Closed MartonaAlvarez closed 1 year ago
isovic
commented
2 years ago Hi @MartonaAlvarez,
Can you please post the entire stderr of the ipa local output (not just this last chunk)?
There seems to be something wrong in the DB construction stage.
Can you also please verify that bothrioHiFi_reads.fastq is a valid FASTQ file?
Best regards, Ivan.
MartonaAlvarez
commented
2 years ago Hi @isovic , thanks for your response. Here is the output complete. Regarding the fastq file, yes, it is valid.
INFO: /home_new/jordi/soft/miniconda3/envs/ipa/bin/ipa local -i bothrioHiFi_reads.fastq --njobs 2 --nthreads 25 --genome-size 4943861964 --coverage 18 --resume
INFO: ipa.py ipa (wrapper) version=1.5.0 ... Checking dependencies ...
INFO: Dependencies
/home_new/jordi/soft/miniconda3/envs/ipa/bin/python3
/home_new/jordi/soft/miniconda3/envs/ipa/bin/ipa2-task
/home_new/jordi/soft/miniconda3/envs/ipa/bin/falconc
/home_new/jordi/soft/miniconda3/envs/ipa/bin/minimap2
/home_new/jordi/soft/miniconda3/envs/ipa/bin/nighthawk
/home_new/jordi/soft/miniconda3/envs/ipa/bin/pancake
/home_new/jordi/soft/miniconda3/envs/ipa/bin/pblayout
/home_new/jordi/soft/miniconda3/envs/ipa/bin/racon
/home_new/jordi/soft/miniconda3/envs/ipa/bin/samtools
/home_new/jordi/soft/miniconda3/envs/ipa/bin/ipa_purge_dups
/home_new/jordi/soft/miniconda3/envs/ipa/bin/ipa_purge_dups_split_fa
snakemake version=7.1.0
ipa2-task 1.5.0 (commit c875fce13bdacbafc2f4f750c6438f4453e1354d)
Machine name: 'Linux'
Copyright (C) 2004-2021 Pacific Biosciences of California, Inc.
This program comes with ABSOLUTELY NO WARRANTY; it is intended for
Research Use Only and not for use in diagnostic procedures.
falconc version=1.13.1+git.f9d1b5651e891efe379bd9727a0fa0931b875d7b, nim-version=1.5.1
minimap2 version=2.24-r1122
Nighthawk 0.1.0 (commit SL-release-10.1.0-7-gbe5dfb1*)
pancake 1.3.0 (commit SEQII-release-10.1.0-432-gf2693fd*)
pblayout 1.0.0 (commit SL-release-10.1.0-152-g66936d1*)
racon version=v1.4.20
samtools 1.15
Using htslib 1.14
ipa_purge_dups Version: 1.2.5
To run this yourself:
/home_new/jordi/soft/miniconda3/envs/ipa/bin/python3 -m snakemake -j 2 -d RUN -p -s /home_new/jordi/soft/miniconda3/envs/ipa/etc/ipa.snakefile --configfile RUN/config.yaml --reason
Starting snakemake ...
CWD:/mnt/iscsi01-copy/userdir/Bothrioplana/ipa/RUN
NPROC:25
NPROC_SERIAL:25
config:{'advanced_options': '', 'coverage': 18, 'genome_size': 4943861964, 'm4filt_high_copy_sample_rate': 1.0, 'max_nchunks': 40, 'nproc': 25, 'phase_run': 1, 'polish_run': 1, 'purge_dups_calcuts': '', 'purge_dups_run': 1, 'reads_fn': 'RUN/input.fofn', 'tmp_dir': '/tmp'}
Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 2
Rules claiming more threads will be scaled down.
Job stats:
job count min threads max threads
---------------------- ------- ------------- -------------
assemble 1 1 1
build_db 1 1 1
final 1 1 1
finish 1 1 1
ovl_asym_merge 1 1 1
ovl_asym_prepare 1 1 1
ovl_filter 1 1 1
phasing_merge 1 1 1
phasing_prepare 1 1 1
polish_merge 1 1 1
polish_prepare 1 1 1
purge_dups_map_merge 1 1 1
purge_dups_map_prepare 1 1 1
purge_dups_paf 1 1 1
separate_p_from_a 1 1 1
total 15 1 1
Select jobs to execute...
[Mon Mar 14 10:15:52 2022]
rule build_db:
input: /mnt/iscsi01-copy/userdir/Bothrioplana/ipa/RUN/input.fofn, 01-generate_config/generated.config
output: 02-build_db/reads.seqdb, 02-build_db/reads.seeddb, 02-build_db/reads.seqdb.0.seq, 02-build_db/reads.seeddb.0.seeds, 02-build_db/input.fofn
jobid: 5
reason: Missing output files: 02-build_db/reads.seqdb
resources: tmpdir=/tmp
wd=$(dirname 02-build_db/reads.seqdb)
mkdir -p $wd
cd $wd
rel=..
input_reads_fn="/mnt/iscsi01-copy/userdir/Bothrioplana/ipa/RUN/input.fofn" params_db_prefix="reads" params_config_sh_fn="$rel/01-generate_config/generated.config" params_num_threads=25 params_log_level="INFO" params_tmp_dir="/tmp" time ipa2-task build_db
/mnt/iscsi01-copy/userdir/Bothrioplana/ipa/RUN /mnt/iscsi01-copy/userdir/Bothrioplana/ipa/RUN/02-build_db
/mnt/iscsi01-copy/userdir/Bothrioplana/ipa/RUN/02-build_db
/mnt/iscsi01-copy/userdir/Bothrioplana/ipa/bothrioHiFi_reads.fastq
>|> 20220314 11:57:02.418 -|- INFO -|- Runner -|- 0x7f35392e5780|| -|- Loading the input DBs.
Command exited with non-zero status 139
5727.91user 404.48system 1:42:15elapsed 99%CPU (0avgtext+0avgdata 2127640maxresident)k
0inputs+46524440outputs (0major+960864minor)pagefaults 0swaps
[Mon Mar 14 11:58:07 2022]
Error in rule build_db:
jobid: 5
output: 02-build_db/reads.seqdb, 02-build_db/reads.seeddb, 02-build_db/reads.seqdb.0.seq, 02-build_db/reads.seeddb.0.seeds, 02-build_db/input.fofn
shell:
wd=$(dirname 02-build_db/reads.seqdb)
mkdir -p $wd
cd $wd
rel=..
input_reads_fn="/mnt/iscsi01-copy/userdir/Bothrioplana/ipa/RUN/input.fofn" params_db_prefix="reads" params_config_sh_fn="$rel/01-generate_config/generated.config" params_num_threads=25 params_log_level="INFO" params_tmp_dir="/tmp" time ipa2-task build_db
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Removing output files of failed job build_db since they might be corrupted:
02-build_db/reads.seqdb.0.seq, 02-build_db/input.fofn
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /mnt/iscsi01-copy/userdir/Bothrioplana/ipa/RUN/.snakemake/log/2022-03-14T101551.012769.snakemake.log
ERROR: Command '/home_new/jordi/soft/miniconda3/envs/ipa/bin/python3 -m snakemake -j 2 -d RUN -p -s /home_new/jordi/soft/miniconda3/envs/ipa/etc/ipa.snakefile --configfile RUN/config.yaml --reason' returned non-zero exit status 1.
Exiting.Thanks,
Marta
MartonaAlvarez
commented
2 years ago Hi,
I solved the first error and managed to get it running, however, it stops at Snakemake step 5 and I don't understand why. This is the message from snakemake:
Error in rule ovl_asym_merge:
jobid: 13
output: 05-ovl_asym_merge/ovl.merged.m4, 05-ovl_asym_merge/ovl.nonlocal.m4
shell:
wd=$(dirname 05-ovl_asym_merge/ovl.merged.m4)
mkdir -p $wd
cd $wd
rel=..
# We must change rel-path names when we chdir.
for fn in 04-ovl_asym_run/18/ovl.sorted.m4 04-ovl_asym_run/32/ovl.sorted.m4 04-ovl_asym_run/12/ovl.sorted.m4 04-ovl_asym_run/16/ovl.sorted.m4 04-ovl_asym_run/30/ovl.sorted.m4 04-ovl_asym_run/29/ovl.sorted.m4 04-ovl_asym_run/23/ovl.sorted.m4 04-ovl_asym_run/31/ovl.sorted.m4 04-ovl_asym_run/1/ovl.sorted.m4 04-ovl_asym_run/5/ovl.sorted.m4 04-ovl_asym_run/25/ovl.sorted.m4 04-ovl_asym_run/0/ovl.sorted.m4 04-ovl_asym_run/4/ovl.sorted.m4 04-ovl_asym_run/37/ovl.sorted.m4 04-ovl_asym_run/38/ovl.sorted.m4 04-ovl_asym_run/6/ovl.sorted.m4 04-ovl_asym_run/2/ovl.sorted.m4 04-ovl_asym_run/9/ovl.sorted.m4 04-ovl_asym_run/33/ovl.sorted.m4 04-ovl_asym_run/10/ovl.sorted.m4 04-ovl_asym_run/17/ovl.sorted.m4 04-ovl_asym_run/14/ovl.sorted.m4 04-ovl_asym_run/3/ovl.sorted.m4 04-ovl_asym_run/24/ovl.sorted.m4 04-ovl_asym_run/27/ovl.sorted.m4 04-ovl_asym_run/20/ovl.sorted.m4 04-ovl_asym_run/35/ovl.sorted.m4 04-ovl_asym_run/13/ovl.sorted.m4 04-ovl_asym_run/19/ovl.sorted.m4 04-ovl_asym_run/26/ovl.sorted.m4 04-ovl_asym_run/34/ovl.sorted.m4 04-ovl_asym_run/39/ovl.sorted.m4 04-ovl_asym_run/36/ovl.sorted.m4 04-ovl_asym_run/8/ovl.sorted.m4 04-ovl_asym_run/28/ovl.sorted.m4 04-ovl_asym_run/11/ovl.sorted.m4 04-ovl_asym_run/22/ovl.sorted.m4 04-ovl_asym_run/15/ovl.sorted.m4 04-ovl_asym_run/21/ovl.sorted.m4 04-ovl_asym_run/7/ovl.sorted.m4; do
echo $rel/$fn
done >| ./sorted.fofn
input_fofn=./sorted.fofn params_num_threads="25" params_db_prefix=reads params_config_sh_fn="$rel/01-generate_config/generated.config" params_log_level="INFO" params_tmp_dir="/tmp" time ipa2-task ovl_asym_merge
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Removing output files of failed job ovl_asym_merge since they might be corrupted:
05-ovl_asym_merge/ovl.merged.m4
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /mnt/iscsi01-copy/userdir/Bothrioplana/ipa/RUN/.snakemake/log/2022-03-15T092702.530410.snakemake.logAny help will be welcome. I have tried rerunning with the --resume flag and tried to run the snakemake commands only. But always get the same error.
Thanks, Marta
isovic
commented
2 years ago Hi Marta,
Can you please describe how you solved the first issue, for future reference?
I solved the first error and managed to get it running, however, it stops at Snakemake step 5 and I don't understand why. This is the message from snakemake:
Is there anything else written to stderr which might provide more info?
Snakemake output, like the one you copy/pasted, is good at telling us that something went wrong, but not exactly what happened.
The actual error messages, if there are any, are usually located just above/below this for an ipa local run, or in the cluster log file for that stage (located in RUN/qsub_log/).
This stage is actually very simple - all it does, literally, is concatenating all overlap files, sorting them and removing local alignments; all of which is done using standard Bash tools.
Is it possible that your disk is full?
Or that the temporary directory is not available on your system or is full (/tmp)?
In this case, try running IPA with this additional parameter: `--tmp-dir "./"
Best regards, Ivan.
MartonaAlvarez
commented
2 years ago Hi Ivan,
thanks for your reply. For getting it running I splitted the input files to the original files I had from the demultiplexing step. It worked well.
It seems that the error this time was the one about the tmp dir, because I changed it to --tmp-dir ${PWD} and it worked.
The RUN/qsub_log/ directory is empty, so I only can give you information about the snakemake log file, I'm afraid.
Now the error is in step 9 (assembly). I've tried to rerun, but it doesn't work this time.
´´´ Finished job 11. 44 of 53 steps (83%) done Select jobs to execute...
[Sun Mar 27 16:45:24 2022] rule assemble: input: /mnt/iscsi01-copy/userdir/Bothrioplana/ipa/RUN/input.fofn, 02-build_db/reads.seqdb, 09-ovl_filter/ovl.final.m4, 08-phasing_merge/ovl.phased.m4, 01-generate_config/generated.config output: 10-assemble/p_ctg.fasta, 10-assemble/a_ctg.fasta, 10-assemble/p_ctg_tiling_path, 10-assemble/a_ctg_tiling_path, 10-assemble/p_ctg.fasta.fai, 10-assemble/a_ctg.fasta.fai, 10-assemble/read_to_contig.paf, 10-assemble/circular_contigs.csv jobid: 10 reason: Missing output files: 10-assemble/p_ctg.fasta, 10-assemble/a_ctg.fasta, 10-assemble/a_ctg.fasta.fai, 10-assemble/read_to_contig.paf, 10-assemble/p_ctg.fasta.fai; Input files updated by another job: 09-ovl_filter/ovl.final.m4, 08-phasing_merge/ovl.phased.m4 resources: tmpdir=/tmp
wd=$(dirname 10-assemble/p_ctg.fasta)
mkdir -p $wd
cd $wd
rel=..
output_read_to_contig=$(basename 10-assemble/read_to_contig.paf) input_seqdb="$rel/02-build_db/reads.seqdb" input_m4="$rel/09-ovl_filter/ovl.final.m4" input_m4_phasing_merge="$rel/08-phasing_merge/ovl.phased.m4" input_reads="/mnt/iscsi01-copy/userdir/Bothrioplana/ipa/RUN/input.fofn" params_ctg_prefix=ctg params_num_threads=25 params_config_sh_fn="$rel/01-generate_config/generated.config" params_log_level="INFO" params_tmp_dir="/mnt/iscsi01-copy/userdir/Bothrioplana/ipa" time ipa2-task assemble[Sun Mar 27 16:45:24 2022] Error in rule assemble: jobid: 10 output: 10-assemble/p_ctg.fasta, 10-assemble/a_ctg.fasta, 10-assemble/p_ctg_tiling_path, 10-assemble/a_ctg_tiling_path, 10-assemble/p_ctg.fasta.fai, 10-assemble/a_ctg.fasta.fai, 10-assemble/read_to_contig.paf, 10-assemble/circular_contigs.csv shell:
wd=$(dirname 10-assemble/p_ctg.fasta)
mkdir -p $wd
cd $wd
rel=..
output_read_to_contig=$(basename 10-assemble/read_to_contig.paf) input_seqdb="$rel/02-build_db/reads.seqdb" input_m4="$rel/09-ovl_filter/ovl.final.m4" input_m4_phasing_merge="$rel/08-phasing_merge/ovl.phased.m4" input_reads="/mnt/iscsi01-copy/userdir/Bothrioplana/ipa/RUN/input.fofn" params_ctg_prefix=ctg params_num_threads=25 params_config_sh_fn="$rel/01-generate_config/generated.config" params_log_level="INFO" params_tmp_dir="/mnt/iscsi01-copy/userdir/Bothrioplana/ipa" time ipa2-task assemble
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message The params used to generate one or several output files has changed: To inspect which output files have changes, run 'snakemake --list-params-changes'. To trigger a re-run, use 'snakemake -R $(snakemake --list-params-changes)'. Complete log: /mnt/iscsi01-copy/userdir/Bothrioplana/ipa/RUN/.snakemake/log/2022-03-22T115640.011885.snakemake.log ´´´
I've tried running : snakemake --list-params-changes and it returns: Error: no Snakefile found, tried Snakefile, snakefile, workflow/Snakefile, workflow/snakefile
Also: snakemake -R $(snakemake --list-params-changes) returns: Error: you need to specify the maximum number of CPU cores to be used at the same time. If you want to use N cores, say --cores N or -cN. For all cores on your system (be sure that this is appropriate) use --cores all. For no parallelization use --cores 1 or -c1.
So, I've tried specifying number of cores, but it doesn't recognise the parameter. So I am lost here, don't know how to get my run finished. Any clue will be welcome.
Thanks
Marta
MartonaAlvarez
commented
1 year ago Hi,
I've seen that my issue has been closed as resolved, but I didn't get any answer about the last problem I had...
Thanks
Marta
Missatge de Armin Töpfer @.***> del dia dl., 14 de nov. 2022 a les 16:29:
Closed #479 https://github.com/PacificBiosciences/pbbioconda/issues/479 as completed.
— Reply to this email directly, view it on GitHub https://github.com/PacificBiosciences/pbbioconda/issues/479#event-7805388603, or unsubscribe https://github.com/notifications/unsubscribe-auth/AT7BTRABAASXPEVO56X3W3LWIJLFJANCNFSM5QPNKZ6A . You are receiving this because you were mentioned.Message ID: @.*** com>
Operating system Which operating system and version are you using? I am working on a server with:
Package name Which package / tool is causing the problem? Which version are you using, use
tool --version. Have you updated to the latest versionconda update package? Have you updated the complete env by runningconda update --all? Have you ensured that your channel priorities are set up according to the bioconda recommendations at https://bioconda.github.io/#set-up-channels?I am using IPA installed with conda with all last versions.
Conda environment What is the result of
conda list? (Try to paste that between triple backticks.)Describe the bug A clear and concise description of what the bug is. I have run the IPA program to assemble a genome with HiFi reads, but it always stops at the same step, giving the same message. This is the code: ipa local -i bothrioHiFi_reads.fastq --njobs 2 --nthreads 25 --genome-size 4943861964 --coverage 18 I have tried to restart it, with the --resume flag, as I have seen in some posts, but it keeps failing. I have also tried to run snakemake alone, with the command line indicated in the log file, but it doesn't work either. miniconda3/envs/ipa/bin/python3 -m snakemake -j 2 -d RUN -p -s miniconda3/envs/ipa/etc/ipa.snakefile --configfile RUN/config.yaml --reason I don't know what could be wrong.
Error message Paste the error message / stack.
To Reproduce Steps to reproduce the behavior. Providing a minimal test dataset on which we can reproduce the behavior will generally lead to quicker turnaround time!
Expected behavior A clear and concise description of what you expected to happen.