[2024-01-24 12:22:48,208] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,209] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,210] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d703e1c-2560-40b8-8ecb-44eeeeb80c55/dqc_reference
[2024-01-24 12:22:49,485] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:49,486] [INFO] Task started: Prodigal
[2024-01-24 12:22:49,486] [INFO] Running command: gunzip -c /var/lib/cwl/stg357de742-dac3-41d0-81d0-7c86e9fe746a/GCF_019457515.1_ASM1945751v1_genomic.fna.gz | prodigal -d GCF_019457515.1_ASM1945751v1_genomic.fna/cds.fna -a GCF_019457515.1_ASM1945751v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:59,349] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:59,349] [INFO] Task started: HMMsearch
[2024-01-24 12:22:59,350] [INFO] Running command: hmmsearch --tblout GCF_019457515.1_ASM1945751v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d703e1c-2560-40b8-8ecb-44eeeeb80c55/dqc_reference/reference_markers.hmm GCF_019457515.1_ASM1945751v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:59,652] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:59,654] [INFO] Found 6/6 markers.
[2024-01-24 12:22:59,690] [INFO] Query marker FASTA was written to GCF_019457515.1_ASM1945751v1_genomic.fna/markers.fasta
[2024-01-24 12:22:59,691] [INFO] Task started: Blastn
[2024-01-24 12:22:59,691] [INFO] Running command: blastn -query GCF_019457515.1_ASM1945751v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d703e1c-2560-40b8-8ecb-44eeeeb80c55/dqc_reference/reference_markers.fasta -out GCF_019457515.1_ASM1945751v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:00,479] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:00,483] [INFO] Selected 15 target genomes.
[2024-01-24 12:23:00,484] [INFO] Target genome list was writen to GCF_019457515.1_ASM1945751v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:00,536] [INFO] Task started: fastANI
[2024-01-24 12:23:00,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg357de742-dac3-41d0-81d0-7c86e9fe746a/GCF_019457515.1_ASM1945751v1_genomic.fna.gz --refList GCF_019457515.1_ASM1945751v1_genomic.fna/target_genomes.txt --output GCF_019457515.1_ASM1945751v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:13,319] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:13,320] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d703e1c-2560-40b8-8ecb-44eeeeb80c55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:13,321] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d703e1c-2560-40b8-8ecb-44eeeeb80c55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:13,336] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:23:13,336] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:23:13,336] [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 colwelliana	strain=ATCC 39565	GCA_000518705.1	23	23	type	True	82.3626	752	1441	95	below_threshold
Shewanella algidipiscicola	strain=LMG 23746	GCA_019655175.1	614070	614070	type	True	81.4452	671	1441	95	below_threshold
Shewanella algidipiscicola	strain=LMG 23746	GCA_003605125.1	614070	614070	type	True	81.4313	700	1441	95	below_threshold
Shewanella loihica	strain=PV-4	GCA_000016065.1	359303	359303	type	True	80.5921	559	1441	95	below_threshold
Shewanella marisflavi	strain=JCM 12192	GCA_023283925.1	260364	260364	type	True	80.2029	620	1441	95	below_threshold
Shewanella aquimarina	strain=JCM 12193	GCA_023349185.1	260365	260365	type	True	80.0387	567	1441	95	below_threshold
Shewanella insulae	strain=JBTF-M18	GCA_009831655.1	2681496	2681496	type	True	79.9703	556	1441	95	below_threshold
Shewanella pealeana	strain=ATCC 700345	GCA_000018285.1	70864	70864	type	True	79.5579	334	1441	95	below_threshold
Shewanella schlegeliana	strain=JCM 11561	GCA_016765635.1	190308	190308	type	True	79.1825	342	1441	95	below_threshold
Shewanella sairae	strain=LMG 21408	GCA_023283535.1	190310	190310	type	True	79.1006	312	1441	95	below_threshold
Shewanella schlegeliana	strain=LMG 21406	GCA_023283605.1	190308	190308	type	True	79.0647	341	1441	95	below_threshold
Shewanella schlegeliana	strain=JCM 11561	GCA_019654995.1	190308	190308	type	True	79.0079	336	1441	95	below_threshold
Shewanella nanhaiensis	strain=NR704-98	GCA_019457885.1	2864872	2864872	type	True	78.8236	363	1441	95	below_threshold
Shewanella fidelis	strain=ATCC BAA-318	GCA_000518605.1	173509	173509	type	True	78.7223	330	1441	95	below_threshold
Shewanella donghaensis	strain=LT17	GCA_007567505.1	238836	238836	type	True	78.6833	229	1441	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:13,338] [INFO] DFAST Taxonomy check result was written to GCF_019457515.1_ASM1945751v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:13,340] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:13,340] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:13,340] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d703e1c-2560-40b8-8ecb-44eeeeb80c55/dqc_reference/checkm_data
[2024-01-24 12:23:13,341] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:13,387] [INFO] Task started: CheckM
[2024-01-24 12:23:13,387] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019457515.1_ASM1945751v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019457515.1_ASM1945751v1_genomic.fna/checkm_input GCF_019457515.1_ASM1945751v1_genomic.fna/checkm_result
[2024-01-24 12:23:47,458] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:47,460] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:47,484] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:47,484] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:47,485] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019457515.1_ASM1945751v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:47,485] [INFO] Task started: Blastn
[2024-01-24 12:23:47,485] [INFO] Running command: blastn -query GCF_019457515.1_ASM1945751v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d703e1c-2560-40b8-8ecb-44eeeeb80c55/dqc_reference/reference_markers_gtdb.fasta -out GCF_019457515.1_ASM1945751v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:48,667] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:48,671] [INFO] Selected 15 target genomes.
[2024-01-24 12:23:48,671] [INFO] Target genome list was writen to GCF_019457515.1_ASM1945751v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:48,686] [INFO] Task started: fastANI
[2024-01-24 12:23:48,686] [INFO] Running command: fastANI --query /var/lib/cwl/stg357de742-dac3-41d0-81d0-7c86e9fe746a/GCF_019457515.1_ASM1945751v1_genomic.fna.gz --refList GCF_019457515.1_ASM1945751v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019457515.1_ASM1945751v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:01,751] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:01,767] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:24:01,767] [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_000518705.1	s__Shewanella colwelliana	82.3685	753	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.91	98.91	0.92	0.92	2	-
GCF_003605125.1	s__Shewanella algidipiscicola	81.3944	705	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.64	98.64	0.92	0.92	2	-
GCF_000016065.1	s__Shewanella loihica	80.5919	559	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.22	95.22	0.91	0.91	2	-
GCF_002215585.1	s__Shewanella marisflavi	80.4142	619	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.20	98.16	0.93	0.93	3	-
GCF_000832025.1	s__Shewanella sp000832025	80.2523	566	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009831655.1	s__Shewanella insulae	79.9604	557	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018285.1	s__Shewanella pealeana	79.5658	334	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518805.1	s__Shewanella waksmanii	79.4665	364	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.84	97.84	0.93	0.93	2	-
GCF_013248905.1	s__Shewanella sp013248905	79.2391	246	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765635.1	s__Shewanella schlegeliana	79.1814	342	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007567505.1	s__Shewanella donghaensis	78.9306	229	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518605.1	s__Shewanella fidelis	78.7504	330	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.11	97.11	0.90	0.90	2	-
GCF_003797125.1	s__Shewanella frigidimarina	78.4691	216	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.50	96.12	0.90	0.86	5	-
GCF_014163735.1	s__Shewanella sp014163735	78.4434	175	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641855.1	s__Shewanella inventionis	78.1603	220	1441	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 12:24:01,770] [INFO] GTDB search result was written to GCF_019457515.1_ASM1945751v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:01,771] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:01,775] [INFO] DFAST_QC result json was written to GCF_019457515.1_ASM1945751v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:01,775] [INFO] DFAST_QC completed!
[2024-01-24 12:24:01,775] [INFO] Total running time: 0h1m14s