No case3 is resolved #50
Comments
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I downloaded from https://zenodo.org/record/8137197 simPhage.zip, it did run successfully, I use "Bandage" compared the two assembly graph, found that they are very similar, what caused my running failure? Is it because I use metaSPAdes? |
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Hi @xtc2002, Thanks for your interest in Phables. Have you properly installed Gurobi and set up the academic license? Case 3 won’t be resolved if Gurobi is not properly set up. As for your simulated dataset, can you please share with me the assembly graph file, read data and the Phables log file (found in logs folder)? I can have a look. Using metaSPAdes should not be the issue (you should since it’s a metagenome). Also, what values of k did you use for assembly? |
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Hi @Vini2 , |
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Hi, I'm xtc2002, I'm sorry to bother you, but I'm really confused. I cannot upload files larger than 25M on GitHub, so I uploaded the file to the following URL. Now let me describe the situation.
I downloaded 'simPhage' dataset from https://zenodo.org/record/8137197, I ran Phables with assembly_graph_after_simplification.gfa and reads provided by simPhage, Phables resolved Case 3 correctly (The results are saved in the phables.out folder). However, when I use hecatomb and metaSPAdes to produce assembly graphs, and use these assembly graph to run Phables, it didn't run correctly, no Case 3 is solved (The results are saved in the phables.outh and phables.outs folders, respectively). What's more, I have tried 'Wastewater' dataset and use its assembly graph (reads are from NCBI), also, no Case 3 is solved.
I tried creating a new conda environment and install Phables and Gurobi again, but the results were the same, and I tried running a new environment in a virtual machine, and the results were the same. Where did it all go wrong? I really want to fix it.
I would appreciate it if you could help me with my problem, thanks!
http://mail.qq.com/cgi-bin/ftnExs_download?t=exs_ftn_download&k=7c393765780029c83f40ff0e1362061f404d5354045a55001509525c514f50060c011a040153511d5a090206545157030a5d0707356d34435154670d5405511e4c58454b5218340d&code=897e5b40
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Hi @xtc2002, Thanks for sharing the data. I'll have a look and get back to you soon. Can you please confirm the Gurobi version you are using? |
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Hi @Vini2 , |
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Hi @xtc2002, Sorry for the delay in getting back to you. Were you able to solve this issue? I checked the data you shared with me and the assembly is quite different from the original assembly I had. Simulation and assembly can cause these differences. Simulators can produce different reads covering the genome. Assembly algorithms can be non-deterministic and can result in differences. The assembly you produced has a self-loop (a repeat) in one of the contigs and there are no paired-end reads spanning across contigs (hence no subpaths). In such cases, phables cannot resolve genomes. Since you are simulating reads of length 300bp, I would recommend using a larger k-size for assembly, something like |
Hi, I'm new to this field, I was recently reading an article called "Phables: from fragmented assemblies to high quality bacteriophage genomes" and I wanted to reproduce some of the results, however, I ran into some problems.
I simulated reads from the following four phages with the respective read coverage values and created a simulated phage dataset.
Then I used metaSPAdes to obtain the assembly graph, I'm sure the assembly graph is correct.
Phables ran successfully, but no case3 is resolved.
`(phables) [wangbo@manager ~]$ phables run --output /data/home/wangbo/XTC/result/test --threads 8 --input /data/home/wangbo/XTC/fga/test/assembly_graph_with_scaffolds.gfa --reads /data/home/wangbo/XTC/data/test
[2024:04:12 16:33:29] Copying system default config to /data/home/wangbo/XTC/result/test/config.yaml
[2024:04:12 16:33:29] Updating config file with new values
[2024:04:12 16:33:29] Writing config file to /data/home/wangbo/XTC/result/test/config.yaml
[2024:04:12 16:33:29] ------------------
[2024:04:12 16:33:29] | Runtime config |
[2024:04:12 16:33:29] ------------------
alpha: 1.2
compcount: 200
conda_prefix: /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda
configfile: /data/home/wangbo/XTC/result/test/config.yaml
covtol: 100
databases: null
evalue: 1.0e-10
input: /data/home/wangbo/XTC/fga/test/assembly_graph_with_scaffolds.gfa
log: /data/home/wangbo/XTC/result/test/phables.log
longreads: false
maxpaths: 10
mgfrac: 0.2
mincov: 10
minlength: 2000
output: /data/home/wangbo/XTC/result/test
prefix: null
profile: null
reads: /data/home/wangbo/XTC/data/test
resources:
jobCPU: 8
jobMem: 16000
seqidentity: 0.3
snake_args: []
snake_default:
system_config: /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/config/config.yaml
threads: 8
use_conda: true
[2024:04:12 16:33:29] ---------------------
[2024:04:12 16:33:29] | Snakemake command |
[2024:04:12 16:33:29] ---------------------
snakemake -s /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/phables.smk --configfile /data/home/wangbo/XTC/result/test/config.yaml --cores 8 --use-conda --conda-prefix /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda --rerun-incomplete --printshellcmds --nolock --show-failed-logs
Config file /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/../config/config.yaml is extended by additional config specified via the command line.
Config file /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/../config/databases.yaml is extended by additional config specified via the command line.
Output files will be saved to directory, /data/home/wangbo/XTC/result/test
Assuming unrestricted shared filesystem usage.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 8
Rules claiming more threads will be scaled down.
Job stats:
job count
all 1
combine_genomes_and_unresolved_edges 1
koverage 1
koverage_genomes 1
koverage_postprocess 1
koverage_tsv 1
run_combine_cov 1
run_gfa2fasta 1
run_phables 1
scan_phrogs 1
scan_smg 1
total 11
Select jobs to execute...
Execute 2 jobs...
[Fri Apr 12 16:34:01 2024]
localrule koverage_tsv:
output: /data/home/wangbo/XTC/result/test/preprocess/phables.samples.tsv
jobid: 3
reason: Missing output files: /data/home/wangbo/XTC/result/test/preprocess/phables.samples.tsv
resources: tmpdir=/tmp
[Fri Apr 12 16:34:01 2024]
localrule run_gfa2fasta:
input: /data/home/wangbo/XTC/fga/test/assembly_graph_with_scaffolds.gfa
output: /data/home/wangbo/XTC/result/test/preprocess/edges.fasta
log: /data/home/wangbo/XTC/result/test/logs/gfa2fasta.log
jobid: 1
reason: Missing output files: /data/home/wangbo/XTC/result/test/preprocess/edges.fasta
resources: tmpdir=/tmp
Output files will be saved to directory, /data/home/wangbo/XTC/result/test
Activating conda environment: miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/873ad7e71dfcd9bb5adf1eb8f8dc2377_
[Fri Apr 12 16:34:03 2024]
Finished job 3.
1 of 11 steps (9%) done
Activating conda environment: miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/873ad7e71dfcd9bb5adf1eb8f8dc2377_
2024-04-12 16:34:09,382 - INFO - Obtaining edge sequences
2024-04-12 16:34:09,407 - INFO - Writing edge sequences to FASTA file
2024-04-12 16:34:09,640 - INFO - The FASTA file with unitig sequences can be found at /data/home/wangbo/XTC/result/test/preprocess/edges.fasta
2024-04-12 16:34:09,641 - INFO - Thank you for using gfa2fasta!
[Fri Apr 12 16:34:09 2024]
Finished job 1.
2 of 11 steps (18%) done
Select jobs to execute...
Execute 1 jobs...
[Fri Apr 12 16:34:09 2024]
localrule koverage:
input: /data/home/wangbo/XTC/result/test/preprocess/phables.samples.tsv, /data/home/wangbo/XTC/result/test/preprocess/edges.fasta
output: /data/home/wangbo/XTC/result/test/preprocess/temp/test.bam, /data/home/wangbo/XTC/result/test/preprocess/temp/test.bam.bai, /data/home/wangbo/XTC/result/test/preprocess/results/sample_coverm_coverage.tsv
jobid: 2
reason: Missing output files: /data/home/wangbo/XTC/result/test/preprocess/results/sample_coverm_coverage.tsv, /data/home/wangbo/XTC/result/test/preprocess/temp/test.bam, /data/home/wangbo/XTC/result/test/preprocess/temp/test.bam.bai; Input files updated by another job: /data/home/wangbo/XTC/result/test/preprocess/edges.fasta, /data/home/wangbo/XTC/result/test/preprocess/phables.samples.tsv
threads: 8
resources: tmpdir=/tmp, mem_mb=15259, mem_mib=15259, mem=16000MB
Activating conda environment: miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_
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[2024:04:12 16:34:12] Copying system default config to /data/home/wangbo/XTC/result/test/preprocess/koverage.config.yaml
[2024:04:12 16:34:12] Updating config file with new values
[2024:04:12 16:34:12] Writing config file to /data/home/wangbo/XTC/result/test/preprocess/koverage.config.yaml
[2024:04:12 16:34:12] ------------------
[2024:04:12 16:34:12] | Runtime config |
[2024:04:12 16:34:12] ------------------
koverage:
args:
bin_width: 100
conda_prefix: /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/lib/python3.11/site-packages/koverage/workflow/conda
configfile: /data/home/wangbo/XTC/result/test/preprocess/koverage.config.yaml
kmer_max: 5000
kmer_min: 50
kmer_sample: 100
kmer_size: 25
log: /data/home/wangbo/XTC/result/test/preprocess/koverage.log
minimap: sr
output: /data/home/wangbo/XTC/result/test/preprocess
pafs: false
reads: /data/home/wangbo/XTC/result/test/preprocess/phables.samples.tsv
ref: /data/home/wangbo/XTC/result/test/preprocess/edges.fasta
report: true
report_max_ctg: 1000
snake_args:
- coverm
system_config: /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/lib/python3.11/site-packages/koverage/config/config.yaml
system_workflow_profile: /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/lib/python3.11/site-packages/koverage/config/profile/config.yaml
threads: 8
use_conda: true
workflow_profile: /data/home/wangbo/XTC/result/test/preprocess/koverage.profile
params:
coverm: -m count -m rpkm -m tpm -m mean -m covered_fraction -m variance
jellyfish: -C -s 1G -c 2 --out-counter-len=2 -L 2
resources:
med:
cpu: 4
mem: 16000
time: 02:00:00
ram:
cpu: 2
mem: 8000
time: 04:00:00
[2024:04:12 16:34:12] Copying system default config to /data/home/wangbo/XTC/result/test/preprocess/koverage.profile/config.yaml
[2024:04:12 16:34:12] ---------------------
[2024:04:12 16:34:12] | Snakemake command |
[2024:04:12 16:34:12] ---------------------
snakemake -s /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/lib/python3.11/site-packages/koverage/workflow/Snakefile --configfile /data/home/wangbo/XTC/result/test/preprocess/koverage.config.yaml --cores 8 --use-conda --conda-prefix /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/lib/python3.11/site-packages/koverage/workflow/conda coverm --workflow-profile /data/home/wangbo/XTC/result/test/preprocess/koverage.profile
Using profile /data/home/wangbo/XTC/result/test/preprocess/koverage.profile and workflow specific profile /data/home/wangbo/XTC/result/test/preprocess/koverage.profile for setting default command line arguments.
Config file /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/lib/python3.11/site-packages/koverage/workflow/../config/config.yaml is extended by additional config specified via the command line.
Config file /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/lib/python3.11/site-packages/koverage/workflow/../config/system_config.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 8
Rules claiming more threads will be scaled down.
Job stats:
job count
coverm 1
coverm_bam2counts 1
coverm_combine 1
coverm_map_pe 1
sample_tsv 1
total 5
Select jobs to execute...
[Fri Apr 12 16:34:32 2024]
rule coverm_map_pe:
input: /data/home/wangbo/XTC/result/test/preprocess/edges.fasta, /data/home/wangbo/XTC/data/test/test_1.fq
output: /data/home/wangbo/XTC/result/test/preprocess/temp/test.bam, /data/home/wangbo/XTC/result/test/preprocess/temp/test.bam.bai
log: /data/home/wangbo/XTC/result/test/preprocess/logs/coverm_map_pe.test.err
jobid: 3
benchmark: /data/home/wangbo/XTC/result/test/preprocess/benchmarks/coverm_map_pe.test.txt
reason: Missing output files: /data/home/wangbo/XTC/result/test/preprocess/temp/test.bam
wildcards: sample=test
threads: 4
resources: tmpdir=/tmp, mem_mb=16000, mem_mib=15259, mem=16000MB, time=02:00:00
{ minimap2 -t 4 -ax sr --secondary=no /data/home/wangbo/XTC/result/test/preprocess/edges.fasta /data/home/wangbo/XTC/data/test/test_1.fq /data/home/wangbo/XTC/data/test/test_2.fq | samtools sort -T test -@ 4 - > /data/home/wangbo/XTC/result/test/preprocess/temp/test.bam; samtools index /data/home/wangbo/XTC/result/test/preprocess/temp/test.bam; } 2> /data/home/wangbo/XTC/result/test/preprocess/logs/coverm_map_pe.test.err
[Fri Apr 12 16:34:32 2024]
rule sample_tsv:
output: /data/home/wangbo/XTC/result/test/preprocess/koverage.samples.tsv
jobid: 4
reason: Missing output files: /data/home/wangbo/XTC/result/test/preprocess/koverage.samples.tsv
resources: tmpdir=/tmp
Activating conda environment: miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/lib/python3.11/site-packages/koverage/workflow/conda/fce0923fcb6faed0d66c7fb8e7a9e927_
Config file /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/lib/python3.11/site-packages/koverage/workflow/../config/config.yaml is extended by additional config specified via the command line.
Config file /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/lib/python3.11/site-packages/koverage/workflow/../config/system_config.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 8
Rules claiming more threads will be scaled down.
Select jobs to execute...
[Fri Apr 12 16:34:45 2024]
Finished job 3.
1 of 5 steps (20%) done
Select jobs to execute...
[Fri Apr 12 16:34:45 2024]
rule coverm_bam2counts:
input: /data/home/wangbo/XTC/result/test/preprocess/temp/test.bam
output: /data/home/wangbo/XTC/result/test/preprocess/temp/test.cov
log: /data/home/wangbo/XTC/result/test/preprocess/logs/coverm_bam2counts.test.err
jobid: 2
benchmark: /data/home/wangbo/XTC/result/test/preprocess/benchmarks/coverm_bam2counts.test.txt
reason: Missing output files: /data/home/wangbo/XTC/result/test/preprocess/temp/test.cov; Input files updated by another job: /data/home/wangbo/XTC/result/test/preprocess/temp/test.bam
wildcards: sample=test
resources: tmpdir=/tmp
coverm contig -b /data/home/wangbo/XTC/result/test/preprocess/temp/test.bam -m count -m rpkm -m tpm -m mean -m covered_fraction -m variance > /data/home/wangbo/XTC/result/test/preprocess/temp/test.cov 2> /data/home/wangbo/XTC/result/test/preprocess/logs/coverm_bam2counts.test.err
Activating conda environment: miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/lib/python3.11/site-packages/koverage/workflow/conda/2b6eada0b2671d4e5851244fb2f8d89b_
[Fri Apr 12 16:34:46 2024]
Finished job 4.
2 of 5 steps (40%) done
[Fri Apr 12 16:34:46 2024]
Finished job 2.
3 of 5 steps (60%) done
Select jobs to execute...
[Fri Apr 12 16:34:46 2024]
rule coverm_combine:
input: /data/home/wangbo/XTC/result/test/preprocess/temp/test.cov
output: /data/home/wangbo/XTC/result/test/preprocess/results/sample_coverm_coverage.tsv
jobid: 1
reason: Missing output files: /data/home/wangbo/XTC/result/test/preprocess/results/sample_coverm_coverage.tsv; Input files updated by another job: /data/home/wangbo/XTC/result/test/preprocess/temp/test.cov
resources: tmpdir=/tmp
Config file /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/lib/python3.11/site-packages/koverage/workflow/../config/config.yaml is extended by additional config specified via the command line.
Config file /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/lib/python3.11/site-packages/koverage/workflow/../config/system_config.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 8
Rules claiming more threads will be scaled down.
Select jobs to execute...
[Fri Apr 12 16:34:48 2024]
Finished job 1.
4 of 5 steps (80%) done
Select jobs to execute...
[Fri Apr 12 16:34:48 2024]
localrule coverm:
input: /data/home/wangbo/XTC/result/test/preprocess/results/sample_coverm_coverage.tsv, /data/home/wangbo/XTC/result/test/preprocess/koverage.samples.tsv
jobid: 0
reason: Input files updated by another job: /data/home/wangbo/XTC/result/test/preprocess/results/sample_coverm_coverage.tsv, /data/home/wangbo/XTC/result/test/preprocess/koverage.samples.tsv
resources: tmpdir=/tmp
[Fri Apr 12 16:34:48 2024]
Finished job 0.
5 of 5 steps (100%) done
Complete log: .snakemake/log/2024-04-12T163416.591559.snakemake.log
cat .snakemake/log/2024-04-12T163416.591559.snakemake.log >> /data/home/wangbo/XTC/result/test/preprocess/koverage.log
[2024:04:12 16:34:49] Snakemake finished successfully
[Fri Apr 12 16:34:49 2024]
Finished job 2.
3 of 11 steps (27%) done
Select jobs to execute...
Execute 1 jobs...
[Fri Apr 12 16:34:49 2024]
localrule scan_phrogs:
input: /data/home/wangbo/XTC/result/test/preprocess/edges.fasta, /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/../../databases/phrogs_mmseqs_db/phrogs_profile_db
output: /data/home/wangbo/XTC/result/test/preprocess/phrogs_annotations.tsv
log: /data/home/wangbo/XTC/result/test/logs/phrogs_scan.log
jobid: 6
reason: Missing output files: /data/home/wangbo/XTC/result/test/preprocess/phrogs_annotations.tsv; Input files updated by another job: /data/home/wangbo/XTC/result/test/preprocess/edges.fasta
threads: 8
resources: tmpdir=/tmp, mem_mb=15259, mem_mib=15259, mem=16000MB
Activating conda environment: miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/d873faecbf16136ae736110f2de1b018_
[Fri Apr 12 16:38:07 2024]
Finished job 6.
4 of 11 steps (36%) done
Select jobs to execute...
Execute 1 jobs...
[Fri Apr 12 16:38:07 2024]
localrule scan_smg:
input: /data/home/wangbo/XTC/result/test/preprocess/edges.fasta, /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/../../databases/marker.hmm
output: /data/home/wangbo/XTC/result/test/preprocess/edges.fasta.hmmout
log: /data/home/wangbo/XTC/result/test/logs/smg_scan_frag_out.log, /data/home/wangbo/XTC/result/test/logs/smg_scan_frag_err.log, /data/home/wangbo/XTC/result/test/logs/smg_scan_hmm_out.log, /data/home/wangbo/XTC/result/test/logs/smg_scan_hmm_err.log
jobid: 5
reason: Missing output files: /data/home/wangbo/XTC/result/test/preprocess/edges.fasta.hmmout; Input files updated by another job: /data/home/wangbo/XTC/result/test/preprocess/edges.fasta
threads: 8
resources: tmpdir=/tmp, mem_mb=15259, mem_mib=15259, mem=16000MB
Activating conda environment: miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/7052f94b534705e142372ab214aafe67_
[Fri Apr 12 16:38:10 2024]
Finished job 5.
5 of 11 steps (45%) done
Select jobs to execute...
Execute 1 jobs...
[Fri Apr 12 16:38:10 2024]
localrule run_combine_cov:
input: /data/home/wangbo/XTC/result/test/preprocess/results/sample_coverm_coverage.tsv
output: /data/home/wangbo/XTC/result/test/preprocess/coverage.tsv
jobid: 4
reason: Missing output files: /data/home/wangbo/XTC/result/test/preprocess/coverage.tsv; Input files updated by another job: /data/home/wangbo/XTC/result/test/preprocess/results/sample_coverm_coverage.tsv
resources: tmpdir=/tmp
[Fri Apr 12 16:38:10 2024]
Finished job 4.
6 of 11 steps (55%) done
Select jobs to execute...
Execute 1 jobs...
[Fri Apr 12 16:38:10 2024]
localrule run_phables:
input: /data/home/wangbo/XTC/fga/test/assembly_graph_with_scaffolds.gfa, /data/home/wangbo/XTC/result/test/preprocess/coverage.tsv, /data/home/wangbo/XTC/result/test/preprocess/phrogs_annotations.tsv, /data/home/wangbo/XTC/result/test/preprocess/edges.fasta.hmmout, /data/home/wangbo/XTC/result/test/preprocess/edges.fasta, /data/home/wangbo/XTC/result/test/preprocess/temp/test.bam, /data/home/wangbo/XTC/result/test/preprocess/temp/test.bam.bai, /data/home/wangbo/XTC/result/test/preprocess/coverage.tsv, /data/home/wangbo/XTC/result/test/preprocess/edges.fasta.hmmout, /data/home/wangbo/XTC/result/test/preprocess/phrogs_annotations.tsv
output: /data/home/wangbo/XTC/result/test/phables/resolved_paths.fasta, /data/home/wangbo/XTC/result/test/phables/resolved_phages, /data/home/wangbo/XTC/result/test/phables/resolved_genome_info.txt, /data/home/wangbo/XTC/result/test/phables/resolved_edges.fasta, /data/home/wangbo/XTC/result/test/phables/resolved_component_info.txt, /data/home/wangbo/XTC/result/test/phables/component_phrogs.txt, /data/home/wangbo/XTC/result/test/phables/unresolved_phage_like_edges.fasta
log: /data/home/wangbo/XTC/result/test/logs/phables_output.log
jobid: 7
reason: Missing output files: /data/home/wangbo/XTC/result/test/phables/component_phrogs.txt, /data/home/wangbo/XTC/result/test/phables/resolved_paths.fasta, /data/home/wangbo/XTC/result/test/phables/unresolved_phage_like_edges.fasta, /data/home/wangbo/XTC/result/test/phables/resolved_genome_info.txt, /data/home/wangbo/XTC/result/test/phables/resolved_component_info.txt; Input files updated by another job: /data/home/wangbo/XTC/result/test/preprocess/edges.fasta.hmmout, /data/home/wangbo/XTC/result/test/preprocess/phrogs_annotations.tsv, /data/home/wangbo/XTC/result/test/preprocess/edges.fasta, /data/home/wangbo/XTC/result/test/preprocess/coverage.tsv, /data/home/wangbo/XTC/result/test/preprocess/temp/test.bam, /data/home/wangbo/XTC/result/test/preprocess/temp/test.bam.bai
threads: 8
resources: tmpdir=/tmp
Activating conda environment: miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/873ad7e71dfcd9bb5adf1eb8f8dc2377_
Activating conda environment: miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/873ad7e71dfcd9bb5adf1eb8f8dc2377_
2024-04-12 16:38:25,399 - INFO - Welcome to Phables: from fragmented assemblies to high-quality bacteriophage genomes.
2024-04-12 16:38:25,401 - INFO - Input arguments:
2024-04-12 16:38:25,401 - INFO - Assembly graph file: /data/home/wangbo/XTC/fga/test/assembly_graph_with_scaffolds.gfa
2024-04-12 16:38:25,401 - INFO - Unitig coverage file: /data/home/wangbo/XTC/result/test/preprocess/coverage.tsv
2024-04-12 16:38:25,401 - INFO - BAM files path: /data/home/wangbo/XTC/result/test/preprocess/temp
2024-04-12 16:38:25,401 - INFO - Unitig .hmmout file: /data/home/wangbo/XTC/result/test/preprocess/edges.fasta.hmmout
2024-04-12 16:38:25,401 - INFO - Unitig phrog annotations file: /data/home/wangbo/XTC/result/test/preprocess/phrogs_annotations.tsv
2024-04-12 16:38:25,402 - INFO - Minimum length of unitigs to consider: 2000
2024-04-12 16:38:25,402 - INFO - Minimum coverage of paths to output: 10
2024-04-12 16:38:25,402 - INFO - Minimum unitig count to consider a component: 200
2024-04-12 16:38:25,402 - INFO - Maximum number of paths to resolve for a component: 10
2024-04-12 16:38:25,402 - INFO - Length threshold to consider single copy marker genes: 0.2
2024-04-12 16:38:25,402 - INFO - Maximum e-value for phrog annotations: 1e-10
2024-04-12 16:38:25,403 - INFO - Minimum sequence identity for phrog annotations: 0.3
2024-04-12 16:38:25,403 - INFO - Coverage tolerance for extending subpaths: 100.0
2024-04-12 16:38:25,403 - INFO - Coverage multipler for flow interval modelling: 1.2
2024-04-12 16:38:25,403 - INFO - Input long reads: False
2024-04-12 16:38:25,403 - INFO - Prefix for genome identifiers: None
2024-04-12 16:38:25,403 - INFO - Number of threads to use: 8
2024-04-12 16:38:25,403 - INFO - Output folder: /data/home/wangbo/XTC/result/test/phables
2024-04-12 16:38:25,423 - INFO - Total number of vertices in the assembly graph: 46
2024-04-12 16:38:25,424 - INFO - Total number of links in the assembly graph: 57
2024-04-12 16:38:25,659 - INFO - Total number of components found: 3
2024-04-12 16:38:25,659 - INFO - Short reads provided
Resolving components: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 3/3 [00:00<00:00, 3.10it/s]
2024-04-12 16:38:27,334 - INFO - Total number of cyclic components found: 1
2024-04-12 16:38:27,334 - INFO - Total number of cyclic components resolved: 0
2024-04-12 16:38:27,334 - INFO - Single unitigs identified: 2
2024-04-12 16:38:27,334 - INFO - Total number of linear components found: 0
2024-04-12 16:38:27,334 - INFO - Total number of linear components resolved: 0
2024-04-12 16:38:27,334 - INFO - Total number of cyclic components found including single unitigs: 3
2024-04-12 16:38:27,334 - INFO - Total number of components resolved: 2
2024-04-12 16:38:27,334 - INFO - Case 1 (resolved/found): 2/2
2024-04-12 16:38:27,334 - INFO - Case 2 (resolved/found): 0/0
2024-04-12 16:38:27,334 - INFO - Case 3 (resolved/found): 0/1
2024-04-12 16:38:27,334 - INFO - Total number of genomes resolved: 2
2024-04-12 16:38:27,335 - INFO - Resolved genomes can be found in /data/home/wangbo/XTC/result/test/phables/resolved_paths.fasta
2024-04-12 16:38:27,346 - INFO - Resolved genome information can be found in /data/home/wangbo/XTC/result/test/phables/resolved_genome_info.txt
2024-04-12 16:38:27,349 - INFO - PHROGs found in resolved components can be found in /data/home/wangbo/XTC/result/test/phables/component_phrogs.txt
2024-04-12 16:38:27,349 - INFO - Elapsed time: 1.9460010528564453 seconds
2024-04-12 16:38:27,350 - INFO - Thank you for using Phables!
[Fri Apr 12 16:38:27 2024]
Finished job 7.
7 of 11 steps (64%) done
Select jobs to execute...
Execute 1 jobs...
[Fri Apr 12 16:38:27 2024]
localrule combine_genomes_and_unresolved_edges:
input: /data/home/wangbo/XTC/result/test/phables/resolved_paths.fasta, /data/home/wangbo/XTC/result/test/phables/unresolved_phage_like_edges.fasta
output: /data/home/wangbo/XTC/result/test/postprocess/genomes_and_unresolved_edges.fasta
jobid: 10
reason: Missing output files: /data/home/wangbo/XTC/result/test/postprocess/genomes_and_unresolved_edges.fasta; Input files updated by another job: /data/home/wangbo/XTC/result/test/phables/unresolved_phage_like_edges.fasta, /data/home/wangbo/XTC/result/test/phables/resolved_paths.fasta
resources: tmpdir=/tmp
[Fri Apr 12 16:38:27 2024]
Finished job 10.
8 of 11 steps (73%) done
Select jobs to execute...
Execute 1 jobs...
[Fri Apr 12 16:38:27 2024]
localrule koverage_genomes:
input: /data/home/wangbo/XTC/result/test/preprocess/phables.samples.tsv, /data/home/wangbo/XTC/result/test/postprocess/genomes_and_unresolved_edges.fasta
output: /data/home/wangbo/XTC/result/test/postprocess/results/sample_coverage.tsv
jobid: 9
reason: Missing output files: /data/home/wangbo/XTC/result/test/postprocess/results/sample_coverage.tsv; Input files updated by another job: /data/home/wangbo/XTC/result/test/preprocess/phables.samples.tsv, /data/home/wangbo/XTC/result/test/postprocess/genomes_and_unresolved_edges.fasta
threads: 8
resources: tmpdir=/tmp, mem_mb=15259, mem_mib=15259, mem=16000MB
Activating conda environment: miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_
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╚═╝ ╚═╝ ╚═════╝ ╚═══╝ ╚══════╝╚═╝ ╚═╝╚═╝ ╚═╝ ╚═════╝ ╚══════╝
[2024:04:12 16:38:28] Copying system default config to /data/home/wangbo/XTC/result/test/postprocess/koverage.config.yaml
[2024:04:12 16:38:28] Updating config file with new values
[2024:04:12 16:38:28] Writing config file to /data/home/wangbo/XTC/result/test/postprocess/koverage.config.yaml
[2024:04:12 16:38:28] ------------------
[2024:04:12 16:38:28] | Runtime config |
[2024:04:12 16:38:28] ------------------
koverage:
args:
bin_width: 100
conda_prefix: /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/lib/python3.11/site-packages/koverage/workflow/conda
configfile: /data/home/wangbo/XTC/result/test/postprocess/koverage.config.yaml
kmer_max: 5000
kmer_min: 50
kmer_sample: 100
kmer_size: 25
log: /data/home/wangbo/XTC/result/test/postprocess/koverage.log
minimap: sr
output: /data/home/wangbo/XTC/result/test/postprocess
pafs: false
reads: /data/home/wangbo/XTC/result/test/preprocess/phables.samples.tsv
ref: /data/home/wangbo/XTC/result/test/postprocess/genomes_and_unresolved_edges.fasta
report: false
report_max_ctg: 1000
snake_args: []
system_config: /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/lib/python3.11/site-packages/koverage/config/config.yaml
system_workflow_profile: /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/lib/python3.11/site-packages/koverage/config/profile/config.yaml
threads: 8
use_conda: true
workflow_profile: /data/home/wangbo/XTC/result/test/postprocess/koverage.profile
params:
coverm: -m count -m rpkm -m tpm -m mean -m covered_fraction -m variance
jellyfish: -C -s 1G -c 2 --out-counter-len=2 -L 2
resources:
med:
cpu: 4
mem: 16000
time: 02:00:00
ram:
cpu: 2
mem: 8000
time: 04:00:00
[2024:04:12 16:38:28] Copying system default config to /data/home/wangbo/XTC/result/test/postprocess/koverage.profile/config.yaml
[2024:04:12 16:38:28] ---------------------
[2024:04:12 16:38:28] | Snakemake command |
[2024:04:12 16:38:28] ---------------------
snakemake -s /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/lib/python3.11/site-packages/koverage/workflow/Snakefile --configfile /data/home/wangbo/XTC/result/test/postprocess/koverage.config.yaml --cores 8 --use-conda --conda-prefix /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/lib/python3.11/site-packages/koverage/workflow/conda --workflow-profile /data/home/wangbo/XTC/result/test/postprocess/koverage.profile
Using profile /data/home/wangbo/XTC/result/test/postprocess/koverage.profile and workflow specific profile /data/home/wangbo/XTC/result/test/postprocess/koverage.profile for setting default command line arguments.
Config file /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/lib/python3.11/site-packages/koverage/workflow/../config/config.yaml is extended by additional config specified via the command line.
Config file /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/lib/python3.11/site-packages/koverage/workflow/../config/system_config.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 8
Rules claiming more threads will be scaled down.
Job stats:
job count
all_sample_coverage 1
combine_coverage 1
faidx_ref 1
idx_ref 1
map 1
raw_coverage 1
sample_coverage 1
sample_tsv 1
total 8
Select jobs to execute...
[Fri Apr 12 16:38:32 2024]
rule idx_ref:
input: /data/home/wangbo/XTC/result/test/postprocess/genomes_and_unresolved_edges.fasta
output: /data/home/wangbo/XTC/result/test/postprocess/genomes_and_unresolved_edges.fasta.idx
log: /data/home/wangbo/XTC/result/test/postprocess/logs/idx_ref.err
jobid: 4
benchmark: /data/home/wangbo/XTC/result/test/postprocess/benchmarks/idx_ref.txt
reason: Missing output files: /data/home/wangbo/XTC/result/test/postprocess/genomes_and_unresolved_edges.fasta.idx
threads: 4
resources: tmpdir=/tmp, mem_mb=16000, mem_mib=15259, mem=16000MB, time=02:00:00
awk 'BEGIN {count=-1} /^>/ { $0 = ">" ++count } 1' /data/home/wangbo/XTC/result/test/postprocess/genomes_and_unresolved_edges.fasta | minimap2 -t 4 -d /data/home/wangbo/XTC/result/test/postprocess/genomes_and_unresolved_edges.fasta.idx - 2> /data/home/wangbo/XTC/result/test/postprocess/logs/idx_ref.err
[Fri Apr 12 16:38:32 2024]
rule faidx_ref:
input: /data/home/wangbo/XTC/result/test/postprocess/genomes_and_unresolved_edges.fasta
output: /data/home/wangbo/XTC/result/test/postprocess/genomes_and_unresolved_edges.fasta.fai
log: /data/home/wangbo/XTC/result/test/postprocess/logs/faidx_ref.err
jobid: 5
benchmark: /data/home/wangbo/XTC/result/test/postprocess/benchmarks/faidx_ref.txt
reason: Missing output files: /data/home/wangbo/XTC/result/test/postprocess/genomes_and_unresolved_edges.fasta.fai
resources: tmpdir=/tmp
samtools faidx /data/home/wangbo/XTC/result/test/postprocess/genomes_and_unresolved_edges.fasta 2> /data/home/wangbo/XTC/result/test/postprocess/logs/faidx_ref.err
Activating conda environment: miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/lib/python3.11/site-packages/koverage/workflow/conda/fce0923fcb6faed0d66c7fb8e7a9e927_
Activating conda environment: miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/lib/python3.11/site-packages/koverage/workflow/conda/fce0923fcb6faed0d66c7fb8e7a9e927_
[Fri Apr 12 16:38:32 2024]
rule sample_tsv:
output: /data/home/wangbo/XTC/result/test/postprocess/koverage.samples.tsv
jobid: 7
reason: Missing output files: /data/home/wangbo/XTC/result/test/postprocess/koverage.samples.tsv
resources: tmpdir=/tmp
[Fri Apr 12 16:38:33 2024]
Finished job 4.
1 of 8 steps (12%) done
[Fri Apr 12 16:38:33 2024]
Finished job 5.
2 of 8 steps (25%) done
Select jobs to execute...
[Fri Apr 12 16:38:33 2024]
rule raw_coverage:
input: /data/home/wangbo/XTC/result/test/postprocess/genomes_and_unresolved_edges.fasta.idx, /data/home/wangbo/XTC/data/test/test_1.fq, /data/home/wangbo/XTC/result/test/postprocess/genomes_and_unresolved_edges.fasta.fai
output: /data/home/wangbo/XTC/result/test/postprocess/temp/test.counts.pkl
log: /data/home/wangbo/XTC/result/test/postprocess/logs/raw_coverage.test.err
jobid: 3
benchmark: /data/home/wangbo/XTC/result/test/postprocess/benchmarks/raw_coverage.test.txt
reason: Missing output files: /data/home/wangbo/XTC/result/test/postprocess/temp/test.counts.pkl; Input files updated by another job: /data/home/wangbo/XTC/result/test/postprocess/genomes_and_unresolved_edges.fasta.idx, /data/home/wangbo/XTC/result/test/postprocess/genomes_and_unresolved_edges.fasta.fai
wildcards: sample=test
threads: 4
resources: tmpdir=/tmp, mem_mb=16000, mem_mib=15259, mem=16000MB, time=02:00:00
Config file /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/lib/python3.11/site-packages/koverage/workflow/../config/config.yaml is extended by additional config specified via the command line.
Config file /data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/lib/python3.11/site-packages/koverage/workflow/../config/system_config.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 8
Rules claiming more threads will be scaled down.
Select jobs to execute...
/data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/bin/python3.11 /data/home/wangbo/.snakemake/scripts/tmpugw_b71y.minimapWrapper.py
Activating conda environment: miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/lib/python3.11/site-packages/koverage/workflow/conda/fce0923fcb6faed0d66c7fb8e7a9e927_
[Fri Apr 12 16:38:35 2024]
Finished job 7.
3 of 8 steps (38%) done
[Fri Apr 12 16:38:39 2024]
Finished job 3.
4 of 8 steps (50%) done
Select jobs to execute...
[Fri Apr 12 16:38:39 2024]
rule sample_coverage:
input: /data/home/wangbo/XTC/result/test/postprocess/temp/test.counts.pkl
output: /data/home/wangbo/XTC/result/test/postprocess/temp/test.cov.tsv
log: /data/home/wangbo/XTC/result/test/postprocess/logs/sample_coverage.test.err
jobid: 2
benchmark: /data/home/wangbo/XTC/result/test/postprocess/benchmarks/sample_coverage.test.txt
reason: Missing output files: /data/home/wangbo/XTC/result/test/postprocess/temp/test.cov.tsv; Input files updated by another job: /data/home/wangbo/XTC/result/test/postprocess/temp/test.counts.pkl
wildcards: sample=test
resources: tmpdir=/tmp
/data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/bin/python3.11 /data/home/wangbo/.snakemake/scripts/tmp1gwbri6f.sampleCoverage.py
[Fri Apr 12 16:38:39 2024]
Finished job 2.
5 of 8 steps (62%) done
Removing temporary output /data/home/wangbo/XTC/result/test/postprocess/temp/test.counts.pkl.
Select jobs to execute...
[Fri Apr 12 16:38:39 2024]
rule all_sample_coverage:
input: /data/home/wangbo/XTC/result/test/postprocess/temp/test.cov.tsv
output: /data/home/wangbo/XTC/result/test/postprocess/results/sample_coverage.tsv
log: /data/home/wangbo/XTC/result/test/postprocess/logs/all_sample_coverage.err
jobid: 1
benchmark: /data/home/wangbo/XTC/result/test/postprocess/benchmarks/all_sample_coverage.txt
reason: Missing output files: /data/home/wangbo/XTC/result/test/postprocess/results/sample_coverage.tsv; Input files updated by another job: /data/home/wangbo/XTC/result/test/postprocess/temp/test.cov.tsv
resources: tmpdir=/tmp
printf 'Sample Contig Count RPM RPKM RPK TPM Mean Median Hitrate Variance
' > /data/home/wangbo/XTC/result/test/postprocess/results/sample_coverage.tsv 2> /data/home/wangbo/XTC/result/test/postprocess/logs/all_sample_coverage.err; cat /data/home/wangbo/XTC/result/test/postprocess/temp/test.cov.tsv >> /data/home/wangbo/XTC/result/test/postprocess/results/sample_coverage.tsv 2> /data/home/wangbo/XTC/result/test/postprocess/logs/all_sample_coverage.err
Benchmark: unable to collect cpu and memory benchmark statistics
[Fri Apr 12 16:38:39 2024]
Finished job 1.
6 of 8 steps (75%) done
Removing temporary output /data/home/wangbo/XTC/result/test/postprocess/temp/test.cov.tsv.
Select jobs to execute...
[Fri Apr 12 16:38:39 2024]
rule combine_coverage:
input: /data/home/wangbo/XTC/result/test/postprocess/results/sample_coverage.tsv, /data/home/wangbo/XTC/result/test/postprocess/genomes_and_unresolved_edges.fasta.fai
output: /data/home/wangbo/XTC/result/test/postprocess/results/all_coverage.tsv
log: /data/home/wangbo/XTC/result/test/postprocess/logs/combine_coverage.err
jobid: 6
benchmark: /data/home/wangbo/XTC/result/test/postprocess/benchmarks/combine_coverage.txt
reason: Missing output files: /data/home/wangbo/XTC/result/test/postprocess/results/all_coverage.tsv; Input files updated by another job: /data/home/wangbo/XTC/result/test/postprocess/results/sample_coverage.tsv, /data/home/wangbo/XTC/result/test/postprocess/genomes_and_unresolved_edges.fasta.fai
resources: tmpdir=/tmp
/data/home/wangbo/miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/ca3b7425db9120b12d2fee9bdfbd3ddc_/bin/python3.11 /data/home/wangbo/.snakemake/scripts/tmpns1unuw_.combineCoverage.py
[Fri Apr 12 16:38:40 2024]
Finished job 6.
7 of 8 steps (88%) done
Select jobs to execute...
[Fri Apr 12 16:38:40 2024]
localrule map:
input: /data/home/wangbo/XTC/result/test/postprocess/results/sample_coverage.tsv, /data/home/wangbo/XTC/result/test/postprocess/results/all_coverage.tsv, /data/home/wangbo/XTC/result/test/postprocess/koverage.samples.tsv
jobid: 0
reason: Input files updated by another job: /data/home/wangbo/XTC/result/test/postprocess/results/all_coverage.tsv, /data/home/wangbo/XTC/result/test/postprocess/results/sample_coverage.tsv, /data/home/wangbo/XTC/result/test/postprocess/koverage.samples.tsv
resources: tmpdir=/tmp
[Fri Apr 12 16:38:40 2024]
Finished job 0.
8 of 8 steps (100%) done
Complete log: .snakemake/log/2024-04-12T163828.648781.snakemake.log
cat .snakemake/log/2024-04-12T163828.648781.snakemake.log >> /data/home/wangbo/XTC/result/test/postprocess/koverage.log
[2024:04:12 16:38:40] Snakemake finished successfully
[Fri Apr 12 16:38:40 2024]
Finished job 9.
9 of 11 steps (82%) done
Select jobs to execute...
Execute 1 jobs...
[Fri Apr 12 16:38:40 2024]
localrule koverage_postprocess:
input: /data/home/wangbo/XTC/result/test/postprocess/results/sample_coverage.tsv, /data/home/wangbo/XTC/result/test/preprocess/phables.samples.tsv, /data/home/wangbo/XTC/result/test/postprocess/genomes_and_unresolved_edges.fasta
output: /data/home/wangbo/XTC/result/test/postprocess/sample_genome_read_counts.tsv
log: /data/home/wangbo/XTC/result/test/logs/format_koverage_results_output.log
jobid: 8
reason: Missing output files: /data/home/wangbo/XTC/result/test/postprocess/sample_genome_read_counts.tsv; Input files updated by another job: /data/home/wangbo/XTC/result/test/postprocess/results/sample_coverage.tsv, /data/home/wangbo/XTC/result/test/preprocess/phables.samples.tsv, /data/home/wangbo/XTC/result/test/postprocess/genomes_and_unresolved_edges.fasta
resources: tmpdir=/tmp
Activating conda environment: miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/873ad7e71dfcd9bb5adf1eb8f8dc2377_
Activating conda environment: miniconda3/envs/phables/lib/python3.11/site-packages/phables/workflow/conda/873ad7e71dfcd9bb5adf1eb8f8dc2377_
2024-04-12 16:38:47,662 - INFO - Samples file: /data/home/wangbo/XTC/result/test/preprocess/phables.samples.tsv
2024-04-12 16:38:47,663 - INFO - Koverage results: /data/home/wangbo/XTC/result/test/postprocess/results/sample_coverage.tsv
2024-04-12 16:38:47,663 - INFO - Output path: /data/home/wangbo/XTC/result/test/postprocess/
2024-04-12 16:38:47,707 - INFO - Raw read counts mapped to resolved genomes can be found in /data/home/wangbo/XTC/result/test/postprocess/sample_genome_read_counts.tsv
2024-04-12 16:38:47,707 - INFO - RPKM values of resolved genomes can be found in /data/home/wangbo/XTC/result/test/postprocess/sample_genome_rpkm.tsv
2024-04-12 16:38:47,707 - INFO - Estimated mean read depth of resolved genomes can be found in /data/home/wangbo/XTC/result/test/postprocess/sample_genome_mean_coverage.tsv
2024-04-12 16:38:47,732 - INFO - Sequence information file can be found in /data/home/wangbo/XTC/result/test/postprocess/genomes_and_unresolved_edges_info.tsv
2024-04-12 16:38:47,732 - INFO - Thank you for using format_koverage_results!
[Fri Apr 12 16:38:47 2024]
Finished job 8.
10 of 11 steps (91%) done
Select jobs to execute...
Execute 1 jobs...
[Fri Apr 12 16:38:47 2024]
localrule all:
input: /data/home/wangbo/XTC/result/test/preprocess/edges.fasta, /data/home/wangbo/XTC/result/test/preprocess/temp/test.bam, /data/home/wangbo/XTC/result/test/preprocess/temp/test.bam.bai, /data/home/wangbo/XTC/result/test/preprocess/coverage.tsv, /data/home/wangbo/XTC/result/test/preprocess/edges.fasta.hmmout, /data/home/wangbo/XTC/result/test/preprocess/phrogs_annotations.tsv, /data/home/wangbo/XTC/result/test/phables/resolved_genome_info.txt, /data/home/wangbo/XTC/result/test/phables/resolved_component_info.txt, /data/home/wangbo/XTC/result/test/phables/component_phrogs.txt, /data/home/wangbo/XTC/result/test/postprocess/sample_genome_read_counts.tsv
jobid: 0
reason: Input files updated by another job: /data/home/wangbo/XTC/result/test/phables/component_phrogs.txt, /data/home/wangbo/XTC/result/test/preprocess/phrogs_annotations.tsv, /data/home/wangbo/XTC/result/test/preprocess/coverage.tsv, /data/home/wangbo/XTC/result/test/preprocess/temp/test.bam, /data/home/wangbo/XTC/result/test/preprocess/edges.fasta.hmmout, /data/home/wangbo/XTC/result/test/phables/resolved_genome_info.txt, /data/home/wangbo/XTC/result/test/preprocess/edges.fasta, /data/home/wangbo/XTC/result/test/phables/resolved_component_info.txt, /data/home/wangbo/XTC/result/test/postprocess/sample_genome_read_counts.tsv, /data/home/wangbo/XTC/result/test/preprocess/temp/test.bam.bai
resources: tmpdir=/tmp
[Fri Apr 12 16:38:47 2024]
Finished job 0.
11 of 11 steps (100%) done
Complete log: .snakemake/log/2024-04-12T163350.806415.snakemake.log
Phables ran successfully!
[2024:04:12 16:38:47] Snakemake finished successfully
`
What's more, I tested real datasets(NCBI BioProject number PRJNA756429, PRJNA866269, PRJNA434744), still, no case3 is resolved.
I used phables version 1.3.2 and my operating system is Linux.
I don't think that's the way it should be, and I really want to solve this problem.
The text was updated successfully, but these errors were encountered: