replikation
commented
2 years ago hi, conda is always a pain -.-
the text you provide is difficult to read but in the end it states mv: no se puede efectuar stat' sobre 'binning_results.eps': No existe el archivo o el directorio mv: no se puede efectuar its not my language so assume its something like there is no file? which means no bins were created. (?)
might be that the conda recipe is still strange?
i would btw recommend you to install via conda singularity itself and use that (-profile singularity,local) or ideally use docker which is the preferred and stable solution. because we preinstalled the programs in containers so stuff like this wont happen.
RVanDamme
H1889
Hi again and sorry for the inconveniences. I have run the test with your last update correcting the problem with the nextflow version. Everything goes well until the installation of the conda enviroment for metawrap. This aspect is discussed at the manual. However, I have realize that in the conda config file the version used is not available: withLabel : metawrap { conda = 'ursky::metawrap-mg=1.3'}
There is not any 1.3 version, I think this is the problem and for that reason the conda environment is not created. I have changed it for: withLabel : metawrap { conda = 'ursky::metawrap-mg=1.3.2'}
and the conda environment is now correctly created!
But after a while a new error is shown:
./nextflow run ./MUFFIN --output MUFFIN_TEST --cpus 32 --memory 128g -profile local,conda,test -resume N E X T F L O W ~ version 21.10.6 Launching
./MUFFIN/main.nf[fabulous_babbage] - revision: ab9fe45525 [- ] process > test - [- ] process > sourmash_download_db - executor > local (2) [b6/541637] process > test [ 0%] 0 of 1 [skipped ] process > sourmash_download_db [100%] 1 of 1, stored: 1 ✔ [skipped ] process > checkm_download_db [100%] 1 of 1, stored: 1 ✔ [- ] process > checkm_setup_db [ 0%] 0 of 1 [- ] process > discard_short - executor > local (3) [b6/541637] process > test [ 0%] 0 of 1 [skipped ] process > sourmash_download_db [100%] 1 of 1, stored: 1 ✔ [skipped ] process > checkm_download_db [100%] 1 of 1, stored: 1 ✔ [8e/2054f3] process > checkm_setup_db [ 0%] 0 of 1 [- ] process > discard_short - executor > local (3) [b6/541637] process > test [ 0%] 0 of 1 [skipped ] process > sourmash_download_db [100%] 1 of 1, stored: 1 ✔ [skipped ] process > checkm_download_db [100%] 1 of 1, stored: 1 ✔ [8e/2054f3] process > checkm_setup_db [100%] 1 of 1 ✔ [- ] process > discard_short - executor > local (3) [b6/541637] process > test [100%] 1 of 1 ✔ [skipped ] process > sourmash_download_db [100%] 1 of 1, stored: 1 ✔ [skipped ] process > checkm_download_db [100%] 1 of 1, stored: 1 ✔ [8e/2054f3] process > checkm_setup_db [100%] 1 of 1 ✔ [- ] process > discard_short - executor > local (4) [b6/541637] process > test [100%] 1 of 1 ✔ [skipped ] process > sourmash_download_db [100%] 1 of 1, stored: 1 ✔ [skipped ] process > checkm_download_db [100%] 1 of 1, stored: 1 ✔ [8e/2054f3] process > checkm_setup_db [100%] 1 of 1 ✔ [- ] process > discard_short - executor > local (5) [b6/541637] process > test [100%] 1 of 1 ✔ [skipped ] process > sourmash_download_db [100%] 1 of 1, stored: 1 ✔ [skipped ] process > checkm_download_db [100%] 1 of 1, stored: 1 ✔ [8e/2054f3] process > checkm_setup_db [100%] 1 of 1 ✔ [d0/bb94a3] process > discard_short (1) [ 0%] 0 of 1 executor > local (5) [b6/541637] process > test [100%] 1 of 1 ✔ [skipped ] process > sourmash_download_db [100%] 1 of 1, stored: 1 ✔ [skipped ] process > checkm_download_db [100%] 1 of 1, stored: 1 ✔ [8e/2054f3] process > checkm_setup_db [100%] 1 of 1 ✔ [d0/bb94a3] process > discard_short (1) [ 0%] 0 of 1 executor > local (6) [b6/541637] process > test [100%] 1 of 1 ✔ [skipped ] process > sourmash_download_db [100%] 1 of 1, stored: 1 ✔ [skipped ] process > checkm_download_db [100%] 1 of 1, stored: 1 ✔ [8e/2054f3] process > checkm_setup_db [100%] 1 of 1 ✔ [d0/bb94a3] process > discard_short (1) [100%] 1 of 1 ✔ executor > local (7) [b6/541637] process > test [100%] 1 of 1 ✔ [skipped ] process > sourmash_download_db [100%] 1 of 1, stored: 1 ✔ [skipped ] process > checkm_download_db [100%] 1 of 1, stored: 1 ✔ [8e/2054f3] process > checkm_setup_db [100%] 1 of 1 ✔ [d0/bb94a3] process > discard_short (1) [100%] 1 of 1 ✔ executor > local (9) [b6/541637] process > test [100%] 1 of 1 ✔ [skipped ] process > sourmash_download_db [100%] 1 of 1, stored: 1 ✔ [skipped ] process > checkm_download_db [100%] 1 of 1, stored: 1 ✔ [8e/2054f3] process > checkm_setup_db [100%] 1 of 1 ✔ [d0/bb94a3] process > discard_short (1) [100%] 1 of 1 ✔ executor > local (10) [b6/541637] process > test [100%] 1 of 1 ✔ [skipped ] process > sourmash_download_db [100%] 1 of 1, stored: 1 ✔ [skipped ] process > checkm_download_db [100%] 1 of 1, stored: 1 ✔ [8e/2054f3] process > checkm_setup_db [100%] 1 of 1 ✔ [d0/bb94a3] process > discard_short (1) [100%] 1 of 1 ✔ executor > local (12) executor > local (14) [b6/541637] process > test [100%] 1 of 1 ✔ [skipped ] process > sourmash_download_db [100%] 1 of 1, stored: 1 ✔ [skipped ] process > checkm_download_db [100%] 1 of 1, stored: 1 ✔ [8e/2054f3] process > checkm_setup_db [100%] 1 of 1 ✔ [d0/bb94a3] process > discard_short (1) [100%] 1 of 1 ✔ [1c/08b812] process > merge (1) [100%] 1 of 1 ✔ [b2/7d1748] process > fastp [100%] 1 of 1 ✔ [ca/962cd9] process > spades (1) [100%] 1 of 1 ✔ [f5/e7011e] process > minimap2 (1) [100%] 1 of 1 ✔ [2b/7af319] process > bwa (1) [100%] 1 of 1 ✔ [42/cc5482] process > metabat2 (1) [100%] 1 of 1 ✔ [c0/3ce58d] process > maxbin2 (1) [100%] 1 of 1 ✔ [13/e0de13] process > concoct (1) [100%] 1 of 1 ✔ [31/153ee2] process > refine3 (1) [ 50%] 1 of 2, failed: 1, retries: 1 [- ] process > checkm - [- ] process > sourmash_bins - [- ] process > sourmash_checkm_parser - [skipped ] process > eggnog_download_db [100%] 1 of 1, stored: 1 ✔ [- ] process > eggnog_bin - [- ] process > parser_bin - [64/e95594] process > readme_output [100%] 1 of 1 ✔Error executing process > 'refine3 (1)'
Caused by: Process
refine3 (1)terminated with an error exit status (1)Command executed:
mem=$(echo 128 GB | sed 's/g//g') path_db=$(cat path_db.txt) echo $path_db which checkm > checkm.txt path=$(cat checkm.txt ) path_strip1=$(dirname $path) path_strip2=$(dirname $path_strip1) sed -i 's#/srv/whitlam/bio/db/checkm_data/1.0.0#'"$path_db"'#' $path_strip2/lib/python2.7/site-packages/checkm/DATA_CONFIG echo "checkm done" metawrap bin_refinement -o refined_bins -A maxbin_bin -B bins_dir -t 32 -m $mem mkdir metawrap_bins/ mv refined_bins/metawrap_70_10_bins/*.fa metawrap_bins/ mv refined_bins/metawrap_70_10_bins.stats subset_binning_stats.txt
Command exit status: 1
Command output:
----- Re-evaluating bin quality after contig de-replication is complete! There are still 0 high ----- ----- quality bins. -----
----- making completion and contamination ranking plots for all refinement iterations -----
Loading completion info.... binsAB.stats binsA.stats binsB.stats binsM.stats binsO.stats Plotting completion data... Loading contamination info... Plotting the contamination data... Saving figures binning_results.eps and binning_results.png ...
########################################################################################################################
MOVING OVER TEMPORARY FILES
########################################################################################################################
----- making completion and contamination ranking plots of final outputs -----
Loading completion info.... bins_dir.stats maxbin_bin.stats metawrap_70_10_bins.stats Plotting completion data... Loading contamination info... Plotting the contamination data... Saving figures binning_results.eps and binning_results.png ...
----- making contig membership files (for Anvio and other applications) -----
summarizing metawrap_70_10_bins ...
########################################################################################################################
BIN_REFINEMENT PIPELINE FINISHED SUCCESSFULLY!
########################################################################################################################
Command error:
executor > local (14) [b6/541637] process > test [100%] 1 of 1 ✔ [skipped ] process > sourmash_download_db [100%] 1 of 1, stored: 1 ✔ [skipped ] process > checkm_download_db [100%] 1 of 1, stored: 1 ✔ [8e/2054f3] process > checkm_setup_db [100%] 1 of 1 ✔ [d0/bb94a3] process > discard_short (1) [100%] 1 of 1 ✔ [1c/08b812] process > merge (1) [100%] 1 of 1 ✔ [b2/7d1748] process > fastp [100%] 1 of 1 ✔ [ca/962cd9] process > spades (1) [100%] 1 of 1 ✔ [f5/e7011e] process > minimap2 (1) [100%] 1 of 1 ✔ [2b/7af319] process > bwa (1) [100%] 1 of 1 ✔ [42/cc5482] process > metabat2 (1) [100%] 1 of 1 ✔ [c0/3ce58d] process > maxbin2 (1) [100%] 1 of 1 ✔ [13/e0de13] process > concoct (1) [100%] 1 of 1 ✔ [31/153ee2] process > refine3 (1) [100%] 2 of 2, failed: 2, retries: 1 ✘ [- ] process > checkm - [- ] process > sourmash_bins - [- ] process > sourmash_checkm_parser - [skipped ] process > eggnog_download_db [100%] 1 of 1, stored: 1 ✔ [- ] process > eggnog_bin - [- ] process > parser_bin - [64/e95594] process > readme_output [100%] 1 of 1 ✔ Error executing process > 'refine3 (1)'
Caused by: Process
refine3 (1)terminated with an error exit status (1)Command executed:
mem=$(echo 128 GB | sed 's/g//g') path_db=$(cat path_db.txt) echo $path_db which checkm > checkm.txt path=$(cat checkm.txt ) path_strip1=$(dirname $path) path_strip2=$(dirname $path_strip1) sed -i 's#/srv/whitlam/bio/db/checkm_data/1.0.0#'"$path_db"'#' $path_strip2/lib/python2.7/site-packages/checkm/DATA_CONFIG echo "checkm done" metawrap bin_refinement -o refined_bins -A maxbin_bin -B bins_dir -t 32 -m $mem mkdir metawrap_bins/ mv refined_bins/metawrap_70_10_bins/*.fa metawrap_bins/ mv refined_bins/metawrap_70_10_bins.stats subset_binning_stats.txt
Command exit status: 1
Command output:
----- Re-evaluating bin quality after contig de-replication is complete! There are still 0 high ----- ----- quality bins. -----
----- making completion and contamination ranking plots for all refinement iterations -----
Loading completion info.... binsAB.stats binsA.stats binsB.stats binsM.stats binsO.stats Plotting completion data... Loading contamination info... Plotting the contamination data... Saving figures binning_results.eps and binning_results.png ...
########################################################################################################################
MOVING OVER TEMPORARY FILES
########################################################################################################################
----- making completion and contamination ranking plots of final outputs -----
Loading completion info.... bins_dir.stats maxbin_bin.stats metawrap_70_10_bins.stats Plotting completion data... Loading contamination info... Plotting the contamination data... Saving figures binning_results.eps and binning_results.png ...
----- making contig membership files (for Anvio and other applications) -----
summarizing metawrap_70_10_bins ...
########################################################################################################################
BIN_REFINEMENT PIPELINE FINISHED SUCCESSFULLY!
########################################################################################################################
Command error:
[CheckM - qa] Tabulating genome statistics.
mv: no se puede efectuar
stat' sobre 'binning_results.eps': No existe el archivo o el directorio mv: no se puede efectuarstat' sobre 'binsC': No existe el archivo o el directorio mv: no se puede efectuar `stat' sobre 'binning_results.eps': No existe el archivo o el directorio cat: 'metawrap_70_10_bins/.fa': No existe el archivo o el directorioreal 16m35,180s user 22m53,817s sys 1m23,580s mv: no se puede efectuar `stat' sobre 'refined_bins/metawrap_70_10_bins/*.fa': No existe el archivo o el directorio
Work dir: /media/yomismo/Datos/work/31/153ee281cd2f483b50b2ab4077aa88
Tip: you can replicate the issue by changing to the process work dir and entering the command
bash .command.runThanks for the help in advance.