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ascheben / msa_pipeline

Multiple sequence alignment pipeline
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Error: Insufficient sites with >0.9 sample coverage in results/tree/roast_noN.fa. #2

Closed polchan closed 12 months ago

polchan commented 12 months ago

Hello! Armin I used the Call_conversation in msa_pipeline, but it errored me as below:

Found Snakefile: workflow/Snakefile. Executing test analysis. Config file config/config.yaml is extended by additional config specified via the command line. Building DAG of jobs... Your conda installation is not configured to use strict channel priorities. This is however crucial for having robust and correct environments (for details, see https://conda-forge.org/docs/user/tipsandtricks.html). Please consider to configure strict priorities by executing 'conda config --set channel_priority strict'. Using shell: /usr/bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Singularity containers: ignored Job stats: job count min threads max threads call_conservation 1 1 1 cds_fold 1 1 1 clean_maf 1 1 1 filtN 1 1 1 filtcols 1 1 1 gerp_clean 1 1 1 maf2fa 1 1 1 maf2fold 1 1 1 maf_split 1 1 1 phylofit 1 1 1 raxml 1 8 8 sitefold2bed 1 1 1 trimcols 1 1 1 total 13 1 8 Select jobs to execute... [Wed Nov 15 12:08:59 2023] rule cds_fold: input: data/MdHF.fa output: results/tree/sitefold.txt log: logs/cds_foldlog.txt jobid: 12 reason: Missing output files: results/tree/sitefold.txt resources: tmpdir=/tmp Activating conda environment: .snakemake/conda/7e29029ac4d1260a5defa3a8c8662fcc Activating conda environment: .snakemake/conda/7e29029ac4d1260a5defa3a8c8662fcc_ [Wed Nov 15 12:17:40 2023] Finished job 12. 1 of 13 steps (8%) done Select jobs to execute... [Wed Nov 15 12:17:40 2023] rule sitefold2bed: input: results/tree/sitefold.txt output: results/tree/sitefold.bed log: logs/sitefold2bed_log.txt jobid: 11 reason: Missing output files: results/tree/sitefold.bed; Input files updated by another job: results/tree/sitefold.txt resources: tmpdir=/tmp [Wed Nov 15 12:17:40 2023] Finished job 11. 2 of 13 steps (15%) done Removing temporary output results/tree/sitefold.txt. Select jobs to execute... [Wed Nov 15 12:17:40 2023] rule maf2fold: input: results/roast/roast.maf, results/tree/sitefold.bed output: results/roast/roast.sitefold.maf log: logs/maf2foldlog.txt jobid: 10 reason: Missing output files: results/roast/roast.sitefold.maf; Input files updated by another job: results/tree/sitefold.bed resources: tmpdir=/tmp Activating conda environment: .snakemake/conda/45029268ad8b9444e2538700341456f4 [Wed Nov 15 12:18:17 2023] Finished job 10. 3 of 13 steps (23%) done Select jobs to execute... [Wed Nov 15 12:18:17 2023] rule clean_maf: input: results/roast/roast.sitefold.maf output: results/roast/roast.sitefold.clean.maf jobid: 9 reason: Missing output files: results/roast/roast.sitefold.clean.maf; Input files updated by another job: results/roast/roast.sitefold.maf resources: tmpdir=/tmp [Wed Nov 15 12:18:17 2023] Finished job 9. 4 of 13 steps (31%) done Removing temporary output results/roast/roast.sitefold.maf. Select jobs to execute... [Wed Nov 15 12:18:17 2023] rule maf2fa: input: results/roast/roast.sitefold.clean.maf output: results/tree/roast.fa log: logs/maf2fa_log.txt jobid: 8 benchmark: benchmark/maf2fabm.txt reason: Missing output files: results/tree/roast.fa; Input files updated by another job: results/roast/roast.sitefold.clean.maf resources: tmpdir=/tmp Activating conda environment: .snakemake/conda/7e29029ac4d1260a5defa3a8c8662fcc Activating conda environment: .snakemake/conda/7e29029ac4d1260a5defa3a8c8662fcc_ [Wed Nov 15 12:18:18 2023] Finished job 8. 5 of 13 steps (38%) done Removing temporary output results/roast/roast.sitefold.clean.maf. Select jobs to execute... [Wed Nov 15 12:18:18 2023] rule filtN: input: results/tree/roast.fa output: results/tree/roast_noN.fa log: logs/filtn_log.txt jobid: 7 benchmark: benchmark/filtn_bm.txt reason: Missing output files: results/tree/roast_noN.fa; Input files updated by another job: results/tree/roast.fa resources: tmpdir=/tmp Benchmark: unable to collect cpu and memory benchmark statistics [Wed Nov 15 12:18:18 2023] Finished job 7. 6 of 13 steps (46%) done Removing temporary output results/tree/roast.fa. Select jobs to execute... [Wed Nov 15 12:18:18 2023] rule filtcols: input: results/tree/roast_noN.fa output: results/tree/roast_mincol.fa log: logs/filtcols_log.txt jobid: 6 benchmark: benchmark/filtcols_bm.txt reason: Missing output files: results/tree/roast_mincol.fa; Input files updated by another job: results/tree/roastnoN.fa resources: tmpdir=/tmp Activating conda environment: .snakemake/conda/7e29029ac4d1260a5defa3a8c8662fcc WARNING: Removing sequence 'MdGDDH' composed only by gaps WARNING: Removing sequence 'MdGala' composed only by gaps WARNING: Removing sequence 'MdHF' composed only by gaps WARNING: Removing sequence 'MdHoney' composed only by gaps WARNING: Removing sequence 'Mbacc' composed only by gaps WARNING: Removing sequence 'MdOregonSpur' composed only by gaps WARNING: Removing sequence 'Mfusca' composed only by gaps WARNING: Removing sequence 'Mprun' composed only by gaps WARNING: Removing sequence 'Msieve' composed only by gaps WARNING: Removing sequence 'Msylve' composed only by gaps WARNING: Removing sequence 'MdRoyal' composed only by gaps WARNING: Removing sequence 'Cpinn' composed only by gaps WARNING: Removing sequence 'Pbret' composed only by gaps WARNING: Removing sequence 'Pcomm' composed only by gaps WARNING: Removing sequence 'PpCuiG' composed only by gaps WARNING: Removing sequence 'Psin' composed only by gaps WARNING: Removing sequence 'Mhupe' composed only by gaps WARNING: Removing sequence 'Erijapo' composed only by gaps WARNING: Removing sequence 'Fichisp' composed only by gaps WARNING: Removing sequence 'Ficmicr' composed only by gaps WARNING: Removing sequence 'Fravesc' composed only by gaps WARNING: Removing sequence 'Prupers' composed only by gaps WARNING: Removing sequence 'Moralba' composed only by gaps WARNING: Removing sequence 'Mornota' composed only by gaps WARNING: Removing sequence 'Moryunn' composed only by gaps WARNING: Removing sequence 'Ddrum' composed only by gaps WARNING: Removing sequence 'Gtrif' composed only by gaps WARNING: Removing sequence 'Parande' composed only by gaps WARNING: Removing sequence 'Prumume' composed only by gaps WARNING: Removing sequence 'Rchin' composed only by gaps WARNING: Removing sequence 'Ridae' composed only by gaps WARNING: Removing sequence 'Rocci' composed only by gaps WARNING: Removing sequence 'Rrugo' composed only by gaps WARNING: Removing sequence 'Treorie' composed only by gaps WARNING: Removing sequence 'Zjuju' composed only by gaps WARNING: Removing sequence 'Zmaur' composed only by gaps WARNING: Removing sequence 'Boenive' composed only by gaps WARNING: Removing sequence 'Casttibe' composed only by gaps WARNING: Removing sequence 'Quacut' composed only by gaps WARNING: Removing sequence 'Viariz' composed only by gaps WARNING: Removing sequence 'Vivisy' composed only by gaps WARNING: Output alignment has not been generated. It is empty. ERROR: Insufficient sites with >0.9 sample coverage in results/tree/roast_noN.fa. Check coverage in multiple alignment results/roast/roast.maf. Note that some highly diverged genomes may require tuning/changing of the aligner to achieve adequate coverage. Waiting at most 5 seconds for missing files. MissingOutputException in rule filtcols in file /ngsproject/bcguo/tools/msa_pipeline/workflow/./rules/call_conservation.smk, line 100: Job 6 completed successfully, but some output files are missing. Missing files after 5 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait: results/tree/roast_mincol.fa Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message

I tried using another reference gff, and this issue no longer occurs. But I wanted to use the original gff file as a reference, How can I solve this issue? Can you help me solve this issue?

best-wish

Bo-Cheng

polchan commented 12 months ago

Sorry, I think I have solve this issue.