
[2023-06-21 15:54:41] INFO: Identifying marker genes in 1 bins with 1 threads:
Finished processing 1 of 1 (100.00%) bins.
[2023-06-21 15:54:47] INFO: Saving HMM info to file.
[2023-06-21 15:54:47] INFO: Calculating genome statistics for 1 bins with 1 threads:
Finished processing 1 of 1 (100.00%) bins.
[2023-06-21 15:54:47] INFO: Extracting marker genes to align.
[2023-06-21 15:54:47] INFO: Parsing HMM hits to marker genes:
Finished parsing hits for 1 of 1 (100.00%) bins.
[2023-06-21 15:54:47] INFO: Extracting 43 HMMs with 1 threads:
Finished extracting 43 of 43 (100.00%) HMMs.
[2023-06-21 15:54:47] INFO: Aligning 43 marker genes with 1 threads:
Finished aligning 43 of 43 (100.00%) marker genes.
[2023-06-21 15:54:47] INFO: Reading marker alignment files.
[2023-06-21 15:54:47] INFO: Concatenating alignments.
[2023-06-21 15:54:47] INFO: Placing 1 bins into the genome tree with pplacer (be patient).
Killed
Uncaught exception: Sys_error("/home/user/testcheckm/results/storage/tree/concatenated.pplacer.json: No such file or directory")
Fatal error: exception Sys_error("/home/user/testcheckm/results/storage/tree/concatenated.pplacer.json: No such file or directory")
[2023-06-21 15:55:14] INFO: { Current stage: 0:00:33.283 || Total: 0:00:33.283 }
[2023-06-21 15:55:14] INFO: [Passed]
[2023-06-21 15:55:14] INFO: [Step 2]: Verifying tree_qa command.
[2023-06-21 15:55:14] INFO: [CheckM - tree_qa] Assessing phylogenetic markers found in each bin.
[2023-06-21 15:55:14] INFO: Reading HMM info from file.
[2023-06-21 15:55:14] INFO: Parsing HMM hits to marker genes:
Finished parsing hits for 1 of 1 (100.00%) bins.
This exception is seen here but shows a defined error instead of a Killed
and then:
[2023-06-21 15:55:14] INFO: [Passed]
[2023-06-21 15:55:14] INFO: [Step 2]: Verifying tree_qa command.
[2023-06-21 15:55:14] INFO: [CheckM - tree_qa] Assessing phylogenetic markers found in each bin.
[2023-06-21 15:55:14] INFO: Reading HMM info from file.
[2023-06-21 15:55:14] INFO: Parsing HMM hits to marker genes:
Finished parsing hits for 1 of 1 (100.00%) bins.
Unexpected error: <class 'FileNotFoundError'>
Traceback (most recent call last):
File "/usr/local/bin/checkm", line 856, in <module>
checkmParser.parseOptions(args)
File "/usr/local/lib/python3.10/dist-packages/checkm/main.py", line 1031, in parseOptions
self.test(options)
File "/usr/local/lib/python3.10/dist-packages/checkm/main.py", line 940, in test
verifyEcoli.run(self, options.output_dir)
File "/usr/local/lib/python3.10/dist-packages/checkm/test/test_ecoli.py", line 75, in run
parser.treeQA(options)
File "/usr/local/lib/python3.10/dist-packages/checkm/main.py", line 225, in treeQA
treeParser.printSummary(
File "/usr/local/lib/python3.10/dist-packages/checkm/treeParser.py", line 45, in printSummary
self.reportBinTaxonomy(outDir, resultsParser, bTabTable, outFile, binStats, bLineageStatistics=False)
File "/usr/local/lib/python3.10/dist-packages/checkm/treeParser.py", line 641, in reportBinTaxonomy
binIdToTaxonomy = self.getBinTaxonomy(outDir, binIds)
File "/usr/local/lib/python3.10/dist-packages/checkm/treeParser.py", line 191, in getBinTaxonomy
tree = dendropy.Tree.get_from_path(treeFile, schema='newick', rooting="force-rooted", preserve_underscores=True)
File "/usr/local/lib/python3.10/dist-packages/dendropy/datamodel/basemodel.py", line 217, in get_from_path
with open(src, *open_args) as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: '/home/user/testcheckm/results/storage/tree/concatenated.tre'
I wonder if the error of @spitfiredd comes from the same killed job of pplacer or if our python error comes from a different previous bug. Maybe mine should be in a different issue.
same issue here
FileNotFoundError: [Errno 2] No such file or directory: 'temp_checkm_dir/storage/tree/concatenated.tre'
command line:
checkm lineage_wf -t 8 -x .fasta temp_checkm_dir --tab_table --file checkm_genome_results.tsv
versions: CheckM v1.2.2 Python 3.10.12
executed on: WSL installed on LAPTOP x86_64 (8 CPUs and 6.087029e+09 RAMs)
I have installed checkm-genome on 3 ubuntu 22.04 systems for numerous times.
All the procedures are following the INSTALLATION wiki.
On the first two systems , when running the following comand:
checkm test ./re
the results showed as the following :
FileNotFoundError: [Errno 2] No such file or directory: ./re/results/storage/tree/concatenated.tre'
However, the last try in the 3rd system had successed.
I am a new in bio-info, I think this issue may be caused by the source code because it had not been updated after 2015.
I have installed checkm-genome on 3 ubuntu 22.04 systems for numerous times. All the procedures are following the INSTALLATION wiki. On the first two systems , when running the following comand:
checkm test ./re
the results showed as the following : FileNotFoundError: [Errno 2] No such file or directory: ./re/results/storage/tree/concatenated.tre'However, the last try in the 3rd system had successed.
I am a new in bio-info, I think this issue may be caused by the source code because it had not been updated after 2015.
你好,这个问题你解决了吗?
I'm experiencing the same problem, do you have a solution for the trouble?
Missing file issues are generally due to the machine running out of memory. You can find the CheckM system requirements here: https://github.com/Ecogenomics/CheckM/wiki/Installation#system-requirements
I am running the following command
Here is my traceback:
When I look in the
checkm_folder/storage/tree
I see aconcatenated.fasta
file but notconcatenated.tre
I am running this from: docker base image:
mambaorg/micromamba:0.27.0
python:3.7.16
nextflow:version 22.10.0 build 5826