[2024-01-24 13:09:43,319] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:43,322] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:43,322] [INFO] DQC Reference Directory: /var/lib/cwl/stgabf6cf0f-39ff-4095-bd8e-d8890f546127/dqc_reference
[2024-01-24 13:09:44,574] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:44,574] [INFO] Task started: Prodigal
[2024-01-24 13:09:44,575] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e23d010-2baf-4c8f-9142-ded3a4da6e82/GCF_002005305.1_ASM200530v1_genomic.fna.gz | prodigal -d GCF_002005305.1_ASM200530v1_genomic.fna/cds.fna -a GCF_002005305.1_ASM200530v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:58,842] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:58,843] [INFO] Task started: HMMsearch
[2024-01-24 13:09:58,843] [INFO] Running command: hmmsearch --tblout GCF_002005305.1_ASM200530v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabf6cf0f-39ff-4095-bd8e-d8890f546127/dqc_reference/reference_markers.hmm GCF_002005305.1_ASM200530v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:59,167] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:59,169] [INFO] Found 6/6 markers.
[2024-01-24 13:09:59,218] [INFO] Query marker FASTA was written to GCF_002005305.1_ASM200530v1_genomic.fna/markers.fasta
[2024-01-24 13:09:59,218] [INFO] Task started: Blastn
[2024-01-24 13:09:59,219] [INFO] Running command: blastn -query GCF_002005305.1_ASM200530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabf6cf0f-39ff-4095-bd8e-d8890f546127/dqc_reference/reference_markers.fasta -out GCF_002005305.1_ASM200530v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:59,957] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:59,960] [INFO] Selected 13 target genomes.
[2024-01-24 13:09:59,961] [INFO] Target genome list was writen to GCF_002005305.1_ASM200530v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:59,966] [INFO] Task started: fastANI
[2024-01-24 13:09:59,966] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e23d010-2baf-4c8f-9142-ded3a4da6e82/GCF_002005305.1_ASM200530v1_genomic.fna.gz --refList GCF_002005305.1_ASM200530v1_genomic.fna/target_genomes.txt --output GCF_002005305.1_ASM200530v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:15,571] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:15,572] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabf6cf0f-39ff-4095-bd8e-d8890f546127/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:15,572] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabf6cf0f-39ff-4095-bd8e-d8890f546127/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:15,589] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:15,589] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:15,590] [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 psychrophila	strain=WP2	GCA_002005305.1	225848	225848	type	True	100.0	2116	2117	95	conclusive
Shewanella psychropiezotolerans	strain=YLB-06	GCA_007197555.1	2593655	2593655	type	True	88.0879	1759	2117	95	below_threshold
Shewanella benthica	strain=DSM 8812	GCA_015069875.1	43661	43661	type	True	86.2989	1044	2117	95	below_threshold
Shewanella violacea	strain=DSS12	GCA_000091325.1	60217	60217	type	True	84.607	1289	2117	95	below_threshold
Shewanella eurypsychrophilus	strain=YLB-08	GCA_007004545.3	2593656	2593656	type	True	82.6373	1113	2117	95	below_threshold
Shewanella atlantica	strain=HAW-EB5	GCA_003966265.1	271099	271099	type	True	79.6183	601	2117	95	below_threshold
Shewanella woodyi	strain=ATCC 51908	GCA_000019525.1	60961	60961	type	True	79.4385	571	2117	95	below_threshold
Shewanella nanhaiensis	strain=NR704-98	GCA_019457885.1	2864872	2864872	type	True	79.0732	569	2117	95	below_threshold
Shewanella hanedai	strain=JCM 20706	GCA_007197645.1	25	25	type	True	78.9721	540	2117	95	below_threshold
Shewanella insulae	strain=JBTF-M18	GCA_009831655.1	2681496	2681496	type	True	78.4073	325	2117	95	below_threshold
Shewanella profunda	strain=DSM 15900	GCA_023283765.1	254793	254793	type	True	77.9106	198	2117	95	below_threshold
Parashewanella hymeniacidonis	strain=202IG2-18	GCA_016900895.1	2807618	2807618	type	True	77.9023	117	2117	95	below_threshold
Shewanella chilikensis	strain=CCUG 57101	GCA_023283475.1	558541	558541	type	True	77.3926	166	2117	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:15,592] [INFO] DFAST Taxonomy check result was written to GCF_002005305.1_ASM200530v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:15,592] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:15,593] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:15,593] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabf6cf0f-39ff-4095-bd8e-d8890f546127/dqc_reference/checkm_data
[2024-01-24 13:10:15,594] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:15,654] [INFO] Task started: CheckM
[2024-01-24 13:10:15,654] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002005305.1_ASM200530v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002005305.1_ASM200530v1_genomic.fna/checkm_input GCF_002005305.1_ASM200530v1_genomic.fna/checkm_result
[2024-01-24 13:11:02,714] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:02,716] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:02,744] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:02,744] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:02,745] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002005305.1_ASM200530v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:02,745] [INFO] Task started: Blastn
[2024-01-24 13:11:02,745] [INFO] Running command: blastn -query GCF_002005305.1_ASM200530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabf6cf0f-39ff-4095-bd8e-d8890f546127/dqc_reference/reference_markers_gtdb.fasta -out GCF_002005305.1_ASM200530v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:03,879] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:03,882] [INFO] Selected 8 target genomes.
[2024-01-24 13:11:03,883] [INFO] Target genome list was writen to GCF_002005305.1_ASM200530v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:03,889] [INFO] Task started: fastANI
[2024-01-24 13:11:03,889] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e23d010-2baf-4c8f-9142-ded3a4da6e82/GCF_002005305.1_ASM200530v1_genomic.fna.gz --refList GCF_002005305.1_ASM200530v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002005305.1_ASM200530v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:15,750] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:15,759] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:15,759] [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_002005305.1	s__Shewanella psychrophila	100.0	2116	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007197555.1	s__Shewanella sp007197555	88.0913	1758	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.43	99.43	0.94	0.94	2	-
GCF_015069875.1	s__Shewanella benthica	86.3048	1043	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.81	96.81	0.66	0.66	2	-
GCF_000172075.1	s__Shewanella benthica_A	85.6162	1134	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.25	96.25	0.86	0.86	2	-
GCA_013214165.1	s__Shewanella sp013214165	85.0732	1144	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000091325.1	s__Shewanella violacea	84.6219	1290	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004545.2	s__Shewanella sp007004545	82.6895	1077	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.97	99.97	0.99	0.99	2	-
GCF_001957125.1	s__Shewanella sp001957125	80.0354	823	2117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:15,761] [INFO] GTDB search result was written to GCF_002005305.1_ASM200530v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:15,762] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:15,767] [INFO] DFAST_QC result json was written to GCF_002005305.1_ASM200530v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:15,767] [INFO] DFAST_QC completed!
[2024-01-24 13:11:15,767] [INFO] Total running time: 0h1m32s