[2024-01-24 14:07:31,197] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:31,199] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:31,200] [INFO] DQC Reference Directory: /var/lib/cwl/stg80adc217-c038-4a7e-92f1-2d4aaf9bef67/dqc_reference
[2024-01-24 14:07:32,462] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:32,463] [INFO] Task started: Prodigal
[2024-01-24 14:07:32,463] [INFO] Running command: gunzip -c /var/lib/cwl/stg885251d9-27ce-40d4-af4e-6fa65cb2c274/GCF_003797885.1_ASM379788v1_genomic.fna.gz | prodigal -d GCF_003797885.1_ASM379788v1_genomic.fna/cds.fna -a GCF_003797885.1_ASM379788v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:42,633] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:42,633] [INFO] Task started: HMMsearch
[2024-01-24 14:07:42,634] [INFO] Running command: hmmsearch --tblout GCF_003797885.1_ASM379788v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80adc217-c038-4a7e-92f1-2d4aaf9bef67/dqc_reference/reference_markers.hmm GCF_003797885.1_ASM379788v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:42,969] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:42,970] [INFO] Found 6/6 markers.
[2024-01-24 14:07:43,016] [INFO] Query marker FASTA was written to GCF_003797885.1_ASM379788v1_genomic.fna/markers.fasta
[2024-01-24 14:07:43,017] [INFO] Task started: Blastn
[2024-01-24 14:07:43,017] [INFO] Running command: blastn -query GCF_003797885.1_ASM379788v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80adc217-c038-4a7e-92f1-2d4aaf9bef67/dqc_reference/reference_markers.fasta -out GCF_003797885.1_ASM379788v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:43,798] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:43,805] [INFO] Selected 8 target genomes.
[2024-01-24 14:07:43,806] [INFO] Target genome list was writen to GCF_003797885.1_ASM379788v1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:43,810] [INFO] Task started: fastANI
[2024-01-24 14:07:43,810] [INFO] Running command: fastANI --query /var/lib/cwl/stg885251d9-27ce-40d4-af4e-6fa65cb2c274/GCF_003797885.1_ASM379788v1_genomic.fna.gz --refList GCF_003797885.1_ASM379788v1_genomic.fna/target_genomes.txt --output GCF_003797885.1_ASM379788v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:52,700] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:52,701] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80adc217-c038-4a7e-92f1-2d4aaf9bef67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:52,701] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80adc217-c038-4a7e-92f1-2d4aaf9bef67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:52,715] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:07:52,715] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:52,716] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Shewanella vesiculosa	strain=LMG 24424	GCA_003797885.1	518738	518738	type	True	100.0	1547	1549	95	conclusive
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	99.982	1547	1549	95	conclusive
Shewanella livingstonensis	strain=LMG 19866	GCA_003855395.1	150120	150120	type	True	85.5954	1235	1549	95	below_threshold
Shewanella psychromarinicola	strain=JCM 32090	GCA_023283865.1	2487742	2487742	type	True	84.4263	1144	1549	95	below_threshold
Shewanella psychromarinicola	strain=M2	GCA_003855155.1	2487742	2487742	type	True	84.4125	1180	1549	95	below_threshold
Shewanella polaris	strain=SM1901	GCA_006385555.1	2588449	2588449	type	True	83.6176	1119	1549	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	81.2941	850	1549	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	81.0334	829	1549	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:52,717] [INFO] DFAST Taxonomy check result was written to GCF_003797885.1_ASM379788v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:52,718] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:52,718] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:52,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80adc217-c038-4a7e-92f1-2d4aaf9bef67/dqc_reference/checkm_data
[2024-01-24 14:07:52,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:52,764] [INFO] Task started: CheckM
[2024-01-24 14:07:52,764] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003797885.1_ASM379788v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003797885.1_ASM379788v1_genomic.fna/checkm_input GCF_003797885.1_ASM379788v1_genomic.fna/checkm_result
[2024-01-24 14:08:29,410] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:29,411] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:29,454] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:29,454] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:29,455] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003797885.1_ASM379788v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:29,455] [INFO] Task started: Blastn
[2024-01-24 14:08:29,455] [INFO] Running command: blastn -query GCF_003797885.1_ASM379788v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80adc217-c038-4a7e-92f1-2d4aaf9bef67/dqc_reference/reference_markers_gtdb.fasta -out GCF_003797885.1_ASM379788v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:30,660] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:30,664] [INFO] Selected 7 target genomes.
[2024-01-24 14:08:30,664] [INFO] Target genome list was writen to GCF_003797885.1_ASM379788v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:30,670] [INFO] Task started: fastANI
[2024-01-24 14:08:30,670] [INFO] Running command: fastANI --query /var/lib/cwl/stg885251d9-27ce-40d4-af4e-6fa65cb2c274/GCF_003797885.1_ASM379788v1_genomic.fna.gz --refList GCF_003797885.1_ASM379788v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003797885.1_ASM379788v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:39,395] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:39,404] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:39,404] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_003797885.1	s__Shewanella vesiculosa	100.0	1546	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.53	98.48	0.92	0.86	17	conclusive
GCF_010092445.1	s__Shewanella sp002836315	85.8969	1257	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.47	98.34	0.91	0.90	4	-
GCF_003855395.1	s__Shewanella livingstonensis	85.6108	1233	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797125.1	s__Shewanella frigidimarina	85.5761	1259	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.50	96.12	0.90	0.86	5	-
GCF_014164505.1	s__Shewanella sp014164505	85.5684	966	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003855155.1	s__Shewanella sp002836275	84.4176	1179	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.14	98.29	0.96	0.92	3	-
GCF_006385555.1	s__Shewanella polaris	83.6194	1120	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.84	97.84	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:39,406] [INFO] GTDB search result was written to GCF_003797885.1_ASM379788v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:39,407] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:39,410] [INFO] DFAST_QC result json was written to GCF_003797885.1_ASM379788v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:39,410] [INFO] DFAST_QC completed!
[2024-01-24 14:08:39,410] [INFO] Total running time: 0h1m8s