Dear PathoFact team, Thanks for your such amazing work. My issue is that I got unknown block on the dvf step when I run PathoFact with a test input genomes.
snakemake log:
Building DAG of jobs...
Updating job 10.
Using shell: /usr/bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 HMM_R_VIR
1 HMM_VIR_classification
1 HMM_VIR_finalformat
1 HMM_VIR_report
1 HMM_correct_format_2
1 HMM_correct_format_2_vir
1 HMM_correct_format_3
1 Plasmid_aggregate
1 R_script
1 SignalPN_aggregate
1 SignalPP_aggregate
1 aggregate_RGI
1 aggregate_VirFinder
1 aggregate_deepARG
1 aggregate_signalP
1 all
1 clean_all
1 combine_AMR
1 combine_AMR_plasmid
1 combine_PathoFact
1 filter_seq
1 format_classifier
1 format_classifier_2
2 generate_ID
1 generate_translation
1 mapping_file
1 merge_SignalPVir
1 run_VirFinder
1 select
1 splitplasmid
2 splitting
1 splittingsignalP
34
[Thu Jun 17 10:22:10 2021]
Job 35: Filter samples on length for PlasFlow predictions: PathoFact_results - ISO_DWRC1-3
Reason: Missing output files: /mnt/nfs/software/PathoFact/Test/PathoFact_results/PathoFact_intermediate/plasmid/ISO_DWRC1-3_filtered.fna
scripts/filter.pl 1000 /mnt/nfs/software/PathoFact/Test/PathoFact_results/PathoFact_intermediate/renamed/ISO_DWRC1-3_Contig_ID.fna > /mnt/nfs/software/PathoFact/Test/PathoFact_results/PathoFact_intermediate/plasmid/ISO_DWRC1-3_filtered.fna 2> /mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_DWRC1-3/plasmid_filtered.log
Activating conda environment: /mnt/nfs/software/Old_PathoFact/.snakemake/conda/f490db85
[Thu Jun 17 10:22:16 2021]
Finished job 35.
1 of 34 steps (3%) done
[Thu Jun 17 10:22:16 2021]
checkpoint splitplasmid:
input: /mnt/nfs/software/PathoFact/Test/PathoFact_results/PathoFact_intermediate/plasmid/ISO_DWRC1-3_filtered.fna
output: /mnt/nfs/software/PathoFact/Test/PathoFact_results/PathoFact_intermediate/MGE/plasmid_splitted/ISO_DWRC1-3/
jobid: 29
reason: Missing output files: /mnt/nfs/software/PathoFact/Test/PathoFact_results/PathoFact_intermediate/MGE/plasmid_splitted/ISO_DWRC1-3/; Input files updated by another job: /mnt/nfs/software/PathoFact/Test/PathoFact_results/PathoFact_intermediate/plasmid/ISO_DWRC1-3_filtered.fna
wildcards: project=PathoFact_results, sample=ISO_DWRC1-3
Downstream jobs will be updated after completion.
python scripts/split.py /mnt/nfs/software/PathoFact/Test/PathoFact_results/PathoFact_intermediate/plasmid/ISO_DWRC1-3_filtered.fna 10000 /mnt/nfs/software/PathoFact/Test/PathoFact_results/PathoFact_intermediate/MGE/plasmid_splitted/ISO_DWRC1-3/
Activating conda environment: /mnt/nfs/software/Old_PathoFact/.snakemake/conda/f490db85
Wrote 5 records to group_1.fasta
Removing temporary output file /mnt/nfs/software/PathoFact/Test/PathoFact_results/PathoFact_intermediate/plasmid/ISO_DWRC1-3_filtered.fna.
Updating job 20.
Creating conda environment envs/PlasFlow.yaml...
Downloading remote packages.
Environment for envs/PlasFlow.yaml created (location: .snakemake/conda/0d925277)
[Thu Jun 17 11:22:31 2021]
Finished job 29.
2 of 33 steps (6%) done
[Thu Jun 17 11:22:32 2021]
Job 41: Executing Deep-VirFinder with 1 threads on the following sample(s): PathoFact_results - ISO_DWRC1-3
Reason: Missing output files: /mnt/nfs/software/PathoFact/Test/PathoFact_results/PathoFact_intermediate/MGE/phage/ISO_DWRC1-3/virfinder/group_1.fasta_gt1bp_dvfpred.txt
python submodules/DeepVirFinder/dvf.py -i /mnt/nfs/software/PathoFact/Test/PathoFact_results/PathoFact_intermediate/contig_splitted/ISO_DWRC1-3/group_1.fasta -o /mnt/nfs/software/PathoFact/Test/PathoFact_results/PathoFact_intermediate/MGE/phage/ISO_DWRC1-3/virfinder -c 1 &> /mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_DWRC1-3/group_1.fasta_gt1bp_dvfpred.log
Activating conda environment: /mnt/nfs/software/Old_PathoFact/.snakemake/conda/45939b1f
It seems blocked in the dvf step,so I check the group_1.fasta_gt1bp_dvfpred.log:
bp_dvfpred.log
Using Theano backend.
WARNING (theano.configdefaults): install mkl with `conda install mkl-service`: No module named 'mkl'
OMP: Info #212: KMP_AFFINITY: decoding x2APIC ids.
OMP: Info #210: KMP_AFFINITY: Affinity capable, using global cpuid leaf 11 info
OMP: Info #154: KMP_AFFINITY: Initial OS proc set respected: 0-255
OMP: Info #156: KMP_AFFINITY: 256 available OS procs
OMP: Info #157: KMP_AFFINITY: Uniform topology
OMP: Info #179: KMP_AFFINITY: 2 packages x 64 cores/pkg x 2 threads/core (128 total cores)
OMP: Info #214: KMP_AFFINITY: OS proc to physical thread map:
OMP: Info #171: KMP_AFFINITY: OS proc 0 maps to package 0 core 0 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 128 maps to package 0 core 0 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 1 maps to package 0 core 1 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 129 maps to package 0 core 1 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 2 maps to package 0 core 2 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 130 maps to package 0 core 2 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 3 maps to package 0 core 3 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 131 maps to package 0 core 3 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 4 maps to package 0 core 4 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 132 maps to package 0 core 4 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 5 maps to package 0 core 5 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 133 maps to package 0 core 5 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 6 maps to package 0 core 6 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 134 maps to package 0 core 6 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 7 maps to package 0 core 7 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 135 maps to package 0 core 7 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 8 maps to package 0 core 8 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 136 maps to package 0 core 8 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 9 maps to package 0 core 9 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 137 maps to package 0 core 9 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 10 maps to package 0 core 10 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 138 maps to package 0 core 10 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 11 maps to package 0 core 11 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 139 maps to package 0 core 11 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 12 maps to package 0 core 12 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 140 maps to package 0 core 12 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 13 maps to package 0 core 13 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 141 maps to package 0 core 13 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 14 maps to package 0 core 14 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 142 maps to package 0 core 14 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 15 maps to package 0 core 15 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 143 maps to package 0 core 15 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 16 maps to package 0 core 16 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 144 maps to package 0 core 16 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 17 maps to package 0 core 17 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 145 maps to package 0 core 17 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 18 maps to package 0 core 18 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 146 maps to package 0 core 18 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 19 maps to package 0 core 19 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 147 maps to package 0 core 19 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 20 maps to package 0 core 20 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 148 maps to package 0 core 20 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 21 maps to package 0 core 21 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 149 maps to package 0 core 21 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 22 maps to package 0 core 22 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 150 maps to package 0 core 22 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 23 maps to package 0 core 23 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 151 maps to package 0 core 23 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 24 maps to package 0 core 24 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 152 maps to package 0 core 24 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 25 maps to package 0 core 25 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 153 maps to package 0 core 25 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 26 maps to package 0 core 26 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 154 maps to package 0 core 26 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 27 maps to package 0 core 27 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 155 maps to package 0 core 27 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 28 maps to package 0 core 28 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 156 maps to package 0 core 28 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 29 maps to package 0 core 29 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 157 maps to package 0 core 29 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 30 maps to package 0 core 30 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 158 maps to package 0 core 30 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 31 maps to package 0 core 31 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 159 maps to package 0 core 31 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 32 maps to package 0 core 32 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 160 maps to package 0 core 32 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 33 maps to package 0 core 33 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 161 maps to package 0 core 33 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 34 maps to package 0 core 34 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 162 maps to package 0 core 34 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 35 maps to package 0 core 35 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 163 maps to package 0 core 35 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 36 maps to package 0 core 36 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 164 maps to package 0 core 36 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 37 maps to package 0 core 37 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 165 maps to package 0 core 37 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 38 maps to package 0 core 38 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 166 maps to package 0 core 38 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 39 maps to package 0 core 39 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 167 maps to package 0 core 39 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 40 maps to package 0 core 40 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 168 maps to package 0 core 40 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 41 maps to package 0 core 41 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 169 maps to package 0 core 41 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 42 maps to package 0 core 42 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 170 maps to package 0 core 42 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 43 maps to package 0 core 43 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 171 maps to package 0 core 43 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 44 maps to package 0 core 44 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 172 maps to package 0 core 44 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 45 maps to package 0 core 45 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 173 maps to package 0 core 45 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 46 maps to package 0 core 46 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 174 maps to package 0 core 46 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 47 maps to package 0 core 47 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 175 maps to package 0 core 47 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 48 maps to package 0 core 48 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 176 maps to package 0 core 48 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 49 maps to package 0 core 49 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 177 maps to package 0 core 49 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 50 maps to package 0 core 50 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 178 maps to package 0 core 50 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 51 maps to package 0 core 51 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 179 maps to package 0 core 51 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 52 maps to package 0 core 52 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 180 maps to package 0 core 52 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 53 maps to package 0 core 53 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 181 maps to package 0 core 53 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 54 maps to package 0 core 54 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 182 maps to package 0 core 54 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 55 maps to package 0 core 55 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 183 maps to package 0 core 55 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 56 maps to package 0 core 56 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 184 maps to package 0 core 56 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 57 maps to package 0 core 57 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 185 maps to package 0 core 57 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 58 maps to package 0 core 58 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 186 maps to package 0 core 58 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 59 maps to package 0 core 59 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 187 maps to package 0 core 59 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 60 maps to package 0 core 60 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 188 maps to package 0 core 60 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 61 maps to package 0 core 61 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 189 maps to package 0 core 61 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 62 maps to package 0 core 62 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 190 maps to package 0 core 62 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 63 maps to package 0 core 63 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 191 maps to package 0 core 63 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 64 maps to package 1 core 0 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 192 maps to package 1 core 0 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 65 maps to package 1 core 1 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 193 maps to package 1 core 1 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 66 maps to package 1 core 2 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 194 maps to package 1 core 2 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 67 maps to package 1 core 3 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 195 maps to package 1 core 3 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 68 maps to package 1 core 4 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 196 maps to package 1 core 4 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 69 maps to package 1 core 5 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 197 maps to package 1 core 5 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 70 maps to package 1 core 6 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 198 maps to package 1 core 6 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 71 maps to package 1 core 7 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 199 maps to package 1 core 7 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 72 maps to package 1 core 8 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 200 maps to package 1 core 8 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 73 maps to package 1 core 9 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 201 maps to package 1 core 9 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 74 maps to package 1 core 10 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 202 maps to package 1 core 10 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 75 maps to package 1 core 11 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 203 maps to package 1 core 11 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 76 maps to package 1 core 12 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 204 maps to package 1 core 12 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 77 maps to package 1 core 13 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 205 maps to package 1 core 13 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 78 maps to package 1 core 14 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 206 maps to package 1 core 14 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 79 maps to package 1 core 15 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 207 maps to package 1 core 15 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 80 maps to package 1 core 16 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 208 maps to package 1 core 16 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 81 maps to package 1 core 17 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 209 maps to package 1 core 17 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 82 maps to package 1 core 18 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 210 maps to package 1 core 18 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 83 maps to package 1 core 19 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 211 maps to package 1 core 19 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 84 maps to package 1 core 20 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 212 maps to package 1 core 20 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 85 maps to package 1 core 21 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 213 maps to package 1 core 21 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 86 maps to package 1 core 22 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 214 maps to package 1 core 22 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 87 maps to package 1 core 23 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 215 maps to package 1 core 23 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 88 maps to package 1 core 24 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 216 maps to package 1 core 24 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 89 maps to package 1 core 25 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 217 maps to package 1 core 25 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 90 maps to package 1 core 26 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 218 maps to package 1 core 26 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 91 maps to package 1 core 27 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 219 maps to package 1 core 27 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 92 maps to package 1 core 28 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 220 maps to package 1 core 28 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 93 maps to package 1 core 29 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 221 maps to package 1 core 29 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 94 maps to package 1 core 30 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 222 maps to package 1 core 30 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 95 maps to package 1 core 31 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 223 maps to package 1 core 31 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 96 maps to package 1 core 32 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 224 maps to package 1 core 32 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 97 maps to package 1 core 33 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 225 maps to package 1 core 33 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 98 maps to package 1 core 34 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 226 maps to package 1 core 34 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 99 maps to package 1 core 35 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 227 maps to package 1 core 35 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 100 maps to package 1 core 36 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 228 maps to package 1 core 36 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 101 maps to package 1 core 37 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 229 maps to package 1 core 37 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 102 maps to package 1 core 38 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 230 maps to package 1 core 38 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 103 maps to package 1 core 39 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 231 maps to package 1 core 39 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 104 maps to package 1 core 40 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 232 maps to package 1 core 40 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 105 maps to package 1 core 41 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 233 maps to package 1 core 41 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 106 maps to package 1 core 42 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 234 maps to package 1 core 42 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 107 maps to package 1 core 43 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 235 maps to package 1 core 43 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 108 maps to package 1 core 44 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 236 maps to package 1 core 44 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 109 maps to package 1 core 45 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 237 maps to package 1 core 45 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 110 maps to package 1 core 46 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 238 maps to package 1 core 46 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 111 maps to package 1 core 47 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 239 maps to package 1 core 47 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 112 maps to package 1 core 48 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 240 maps to package 1 core 48 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 113 maps to package 1 core 49 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 241 maps to package 1 core 49 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 114 maps to package 1 core 50 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 242 maps to package 1 core 50 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 115 maps to package 1 core 51 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 243 maps to package 1 core 51 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 116 maps to package 1 core 52 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 244 maps to package 1 core 52 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 117 maps to package 1 core 53 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 245 maps to package 1 core 53 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 118 maps to package 1 core 54 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 246 maps to package 1 core 54 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 119 maps to package 1 core 55 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 247 maps to package 1 core 55 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 120 maps to package 1 core 56 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 248 maps to package 1 core 56 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 121 maps to package 1 core 57 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 249 maps to package 1 core 57 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 122 maps to package 1 core 58 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 250 maps to package 1 core 58 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 123 maps to package 1 core 59 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 251 maps to package 1 core 59 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 124 maps to package 1 core 60 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 252 maps to package 1 core 60 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 125 maps to package 1 core 61 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 253 maps to package 1 core 61 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 126 maps to package 1 core 62 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 254 maps to package 1 core 62 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 127 maps to package 1 core 63 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 255 maps to package 1 core 63 thread 1
OMP: Info #250: KMP_AFFINITY: pid 2526244 tid 2526244 thread 0 bound to OS proc set 0
1. Loading Models.
model directory /mnt/nfs/software/Old_PathoFact/submodules/DeepVirFinder/models
2. Encoding and Predicting Sequences.
processing line 1
processing line 61512
/mnt/nfs/software/Old_PathoFact/.snakemake/conda/45939b1f/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:516: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint8 = np.dtype([("qint8", np.int8, 1)])
/mnt/nfs/software/Old_PathoFact/.snakemake/conda/45939b1f/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:517: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint8 = np.dtype([("quint8", np.uint8, 1)])
/mnt/nfs/software/Old_PathoFact/.snakemake/conda/45939b1f/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:518: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint16 = np.dtype([("qint16", np.int16, 1)])
/mnt/nfs/software/Old_PathoFact/.snakemake/conda/45939b1f/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:519: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint16 = np.dtype([("quint16", np.uint16, 1)])
/mnt/nfs/software/Old_PathoFact/.snakemake/conda/45939b1f/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:520: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint32 = np.dtype([("qint32", np.int32, 1)])
/mnt/nfs/software/Old_PathoFact/.snakemake/conda/45939b1f/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:525: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
np_resource = np.dtype([("resource", np.ubyte, 1)])
/mnt/nfs/software/Old_PathoFact/.snakemake/conda/45939b1f/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:541: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint8 = np.dtype([("qint8", np.int8, 1)])
/mnt/nfs/software/Old_PathoFact/.snakemake/conda/45939b1f/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:542: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint8 = np.dtype([("quint8", np.uint8, 1)])
/mnt/nfs/software/Old_PathoFact/.snakemake/conda/45939b1f/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:543: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint16 = np.dtype([("qint16", np.int16, 1)])
/mnt/nfs/software/Old_PathoFact/.snakemake/conda/45939b1f/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:544: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint16 = np.dtype([("quint16", np.uint16, 1)])
/mnt/nfs/software/Old_PathoFact/.snakemake/conda/45939b1f/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:545: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint32 = np.dtype([("qint32", np.int32, 1)])
/mnt/nfs/software/Old_PathoFact/.snakemake/conda/45939b1f/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:550: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
np_resource = np.dtype([("resource", np.ubyte, 1)])
The pipline stop above step for long time(up to 7 days) and seems hardly finished.
Looking forward your reply, Thanks a lot.
the log status is still on the "449 of 401 steps (112%) done" from last check(about 12h elapsed) but just 8 input normal bacteria genomes.Strangely, the job does not stop,I can see the jobs is still work by jobs
command, but we can see many associated python process on S
by top
:
进程号 USER PR NI VIRT RES SHR %CPU %MEM TIME+ COMMAND
1664371 yut 20 0 6833400 1.1g 9896 S 0.0 0.1 1:10.97 python
1665997 yut 20 0 6848376 1.1g 9900 S 0.0 0.1 0:34.00 python
1667545 yut 20 0 6837204 1.1g 9896 S 0.0 0.1 0:17.44 python
1668958 yut 20 0 6837204 1.1g 9896 S 0.0 0.1 0:15.66 python
1670520 yut 20 0 6837204 1.1g 9896 S 0.0 0.1 0:17.22 python
1672231 yut 20 0 6837204 1.1g 9896 S 0.0 0.1 0:15.99 python
1673805 yut 20 0 6837204 1.1g 9876 S 0.0 0.1 0:19.74 python
1675501 yut 20 0 6842828 1.1g 9804 S 0.0 0.1 0:08.28 python
1677644 yut 20 0 5793660 1.1g 4092 S 0.0 0.1 0:00.00 python
and I strace one of process by sudo strace -cp 1665997
, but without any output informations
There is no other python associated jobs,so I run
dmesg |grep python
and, the reults as below:
(PathoFact) [u@h@PathoFact]$ dmesg |grep python
[8131398.716922] [ 281263] 1001 281263 6514 1954 86016 0 0 python
[10199444.589070] [2808526] 0 2808526 180056 11265 397312 0 0 python
[10199444.589071] [2808534] 0 2808534 124551 11127 290816 0 0 python
[10199444.589073] [2808535] 0 2808535 124551 11128 290816 0 0 python
[10199444.589074] [2808536] 0 2808536 124551 11129 290816 0 0 python
[10199444.589075] [2808540] 0 2808540 237446 12204 434176 0 0 python
[10199444.589076] [2808548] 0 2808548 124550 11130 290816 0 0 python
[10199444.589078] [2808549] 0 2808549 125744 12279 331776 0 0 python
[10199444.589079] [2808550] 0 2808550 124486 11068 286720 0 0 python
[10653697.161368] [2808526] 0 2808526 180056 11265 397312 0 0 python
[10653697.161375] [2808534] 0 2808534 124551 11127 290816 0 0 python
[10653697.161382] [2808535] 0 2808535 124551 11128 290816 0 0 python
[10653697.161388] [2808536] 0 2808536 124551 11129 290816 0 0 python
[10653697.161396] [2808540] 0 2808540 237446 12204 434176 0 0 python
[10653697.161402] [2808548] 0 2808548 124550 11130 290816 0 0 python
[10653697.161408] [2808549] 0 2808549 125744 12279 331776 0 0 python
[10653697.161414] [2808550] 0 2808550 124486 11068 286720 0 0 python
[11231202.275383] python[1308340]: segfault at 7fb1a8849030 ip 00007fb72acead00 sp 00007fffe055ac00 error 4 in m4838fd7e383dc3e41c316488e48e8e2b2c422d8d3336c35991d1ba7f7bec1027.so[7fb72ace9000+3000]
[11231246.533843] python[1593230]: segfault at 7fa11edbe480 ip 00007fa713bfbd00 sp 00007ffd85a3b100 error 4 in m4838fd7e383dc3e41c316488e48e8e2b2c422d8d3336c35991d1ba7f7bec1027.so[7fa713bfa000+3000]
[11233238.054619] python[1376604]: segfault at 7f59b61cd368 ip 00007f5f270cbd00 sp 00007ffdaf14c1c0 error 4 in m4838fd7e383dc3e41c316488e48e8e2b2c422d8d3336c35991d1ba7f7bec1027.so[7f5f270ca000+3000]
[11240043.888795] python[2256383]: segfault at 7f2002ca28e4 ip 00007f25b1286d00 sp 00007ffd56decda0 error 4 in m4838fd7e383dc3e41c316488e48e8e2b2c422d8d3336c35991d1ba7f7bec1027.so[7f25b1285000+3000]
[11275302.457741] python[3227889]: segfault at 7f5e28334480 ip 00007f6414b61d00 sp 00007ffc65f97520 error 4 in m4838fd7e383dc3e41c316488e48e8e2b2c422d8d3336c35991d1ba7f7bec1027.so[7f6414b60000+3000]
[11433634.524880] python[2385481]: segfault at 7f87dbab0480 ip 00007f8dc85a9d00 sp 00007ffe78c1e6e0 error 4 in m4838fd7e383dc3e41c316488e48e8e2b2c422d8d3336c35991d1ba7f7bec1027.so[7f8dc85a8000+3000]
[11433647.391418] python[2452736]: segfault at 7fd2f10cc030 ip 00007fd85f324d00 sp 00007fff8fbfc080 error 4 in m4838fd7e383dc3e41c316488e48e8e2b2c422d8d3336c35991d1ba7f7bec1027.so[7fd85f323000+3000]
[11434624.244961] python[860759]: segfault at 7fe5a6149368 ip 00007feb1142fd00 sp 00007ffc6a0d8b00 error 4 in m4838fd7e383dc3e41c316488e48e8e2b2c422d8d3336c35991d1ba7f7bec1027.so[7feb1142e000+3000]
[11438923.448994] python[671784]: segfault at 7f938e5d08e4 ip 00007f9939266d00 sp 00007fff0abaf380 error 4 in m4838fd7e383dc3e41c316488e48e8e2b2c422d8d3336c35991d1ba7f7bec1027.so[7f9939265000+3000]
[11445963.187549] ptrace attach of "python submodules/DeepVirFinder/dvf.py -i /mnt/nfs/software/PathoFact/Test/PathoFact_results/PathoFact_intermediate/contig_splitted/ISO_AS5674-3/group_1.fasta -o /mnt/nfs/software/PathoFact/Test/PathoFact_results/PathoFact_intermediate/MGE/phage/ISO_AS5674-3/virfinder -c 10"[672295] was attempted by "strace -cp 672295"[2233713]
[11446006.954394] ptrace attach of "python submodules/DeepVirFinder/dvf.py -i /mnt/nfs/software/PathoFact/Test/PathoFact_results/PathoFact_intermediate/contig_splitted/ISO_AS5674-3/group_1.fasta -o /mnt/nfs/software/PathoFact/Test/PathoFact_results/PathoFact_intermediate/MGE/phage/ISO_AS5674-3/virfinder -c 10"[672295] was attempted by "strace -p 672295"[2233718]
[11533881.124729] python[1195346]: segfault at 7efb04468a5c ip 00007f003e29dd00 sp 00007ffc6239d1e0 error 4 in m4838fd7e383dc3e41c316488e48e8e2b2c422d8d3336c35991d1ba7f7bec1027.so[7f003e29c000+3000]
[11534129.002131] python[1932251]: segfault at 7fe8eee5969c ip 00007fee4b91fd00 sp 00007fffeaa5cf00 error 4 in m4838fd7e383dc3e41c316488e48e8e2b2c422d8d3336c35991d1ba7f7bec1027.so[7fee4b91e000+3000]
[11534140.557561] python[1905474]: segfault at 7fcd46789b34 ip 00007fd389c0bd00 sp 00007fffd4d46cc0 error 4 in m4838fd7e383dc3e41c316488e48e8e2b2c422d8d3336c35991d1ba7f7bec1027.so[7fd389c0a000+3000]
[11536895.829768] python[320442]: segfault at 7f73840a3b34 ip 00007f79cbccbd00 sp 00007fff65dc9d80 error 4 in m4838fd7e383dc3e41c316488e48e8e2b2c422d8d3336c35991d1ba7f7bec1027.so[7f79cbcca000+3000]
[11536918.216201] python[389823]: segfault at 7fc901f0769c ip 00007fce633f1d00 sp 00007ffeb0aa7800 error 4 in m4838fd7e383dc3e41c316488e48e8e2b2c422d8d3336c35991d1ba7f7bec1027.so[7fce633f0000+3000]
[11536921.044614] python[404030]: segfault at 7fa450d0ba5c ip 00007fa993306d00 sp 00007ffe95d30a80 error 4 in m4838fd7e383dc3e41c316488e48e8e2b2c422d8d3336c35991d1ba7f7bec1027.so[7fa993305000+3000]
[11574772.204849] python[1336602]: segfault at 7f2a86620a5c ip 00007f2fb491cd00 sp 00007ffc0ef240c0 error 4 in m4838fd7e383dc3e41c316488e48e8e2b2c422d8d3336c35991d1ba7f7bec1027.so[7f2fb491b000+3000]
[11615043.576216] python[1662468]: segfault at 7ff01d5e869c ip 00007ff58c1a3d00 sp 00007ffc695ee5c0 error 4 in m4838fd7e383dc3e41c316488e48e8e2b2c422d8d3336c35991d1ba7f7bec1027.so[7ff58c1a2000+3000]
[11615069.921786] python[1866509]: segfault at 7f661f9e6a5c ip 00007f6b5c77cd00 sp 00007ffdc563f0c0 error 4 in m4838fd7e383dc3e41c316488e48e8e2b2c422d8d3336c35991d1ba7f7bec1027.so[7f6b5c77b000+3000]
[11615088.317810] python[1984413]: segfault at 7f4409dc4b34 ip 00007f4a21fc8d00 sp 00007ffd5ba04700 error 4 in m4838fd7e383dc3e41c316488e48e8e2b2c422d8d3336c35991d1ba7f7bec1027.so[7f4a21fc7000+3000]
[11620203.758320] ptrace attach of "python submodules/DeepVirFinder/dvf.py -i /mnt/nfs/software/PathoFact/Test/PathoFact_results/PathoFact_intermediate/contig_splitted/ISO_194-2/group_1.fasta -o /mnt/nfs/software/PathoFact/Test/PathoFact_results/PathoFact_intermediate/MGE/phage/ISO_194-2/virfinder -c 10"[1664371] was attempted by "strace -cp 1664371"[782840]
[11662711.535137] ptrace attach of "python submodules/DeepVirFinder/dvf.py -i /mnt/nfs/software/PathoFact/Test/PathoFact_results/PathoFact_intermediate/contig_splitted/ISO_194-2/group_1.fasta -o /mnt/nfs/software/PathoFact/Test/PathoFact_results/PathoFact_intermediate/MGE/phage/ISO_194-2/virfinder -c 10"[1665997] was attempted by "strace -cp 1665997"[804963]
Thanks for your reply in time, it seems stop in clean_all
step
the log as below:
[Tue May 11 21:17:57 2021]
Job 20: Generate PathoFact report on the following sample(s): PathoFact_results - ISO_20-2-1.002
Rscript --vanilla /mnt/nfs/software/PathoFact/.snakemake/scripts/tmp4qwu215u.PathoFact.R
Activating conda environment: /mnt/nfs/software/PathoFact/.snakemake/conda/1deab78b
[Tue May 11 21:18:01 2021]
Finished job 20.
448 of 401 steps (112%) done
[Tue May 11 21:18:01 2021]
rule clean_all:
input: /mnt/nfs/software/PathoFact/Test/PathoFact_results/PathoFact_report/PathoFact_ISO_20-2-1.002_predictions.tsv
output: /mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002_compressed.zip
jobid: 28
wildcards: project=PathoFact_results, sample=ISO_20-2-1.002
zip -rm /mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002_compressed.zip /mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002
rm -rf /mnt/nfs/software/PathoFact/Test/PathoFact_results/splitted/ISO_20-2-1.002
rm -rf /mnt/nfs/software/PathoFact/Test/PathoFact_results/contig_splitted/ISO_20-2-1.002_dir
rm -rf /mnt/nfs/software/PathoFact/Test/PathoFact_results/PathoFact_intermediate/SignalP/splitted/ISO_20-2-1.002
rm -rf /mnt/nfs/software/PathoFact/Test/PathoFact_results/PathoFact_intermediate/MGE/plasmid_splitted/ISO_20-2-1.002
find /mnt/nfs/software/PathoFact/Test/PathoFact_results -type d -empty -delete
adding: mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002/ (stored 0%)
adding: mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002/Prodigal.log (deflated 60%)
adding: mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002/plasmid_filtered.log (stored 0%)
adding: mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002/VIRSorter_global-phage-signal.log (deflated 89%)
adding: mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002/split_contig.log (stored 0%)
adding: mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002/group_1_plasflow_prediction.log (deflated 62%)
adding: mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002/split_ORF.log (stored 0%)
adding: mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002/SignalP_split.log (deflated 31%)
adding: mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002/SignalP_p_group_2.log (deflated 29%)
adding: mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002/SignalP_n_group_1.log (deflated 30%)
adding: mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002/group_1_CTDC.log (stored 0%)
adding: mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002/group_1_DPC.log (stored 0%)
adding: mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002/group_1_AAC.log (stored 0%)
adding: mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002/group_1_CTDD.log (stored 0%)
adding: mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002/SignalP_p_group_1.log (deflated 29%)
adding: mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002/SignalP_n_group_2.log (deflated 29%)
adding: mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002/group_1.log (deflated 88%)
adding: mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002/group_1_CTDT.log (stored 0%)
adding: mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002/group_1.fasta_gt1bp_dvfpred.log (deflated 90%)
adding: mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002/group_1_classifier_prediction.log (stored 0%)
adding: mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002/SignalP_temp.log (deflated 56%)
adding: mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002/gene_table_library.log (deflated 55%)
adding: mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002/hmm_results.log (deflated 53%)
adding: mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002/combine_virulence_results.log (deflated 58%)
adding: mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002/MGE_AMR_prediction_detail_temp.log (deflated 58%)
adding: mnt/nfs/software/PathoFact/Test/PathoFact_results/logs/ISO_20-2-1.002/PathoFact_predictions.log (deflated 57%)
[Tue May 11 21:18:02 2021]
Finished job 28.
449 of 401 steps (112%) done
and stay 449 of 401 steps (112%) done
step long time.
Dear PathoFact team, Thanks for your such amazing work. My issue is that I got unknown job termination when I run PathoFact with multiple input genomes.
command
nohup time snakemake -s Snakefile --configfile config.yaml --cores --use-conda -p &>iso.log&
config.yaml
(PathoFact) [u@h@PathoFact]$ cat config.yaml
pathofact:
sample: ["ISO_102-3","ISO_1051","ISO_108-2","ISO_10SP3-6-1","ISO_10SP3-6-3","ISO_130","ISO_138","ISO_167","ISO_174","ISO_194-2","ISO_197","ISO_20-2-1.001","ISO_20-2-1.002","ISO_32-3-3","ISO_83-1","ISO_83-3-2","ISO_95"]
project: PathoFact_results # requires user input
datadir: "/mnt/nfs/software/PathoFact/Test" # requires user input
workflow: "complete" #options: "complete", "AMR", "Tox", "Vir"
size_fasta: 10000 #Adjustable to preference
scripts: "scripts"
signalp: "/mnt/nfs/software/signalp-5.0b/bin" # requires user input
deepvirfinder: "submodules/DeepVirFinder/dvf.py"
tox_hmm: "databases/toxins/combined_Toxin.hmm"
tox_lib: "databases/library_HMM_Toxins.csv"
tox_threshold: 40 #Bitscore threshold of the toxin prediction, adjustable by user to preference
vir_hmm: "databases/virulence/Virulence_factor.hmm"
vir_domains: "databases/models_and_domains"
plasflow_threshold: 0.7
plasflow_minlen: 1000
runtime:
short: "00:10:00"
medium: "01:00:00"
long: "02:00:00"
mem:
normal_mem_per_core_gb: "10G"
big_mem_cores: 10
big_mem_per_core_gb: "30G"
Logs(part)
17 HMM_VIR_report
17 HMM_correct_format_2
17 HMM_correct_format_2_vir
17 HMM_correct_format_3
17 Plasmid_aggregate
34 Prodigal
17 R_script
17 SignalPN_aggregate
17 SignalPP_aggregate
17 aggregate_RGI
17 aggregate_VirFinder
17 aggregate_VirSorter
17 aggregate_deepARG
17 aggregate_signalP
1 all
17 clean_all
17 combine_AMR
17 combine_AMR_plasmid
17 combine_PathoFact
17 filter_seq
17 format_classifier
17 format_classifier_2
17 generate_ContigTranslation
34 generate_ID
17 generate_contigID
17 generate_translation
17 mapping_file
17 merge_SignalPVir
17 run_VirSorter
17 select
17 splitcontig
17 splitplasmid
34 splitting
17 splittingsignalP
664
767 of 857 steps (89%) done
[Tue May 11 10:01:52 2021]
Finished job 326.
768 of 857 steps (90%) done
[Tue May 11 10:02:28 2021]
Finished job 270.
769 of 857 steps (90%) done
[Tue May 11 10:03:00 2021]
Finished job 278.
770 of 857 steps (90%) done
[Tue May 11 10:03:22 2021]
Finished job 342.
771 of 857 steps (90%) done
[Tue May 11 10:05:56 2021]
Finished job 246.
772 of 857 steps (90%) done
[Tue May 11 10:07:47 2021]
Finished job 294.
773 of 857 steps (90%) done
It blocked on the 90% step, and I checked the output reasult no other error message. I am looking forward your reply, Thanks a lot