Open mlpereira87 opened 10 months ago
Hello can you replace your image to this image:
cd /home/aicampos/miniconda3/envs/Culebront/lib/python3.10/sitepackages/culebrONT/containers
rm Singularity.culebront_tools.sif
singularity pull Singularity.culebront_tools.sif oras://registry.forge.ird.fr/diade/culebront_pipeline/apptainer/apptainer.culebront_tools.sif:0.0.1
Thank you for the reply. I was able to download the image and use it but I am facing another problem:
I could only run the pipeline test if I install the test folder in /tmp directory: culebrONT test_install -d /tmp/
If I install it in another directory, for example in my user home dir: culebrONT test_install -d /home/aicampos/
The pipeline cannot find the input fastq:
Error in rule run_flye:
jobid: 7
input: /home/aicampos/test_temp/Data-Xoo-sub/fastq/5PXoo1.fastq.gz
output: /home/aicampos/test_temp/culebrONT_OUTPUT/5PXoo1/ASSEMBLERS/FLYE/ASSEMBLER/assembly.fasta, /home/aicampos/test_temp/culebrONT_OUTPUT/5PXoo1/ASSEMBLERS/FLYE/ASSEMBLER/assembly_info.txt, /home/aicampos/test_temp/culebrONT_OUTPUT/5PXoo1/ASSEMBLERS/FLYE/ASSEMBLER/FLYE-version.txt
log: /home/aicampos/test_temp/culebrONT_OUTPUT/5PXoo1/ASSEMBLERS/FLYE/ASSEMBLER/LOGS/5PXoo1_FLYE.o, /home/aicampos/test_temp/culebrONT_OUTPUT/5PXoo1/ASSEMBLERS/FLYE/ASSEMBLER/LOGS/5PXoo1_FLYE.e (check log file(s) for error details)
shell:
[ ! -f /home/aicampos/test_temp/culebrONT_OUTPUT/5PXoo1/ASSEMBLERS/FLYE/ASSEMBLER/FLYE-version.txt ] && [ ! -d versions ] && mkdir -p versions; flye --version > /home/aicampos/test_temp/culebrONT_OUTPUT/5PXoo1/ASSEMBLERS/FLYE/ASSEMBLER/FLYE-version.txt
ln -s -f /home/aicampos/test_temp/culebrONT_OUTPUT/5PXoo1/ASSEMBLERS/FLYE/ASSEMBLER/FLYE-version.txt /home/aicampos/test_temp/culebrONT_OUTPUT/versions/FLYE-version.txt
(flye --nano-raw /home/aicampos/test_temp/Data-Xoo-sub/fastq/5PXoo1.fastq.gz --genome-size 4.8m --out-dir /home/aicampos/test_temp/culebrONT_OUTPUT/5PXoo1/ASSEMBLERS/FLYE/ASSEMBLER/ --threads 1;
echo /home/aicampos/test_temp/culebrONT_OUTPUT/5PXoo1/ASSEMBLERS/FLYE/ASSEMBLER//assembly.fasta /home/aicampos/test_temp/culebrONT_OUTPUT/5PXoo1/ASSEMBLERS/FLYE/ASSEMBLER/assembly.fasta) 1>/home/aicampos/test_temp/culebrONT_OUTPUT/5PXoo1/ASSEMBLERS/FLYE/ASSEMBLER/LOGS/5PXoo1_FLYE.o 2>/home/aicampos/test_temp/culebrONT_OUTPUT/5PXoo1/ASSEMBLERS/FLYE/ASSEMBLER/LOGS/5PXoo1_FLYE.e
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Logfile /home/aicampos/test_temp/culebrONT_OUTPUT/5PXoo1/ASSEMBLERS/FLYE/ASSEMBLER/LOGS/5PXoo1_FLYE.o: empty file
The error file /home/aicampos/test_temp/culebrONT_OUTPUT/5PXoo1/ASSEMBLERS/FLYE/ASSEMBLER/LOGS/5PXoo1_FLYE.e contains the following:
[2023-10-23 15:14:30] INFO: Starting Flye 2.9.2-b1786
[2023-10-23 15:14:30] ERROR: Can't open /home/aicampos/test_temp/Data-Xoo-sub/fastq/5PXoo1.fastq.gz
[2023-10-23 15:14:30] ERROR: Pipeline aborted
However the fastq file exist. Also, if i run the Flye command with singularity but without using the culebrONT main command it works:
singularity exec /home/aicampos/miniconda3/envs/Culebront/lib/python3.10/site-packages/culebrONT/containers/Singularity.culebront_tools.sif flye --nano-raw /home/aicampos/test_temp/Data-Xoo-sub/fastq/5PXoo1.fastq.gz --genome-size 4.8m --out-dir /home/aicampos/test_temp/culebrONT_OUTPUT/5PXoo1/ASSEMBLERS/FLYE/ASSEMBLER/ --threads 1
Output:
[2023-10-23 15:18:08] INFO: Starting Flye 2.9.2-b1786
[2023-10-23 15:18:08] INFO: >>>STAGE: configure
[2023-10-23 15:18:08] INFO: Configuring run
[2023-10-23 15:18:09] INFO: Total read length: 63698302
[2023-10-23 15:18:09] INFO: Input genome size: 4800000
[2023-10-23 15:18:09] INFO: Estimated coverage: 13
[2023-10-23 15:18:09] INFO: Reads N50/N90: 16019 / 4163
[2023-10-23 15:18:09] INFO: Minimum overlap set to 4000
[2023-10-23 15:18:09] INFO: >>>STAGE: assembly
[2023-10-23 15:18:09] INFO: Assembling disjointigs
[2023-10-23 15:18:09] INFO: Reading sequences
The same happen if I try to run CulebrONT with my data.
Maybe there is a problem with Snakemake not recognizing some directories...
How do you configure binding of singularity? https://apptainer.org/docs/user/main/bind_paths_and_mounts.html https://snakemake.readthedocs.io/en/stable/executing/cli.html#singularity https://culebront-pipeline.readthedocs.io/en/latest/FAQ.html#frequently-asked-questions
please try with
culebrONT run_local -c /home/aicampos/test_temp/data_test_config.yaml --singularity-args "--bind /$HOME:/$HOME"
Thank you for the reply! The pipeline can recognize my data now, but another problem was detected:
When I try to run with these configurations (1 nanopore fastq file and no illumina):
############ TOOLS ################
ASSEMBLY:
CANU: false
FLYE: true
MINIASM: true
RAVEN: true
SMARTDENOVO: true
SHASTA: true
POLISHING:
RACON: false
CIRCULAR: false
CORRECTION:
NANOPOLISH: false
MEDAKA: true
PILON: false
FIXSTART: false
# BUSCO and QUAST will be launched on all activated steps (ASSEMBLY, POLISHING, CORRECTION)
QUALITY:
BUSCO: true
QUAST: true
#### Others quality tools are launched only in last assemblies
BLOBTOOLS: true
ASSEMBLYTICS: true
#### Others quality soft but illumina reads are required
FLAGSTATS: false
KAT: false
MERQURY : false
#### Alignment of the various assemblies derived from a fastq file for small genomes (<10-20Mbp);
MSA:
MAUVE: false
############ PARAMS ################
params:
#### ASSEMBLY
MINIMAP2:
PRESET_OPTION: 'map-ont' # -x minimap2 preset option is map-pb by default (map-pb, map-ont etc)
FLYE:
MODE : '--nano-raw'
OPTIONS: '' ## use --scaffold if flye>=2.9 # you can also use --resume option
CANU:
MODE : '-nanopore'
OPTIONS: 'useGrid=false'
SMARTDENOVO:
KMER_SIZE: 16
OPTIONS: '-J 5000'
SHASTA:
MEM_MODE: 'filesystem'
MEM_BACKING: 'disk'
OPTIONS: '--Reads.minReadLength 0 --config Nanopore-May2022'
#### CIRCULAR
CIRCLATOR:
OPTIONS: ''
#### POLISHING
RACON:
RACON_ROUNDS: 2 #1 to 9
#### CORRECTION
CORRECTION_SEGMENTATION:
SEGMENT_LEN: 50000 # segment length to split assembly and correct it default=50000
OVERLAP_LEN: 200 # overlap length between segments default=200
NANOPOLISH:
OPTIONS: ''
MEDAKA:
SEGMENTATION: false # if false, there is no segmentation of contigs for medaka
MEDAKA_TRAIN_WITH_REF: false # if 'MEDAKA_TRAIN_WITH_REF' is True, training uses reference to found in DATA REF param.
# Medaka does not take in count other parameters below if MEDAKA_TRAIN_WITH_REF is TRUE.
MEDAKA_MODEL_PATH: 'r104_e81_sup_g5015' # use a path if you have downloaded a model (or you want to use your own trained model) OR a simple string like 'r941_min_high_g303'
MEDAKA_FEATURES_OPTIONS: '--batch_size 10 --chunk_len 100 --chunk_ovlp 10'
MEDAKA_TRAIN_OPTIONS: '--batch_size 10 --epochs 500 '
MEDAKA_CONSENSUS_OPTIONS: '--batch 200 '
PILON:
PILON_ROUNDS: 2 #1 to 9
OPTIONS: ''
#### QUALITY
BUSCO:
#DATABASE: "DATA_DIR/Data-Xoo-sub/bacteria_odb10"
DATABASE: 'bacteria_odb10 --update-data ' # use a path if you have downloaded a taxonomic database from busco OR a simple string like 'bacteria_odb10'
MODEL: 'genome'
SP: '' #--augustus-specie parameter on busco
QUAST:
GFF: ''
OPTIONS: '--large'
DIAMOND:
DATABASE: '/data/BioISIGenomics_local/References/nr_DIAMOND/nr.dmnd'
MUMMER:
MINMATCH: 100 # is -l option with default 20 on MUMMER
MINCLUSTER: 500 # is -c option with default 65 on MUMMER
ASSEMBLYTICS:
UNIQUE_ANCHOR_LEN: 10000
MIN_VARIANT_SIZE: 50
MAX_VARIANT_SIZE: 10000
BLOBTOOLS:
NAMES: '/data/BioISIGenomics_local/Azure_Devops/jupyter/users/aicampos/X2023/bacteria_empty/3Assembly/Taxon_nodes_names/names.dmp'
NODES: '/data/BioISIGenomics_local/Azure_Devops/jupyter/users/aicampos/X2023/bacteria_empty/3Assembly/Taxon_nodes_names/nodes.dmp'
It could run several jobs except this:
Job 34:
Launching run_shasta
threads: 256
input:
fastq: /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/MISC/FASTQ2FASTA/barcode61.fasta
output:
fasta: /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/ASSEMBLER/assemblyCIRCULARISEDTMPTAG.fasta
params:
ln -s /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/ASSEMBLER/ShastaRun/Assembly.fasta /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/ASSEMBLER/assemblyCIRCULARISED.fasta
ln -s /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/ASSEMBLER/ShastaRun/Assembly.gfa /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/ASSEMBLER/assembly_info.txt
log:
output: /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/ASSEMBLER/LOGS/barcode61_SHASTA.o
error: /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/ASSEMBLER/LOGS/barcode61_SHASTA.e
Reason: Missing output files: /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/ASSEMBLER/SHASTA-version.txt, /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/ASSEMBLER/assemblyCIRCULARISEDTMPTAG.fasta, /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/BENCHMARK/ASSEMBLER/SHASTA.txt, /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/ASSEMBLER/assembly_info.txt; Input files updated by another job: /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/MISC/FASTQ2FASTA/barcode61.fasta
[ ! -f /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/ASSEMBLER/SHASTA-version.txt ] && [ ! -d versions ] && mkdir -p versions; shasta --version | head -n1 > /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/ASSEMBLER/SHASTA-version.txt
ln -s -f /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/ASSEMBLER/SHASTA-version.txt /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/versions/SHASTA-version.txt
(cd /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/ASSEMBLER/;
rm -rf ShastaRun/;
shasta --command assemble --input /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/MISC/FASTQ2FASTA/barcode61.fasta --memoryMode filesystem --memoryBacking disk --threads 256 --Reads.minReadLength 0 --config Nanopore-May2022;
ln -s /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/ASSEMBLER/ShastaRun/Assembly.fasta /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/ASSEMBLER/assemblyCIRCULARISED.fasta ;
ln -s /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/ASSEMBLER/ShastaRun/Assembly.gfa /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/ASSEMBLER/assembly_info.txt ) 1>/home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/ASSEMBLER/LOGS/barcode61_SHASTA.o 2>/home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/ASSEMBLER/LOGS/barcode61_SHASTA.e
Activating singularity image /home/aicampos/miniconda3/envs/Culebront/lib/python3.10/site-packages/culebrONT/containers/Singularity.culebront_tools.sif
Waiting at most 1296000 seconds for missing files.
It keeps waiting for the missing files and nothing happens.
Then I tried to deactivate Circulator:
´´´ CIRCULAR: false ´´´
This happened:
Job 87:
Launching run_blobtools ...
threads: 1
input:
fasta: /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/AGGREGATED_QC/DATA/barcode61-SHASTA-MEDAKA.fasta
sorted_bam: /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/QUALITY/MEDAKA/MINIMAP2/minimap2mapping.bam
diamond: /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/QUALITY/MEDAKA/DIAMOND/diamond.csv
output:
table: /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/QUALITY/MEDAKA/BLOBTOOLS/barcode61_SHASTA_MEDAKA.txt
params:
names: /data/BioISIGenomics_local/References/culebrONT/test/Data-Xoo-sub/blobtools/names.dmp
nodes: /data/BioISIGenomics_local/References/culebrONT/test/Data-Xoo-sub/blobtools/nodes.dmp
log:
output: /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/QUALITY/MEDAKA/BLOBTOOLS/LOGS/barcode61_SHASTA_MEDAKA_BLOBTOOLS.o
error: /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/QUALITY/MEDAKA/BLOBTOOLS/LOGS/barcode61_SHASTA_MEDAKA_BLOBTOOLS.e
Reason: Missing output files: /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/QUALITY/MEDAKA/BLOBTOOLS/barcode61_SHASTA_MEDAKA.txt; Input files updated by another job: /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/AGGREGATED_QC/DATA/barcode61-SHASTA-MEDAKA.fasta, /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/QUALITY/MEDAKA/MINIMAP2/minimap2mapping.bam, /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/QUALITY/MEDAKA/DIAMOND/diamond.csv
[ ! -f /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/QUALITY/MEDAKA/BLOBTOOLS/BLOBTOOLS-version.txt ] && [ ! -d versions ] && mkdir -p versions; blobtools --version > /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/QUALITY/MEDAKA/BLOBTOOLS/BLOBTOOLS-version.txt
ln -s -f /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/QUALITY/MEDAKA/BLOBTOOLS/BLOBTOOLS-version.txt /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/versions/BLOBTOOLS-version.txt
(cd /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/QUALITY/MEDAKA/BLOBTOOLS/ ;
blobtools create -i /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/AGGREGATED_QC/DATA/barcode61-SHASTA-MEDAKA.fasta -b /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/QUALITY/MEDAKA/MINIMAP2/minimap2mapping.bam -t /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/QUALITY/MEDAKA/DIAMOND/diamond.csv -o quality --names /data/BioISIGenomics_local/References/culebrONT/test/Data-Xoo-sub/blobtools/names.dmp --nodes /data/BioISIGenomics_local/References/culebrONT/test/Data-Xoo-sub/blobtools/nodes.dmp --db nodesDB.txt;
blobtools view -i quality.blobDB.json --cov -o output;
blobtools plot -i quality.blobDB.json;
mv quality.blobDB.*.blobplot.read_cov.bam0.png /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/QUALITY/MEDAKA/BLOBTOOLS/read_cov.png;
mv quality.blobDB.*.blobplot.bam0.png /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/QUALITY/MEDAKA/BLOBTOOLS/blob.png) 1>/home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/QUALITY/MEDAKA/BLOBTOOLS/LOGS/barcode61_SHASTA_MEDAKA_BLOBTOOLS.o 2>/home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/QUALITY/MEDAKA/BLOBTOOLS/LOGS/barcode61_SHASTA_MEDAKA_BLOBTOOLS.e
mv /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/QUALITY/MEDAKA/BLOBTOOLS/output.quality.blobDB.table.txt /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/SHASTA/QUALITY/MEDAKA/BLOBTOOLS/barcode61_SHASTA_MEDAKA.txt
Activating singularity image /home/aicampos/miniconda3/envs/Culebront/lib/python3.10/site-packages/culebrONT/containers/Singularity.culebront_tools.sif
Waiting at most 1296000 seconds for missing files.
Now it hangs on Blobtools but with a Shasta input... is there any problem with Shasta?
By last I decided to deactivate both Circulator and Shasta and this happened:
Job 44:
Launching run_assemblytics ...
threads: 1
input:
delta: /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/FLYE/QUALITY/MEDAKA/MUMMER/mummer.delta.gz
output:
summary: /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/FLYE/QUALITY/MEDAKA/ASSEMBLYTICS/barcode61__FLYE__MEDAKA.Assemblytics_structural_variants.summary
params:
unique_anchor_length = 10000
min_variant_size = 50
max_variant_size = 10000
prefix: barcode61__FLYE__MEDAKA
log:
output: /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/FLYE/QUALITY/MEDAKA/ASSEMBLYTICS/LOGS/barcode61_FLYE_MEDAKA_ASSEMBLYTICS.o
error: /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/FLYE/QUALITY/MEDAKA/ASSEMBLYTICS/LOGS/barcode61_FLYE_MEDAKA_ASSEMBLYTICS.e
Reason: Missing output files: /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/FLYE/QUALITY/MEDAKA/ASSEMBLYTICS/ASSEMBLYTICS-version.txt, /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/FLYE/QUALITY/MEDAKA/ASSEMBLYTICS/barcode61__FLYE__MEDAKA.Assemblytics_structural_variants.summary; Input files updated by another job: /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/FLYE/QUALITY/MEDAKA/MUMMER/mummer.delta.gz
[ ! -f /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/FLYE/QUALITY/MEDAKA/ASSEMBLYTICS/ASSEMBLYTICS-version.txt ] && [ ! -d versions ] && mkdir -p versions; whereis Assemblytics > /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/FLYE/QUALITY/MEDAKA/ASSEMBLYTICS/ASSEMBLYTICS-version.txt
cp -f /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/FLYE/QUALITY/MEDAKA/ASSEMBLYTICS/ASSEMBLYTICS-version.txt /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/versions/ASSEMBLYTICS-version.txt
(cd /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/FLYE/QUALITY/MEDAKA/ASSEMBLYTICS/;
Assemblytics /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/FLYE/QUALITY/MEDAKA/MUMMER/mummer.delta.gz barcode61__FLYE__MEDAKA 10000 50 10000) 1>/home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/FLYE/QUALITY/MEDAKA/ASSEMBLYTICS/LOGS/barcode61_FLYE_MEDAKA_ASSEMBLYTICS.o 2>/home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/FLYE/QUALITY/MEDAKA/ASSEMBLYTICS/LOGS/barcode61_FLYE_MEDAKA_ASSEMBLYTICS.e
Activating singularity image /home/aicampos/miniconda3/envs/Culebront/lib/python3.10/site-packages/culebrONT/containers/Singularity.culebront_tools.sif
Waiting at most 1296000 seconds for missing files.
It is hanging again. I checked the stderr file: /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/FLYE/QUALITY/MEDAKA/ASSEMBLYTICS/LOGS/barcode61_FLYE_MEDAKA_ASSEMBLYTICS.e
And it contains this:
Input delta file: /home/aicampos/X2023/validacoes_X/bacteria/validacoes_experimentais/barcode61_X/3Assembly/culebrONT_OUTPUT/barcode61/ASSEMBLERS/FLYE/QUALITY/MEDAKA/MUMMER/mummer.delta.gz
Output prefix: barcode61__FLYE__MEDAKA
Unique anchor length: 10000
Minimum variant size to call: 50
Maximum variant size to call: 10000
Logging progress updates in barcode61__FLYE__MEDAKA/progress.log
1. Filter delta file
2. Finding variants between alignments
Loaded 2 alignments
3. Finding variants within alignments
4. Combine variants between and within alignments
Warning message:
package 'ggplot2' was built under R version 4.2.3
Warning message:
package 'plyr' was built under R version 4.2.3
Warning message:
package 'RColorBrewer' was built under R version 4.2.3
Error in revalue(bed$type, c(Repeat_expansion = "Repeat expansion", Repeat_contraction = "Repeat contraction", :
x is not a factor or a character vector.
Execution halted
Warning message:
package 'ggplot2' was built under R version 4.2.3
Warning messages:
1: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
i Please use `linewidth` instead.
2: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
i Please use the `linewidth` argument instead.
Warning message:
package 'ggplot2' was built under R version 4.2.3
Warning message:
package 'scales' was built under R version 4.2.3
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
i Please use `linewidth` instead.
/usr/local/mamba/mamba/envs/assemblytics/bin/Assemblytics: line 120: zip: command not found
/usr/local/mamba/mamba/envs/assemblytics/bin/Assemblytics: line 123: column: command not found
singularity exec /home/aicampos/miniconda3/envs/Culebront/lib/python3.10/sitepackages/culebrONT/containers/Singularity.culebront_tools.sif circlator all
Traceback (most recent call last): File "/usr/local/miniconda/miniconda3/envs/mamba/envs/circlator/bin/circlator", line 57, in
exec('import circlator.tasks.' + task)
File "", line 1, in
File "/usr/local/miniconda/miniconda3/envs/mamba/envs/circlator/lib/python3.5/site-packages/circlator/init.py", line 26, in
from circlator import
File "/usr/local/miniconda/miniconda3/envs/mamba/envs/circlator/lib/python3.5/site-packages/circlator/bamfilter.py", line 2, in
import pysam
File "/usr/local/miniconda/miniconda3/envs/mamba/envs/circlator/lib/python3.5/site-packages/pysam/init.py", line 5, in
from pysam.libchtslib import
ImportError: libhts.so.2: cannot open shared object file: No such file or directory