[2024-01-24 10:47:06,596] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,605] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,606] [INFO] DQC Reference Directory: /var/lib/cwl/stg9065413f-e02f-4623-be22-5989f139eacd/dqc_reference
[2024-01-24 10:47:12,683] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,798] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,798] [INFO] Running command: gunzip -c /var/lib/cwl/stge8ad3540-97ad-4b06-a85f-bad10ae8daa3/GCF_019457595.1_ASM1945759v1_genomic.fna.gz | prodigal -d GCF_019457595.1_ASM1945759v1_genomic.fna/cds.fna -a GCF_019457595.1_ASM1945759v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:22,709] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:22,710] [INFO] Task started: HMMsearch
[2024-01-24 10:47:22,710] [INFO] Running command: hmmsearch --tblout GCF_019457595.1_ASM1945759v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9065413f-e02f-4623-be22-5989f139eacd/dqc_reference/reference_markers.hmm GCF_019457595.1_ASM1945759v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:23,007] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:23,008] [INFO] Found 6/6 markers.
[2024-01-24 10:47:23,046] [INFO] Query marker FASTA was written to GCF_019457595.1_ASM1945759v1_genomic.fna/markers.fasta
[2024-01-24 10:47:23,047] [INFO] Task started: Blastn
[2024-01-24 10:47:23,047] [INFO] Running command: blastn -query GCF_019457595.1_ASM1945759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9065413f-e02f-4623-be22-5989f139eacd/dqc_reference/reference_markers.fasta -out GCF_019457595.1_ASM1945759v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:23,883] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:23,886] [INFO] Selected 15 target genomes.
[2024-01-24 10:47:23,886] [INFO] Target genome list was writen to GCF_019457595.1_ASM1945759v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:24,418] [INFO] Task started: fastANI
[2024-01-24 10:47:24,418] [INFO] Running command: fastANI --query /var/lib/cwl/stge8ad3540-97ad-4b06-a85f-bad10ae8daa3/GCF_019457595.1_ASM1945759v1_genomic.fna.gz --refList GCF_019457595.1_ASM1945759v1_genomic.fna/target_genomes.txt --output GCF_019457595.1_ASM1945759v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:37,851] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:37,851] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9065413f-e02f-4623-be22-5989f139eacd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:37,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9065413f-e02f-4623-be22-5989f139eacd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:37,864] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:47:37,864] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:47:37,865] [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 marisflavi	strain=JCM 12192	GCA_023283925.1	260364	260364	type	True	82.1229	642	1456	95	below_threshold
Shewanella colwelliana	strain=ATCC 39565	GCA_000518705.1	23	23	type	True	81.6403	690	1456	95	below_threshold
Shewanella algidipiscicola	strain=LMG 23746	GCA_003605125.1	614070	614070	type	True	81.2998	670	1456	95	below_threshold
Shewanella algidipiscicola	strain=LMG 23746	GCA_019655175.1	614070	614070	type	True	81.1835	666	1456	95	below_threshold
Shewanella loihica	strain=PV-4	GCA_000016065.1	359303	359303	type	True	80.3968	537	1456	95	below_threshold
Shewanella aquimarina	strain=JCM 12193	GCA_023349185.1	260365	260365	type	True	79.9873	520	1456	95	below_threshold
Shewanella waksmanii	strain=ATCC BAA-643	GCA_000518805.1	213783	213783	type	True	79.1821	358	1456	95	below_threshold
Shewanella marinintestina	strain=LMG 21403	GCA_023283845.1	190305	190305	type	True	78.8488	326	1456	95	below_threshold
Shewanella sairae	strain=LMG 21408	GCA_023283535.1	190310	190310	type	True	78.7747	318	1456	95	below_threshold
Shewanella baltica	strain=NCTC10735	GCA_900456975.1	62322	62322	type	True	78.649	289	1456	95	below_threshold
Shewanella inventionis	strain=CGMCC 1.15339	GCA_014641855.1	1738770	1738770	type	True	78.2392	203	1456	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	78.0912	204	1456	95	below_threshold
Shewanella morhuae	strain=ATCC BAA-1205	GCA_900156405.1	365591	365591	type	True	77.9535	245	1456	95	below_threshold
Shewanella profunda	strain=DSM 15900	GCA_023283765.1	254793	254793	type	True	77.8667	274	1456	95	below_threshold
Shewanella glacialipiscicola	strain=LMG 23744	GCA_023283485.1	614069	614069	type	True	77.8285	254	1456	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:37,866] [INFO] DFAST Taxonomy check result was written to GCF_019457595.1_ASM1945759v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:37,867] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:37,867] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:37,867] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9065413f-e02f-4623-be22-5989f139eacd/dqc_reference/checkm_data
[2024-01-24 10:47:37,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:37,912] [INFO] Task started: CheckM
[2024-01-24 10:47:37,913] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019457595.1_ASM1945759v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019457595.1_ASM1945759v1_genomic.fna/checkm_input GCF_019457595.1_ASM1945759v1_genomic.fna/checkm_result
[2024-01-24 10:48:12,603] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:12,604] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:12,623] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:12,623] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:12,624] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019457595.1_ASM1945759v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:12,624] [INFO] Task started: Blastn
[2024-01-24 10:48:12,624] [INFO] Running command: blastn -query GCF_019457595.1_ASM1945759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9065413f-e02f-4623-be22-5989f139eacd/dqc_reference/reference_markers_gtdb.fasta -out GCF_019457595.1_ASM1945759v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:13,891] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:13,897] [INFO] Selected 15 target genomes.
[2024-01-24 10:48:13,897] [INFO] Target genome list was writen to GCF_019457595.1_ASM1945759v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:13,924] [INFO] Task started: fastANI
[2024-01-24 10:48:13,925] [INFO] Running command: fastANI --query /var/lib/cwl/stge8ad3540-97ad-4b06-a85f-bad10ae8daa3/GCF_019457595.1_ASM1945759v1_genomic.fna.gz --refList GCF_019457595.1_ASM1945759v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019457595.1_ASM1945759v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:27,073] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:27,098] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:48:27,098] [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_002215585.1	s__Shewanella marisflavi	82.4856	645	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.20	98.16	0.93	0.93	3	-
GCF_000518705.1	s__Shewanella colwelliana	81.6616	689	1456	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	81.307	669	1456	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	80.3851	537	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.22	95.22	0.91	0.91	2	-
GCF_009831655.1	s__Shewanella insulae	80.3737	499	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000832025.1	s__Shewanella sp000832025	80.0012	541	1456	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	79.1902	357	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.84	97.84	0.93	0.93	2	-
GCF_000019185.1	s__Shewanella halifaxensis	79.1402	344	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900456975.1	s__Shewanella baltica	78.7565	291	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.88	96.32	0.89	0.85	16	-
GCF_009828585.1	s__Shewanella litoralis	78.2564	229	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014641855.1	s__Shewanella inventionis	78.2393	203	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014163735.1	s__Shewanella sp014163735	78.198	210	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000217915.1	s__Shewanella sp000217915	78.1186	233	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648295.1	s__Shewanella saliphila	78.0573	218	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_900156405.1	s__Shewanella morhuae	77.9562	246	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.45	98.44	0.93	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:27,102] [INFO] GTDB search result was written to GCF_019457595.1_ASM1945759v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:27,103] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:27,109] [INFO] DFAST_QC result json was written to GCF_019457595.1_ASM1945759v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:27,109] [INFO] DFAST_QC completed!
[2024-01-24 10:48:27,109] [INFO] Total running time: 0h1m21s