[2024-01-24 13:49:27,547] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:27,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:27,551] [INFO] DQC Reference Directory: /var/lib/cwl/stge963029a-79f5-4365-9791-cf482140ff9e/dqc_reference
[2024-01-24 13:49:28,892] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:28,893] [INFO] Task started: Prodigal
[2024-01-24 13:49:28,894] [INFO] Running command: gunzip -c /var/lib/cwl/stgee15e0a4-1ee6-430a-bbfd-e97412d8e75f/GCF_016469335.1_ASM1646933v1_genomic.fna.gz | prodigal -d GCF_016469335.1_ASM1646933v1_genomic.fna/cds.fna -a GCF_016469335.1_ASM1646933v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:37,396] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:37,396] [INFO] Task started: HMMsearch
[2024-01-24 13:49:37,396] [INFO] Running command: hmmsearch --tblout GCF_016469335.1_ASM1646933v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge963029a-79f5-4365-9791-cf482140ff9e/dqc_reference/reference_markers.hmm GCF_016469335.1_ASM1646933v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:37,735] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:37,737] [INFO] Found 6/6 markers.
[2024-01-24 13:49:37,777] [INFO] Query marker FASTA was written to GCF_016469335.1_ASM1646933v1_genomic.fna/markers.fasta
[2024-01-24 13:49:37,777] [INFO] Task started: Blastn
[2024-01-24 13:49:37,777] [INFO] Running command: blastn -query GCF_016469335.1_ASM1646933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge963029a-79f5-4365-9791-cf482140ff9e/dqc_reference/reference_markers.fasta -out GCF_016469335.1_ASM1646933v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:38,678] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:38,682] [INFO] Selected 27 target genomes.
[2024-01-24 13:49:38,683] [INFO] Target genome list was writen to GCF_016469335.1_ASM1646933v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:38,699] [INFO] Task started: fastANI
[2024-01-24 13:49:38,699] [INFO] Running command: fastANI --query /var/lib/cwl/stgee15e0a4-1ee6-430a-bbfd-e97412d8e75f/GCF_016469335.1_ASM1646933v1_genomic.fna.gz --refList GCF_016469335.1_ASM1646933v1_genomic.fna/target_genomes.txt --output GCF_016469335.1_ASM1646933v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:57,498] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:57,498] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge963029a-79f5-4365-9791-cf482140ff9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:57,499] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge963029a-79f5-4365-9791-cf482140ff9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:57,520] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:57,520] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:57,520] [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
Flocculibacter collagenilyticus	strain=SM1988	GCA_016469335.1	2744479	2744479	type	True	100.0	1323	1324	95	conclusive
Pseudoalteromonas phenolica	strain=KCTC 12086	GCA_001444405.1	161398	161398	suspected-type	True	79.022	81	1324	95	below_threshold
Pseudoalteromonas phenolica	strain=O-BC30	GCA_014925335.1	161398	161398	suspected-type	True	78.9432	82	1324	95	below_threshold
Pseudoalteromonas piscicida	strain=JCM 20779	GCA_000238315.4	43662	43662	type	True	78.5844	85	1324	95	below_threshold
Shewanella psychromarinicola	strain=M2	GCA_003855155.1	2487742	2487742	type	True	78.1261	61	1324	95	below_threshold
Pseudoalteromonas citrea	strain=DSM 8771	GCA_000238375.4	43655	43655	type	True	78.1203	89	1324	95	below_threshold
Pseudoalteromonas arctica	strain=A 37-1-2	GCA_000238395.4	394751	394751	type	True	77.9817	92	1324	95	below_threshold
Pseudoalteromonas espejiana	strain=ATCC 29659	GCA_002221525.1	28107	28107	type	True	77.9481	100	1324	95	below_threshold
Shewanella japonica	strain=KCTC 22435	GCA_002075795.1	93973	93973	type	True	77.8876	75	1324	95	below_threshold
Pseudoalteromonas spongiae	strain=UST010723-006	GCA_000238255.4	298657	298657	type	True	77.8125	112	1324	95	below_threshold
Pseudoalteromonas aliena	strain=SW19	GCA_014905615.1	247523	247523	type	True	77.6188	92	1324	95	below_threshold
Pseudoalteromonas arabiensis	strain=JCM 17292	GCA_001550155.1	874454	874454	type	True	77.421	97	1324	95	below_threshold
Pseudoalteromonas tunicata	strain=D2	GCA_000153245.1	314281	314281	type	True	77.3845	104	1324	95	below_threshold
Pseudoalteromonas piscicida	strain=ATCC 15057	GCA_000382005.1	43662	43662	type	True	77.3777	78	1324	95	below_threshold
Pseudoalteromonas phenolica	strain=O-BC30	GCA_004103265.1	161398	161398	suspected-type	True	77.3556	68	1324	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	77.3126	85	1324	95	below_threshold
Pseudoalteromonas espejiana	strain=NBRC 102222	GCA_007989585.1	28107	28107	type	True	76.9033	88	1324	95	below_threshold
Pseudoalteromonas profundi	strain=CGMCC 1.15394	GCA_014642695.1	1774956	1774956	type	True	76.8595	77	1324	95	below_threshold
Pseudoalteromonas fuliginea	strain=KMM 216	GCA_000690055.1	1872678	1872678	type	True	76.6652	89	1324	95	below_threshold
Pseudoalteromonas denitrificans	strain=DSM 6059	GCA_900112265.1	43656	43656	type	True	76.5526	92	1324	95	below_threshold
Shewanella psychromarinicola	strain=JCM 32090	GCA_023283865.1	2487742	2487742	type	True	76.2238	53	1324	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:57,522] [INFO] DFAST Taxonomy check result was written to GCF_016469335.1_ASM1646933v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:57,523] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:57,523] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:57,523] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge963029a-79f5-4365-9791-cf482140ff9e/dqc_reference/checkm_data
[2024-01-24 13:49:57,525] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:57,573] [INFO] Task started: CheckM
[2024-01-24 13:49:57,573] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016469335.1_ASM1646933v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016469335.1_ASM1646933v1_genomic.fna/checkm_input GCF_016469335.1_ASM1646933v1_genomic.fna/checkm_result
[2024-01-24 13:50:30,217] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:30,219] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:30,243] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:30,243] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:30,244] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016469335.1_ASM1646933v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:30,244] [INFO] Task started: Blastn
[2024-01-24 13:50:30,245] [INFO] Running command: blastn -query GCF_016469335.1_ASM1646933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge963029a-79f5-4365-9791-cf482140ff9e/dqc_reference/reference_markers_gtdb.fasta -out GCF_016469335.1_ASM1646933v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:31,504] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:31,509] [INFO] Selected 28 target genomes.
[2024-01-24 13:50:31,509] [INFO] Target genome list was writen to GCF_016469335.1_ASM1646933v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:31,554] [INFO] Task started: fastANI
[2024-01-24 13:50:31,555] [INFO] Running command: fastANI --query /var/lib/cwl/stgee15e0a4-1ee6-430a-bbfd-e97412d8e75f/GCF_016469335.1_ASM1646933v1_genomic.fna.gz --refList GCF_016469335.1_ASM1646933v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016469335.1_ASM1646933v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:50,941] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:50,969] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:50,969] [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_016469335.1	s__Flocculibacter collagenilyticus	100.0	1324	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Flocculibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009176705.1	s__Pseudoalteromonas sp009176705	79.4742	80	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001444405.1	s__Pseudoalteromonas phenolica	78.7249	82	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.52	98.61	0.97	0.92	4	-
GCF_002850255.1	s__Pseudoalteromonas sp002850255	78.3314	88	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.4968	98.33	98.31	0.92	0.91	5	-
GCF_000238275.3	s__Pseudoalteromonas undina	78.1819	103	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	96.09	0.91	0.86	14	-
GCF_003390395.1	s__Thalassotalea euphylliae_C	78.1562	81	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238375.3	s__Pseudoalteromonas citrea	78.1304	87	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002221505.1	s__Pseudoalteromonas nigrifaciens	78.1155	97	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0242	98.65	98.00	0.90	0.81	15	-
GCF_002221525.1	s__Pseudoalteromonas espejiana	78.1086	101	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000196495.1	s__Aliivibrio salmonicida_A	77.98	60	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	97.90	97.13	0.84	0.80	5	-
GCF_001465295.1	s__Pseudoalteromonas translucida	77.9755	99	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0242	N/A	N/A	N/A	N/A	1	-
GCF_002310815.1	s__Pseudoalteromonas tunicata	77.9746	101	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.99	99.99	0.99	0.99	3	-
GCF_000238395.3	s__Pseudoalteromonas arctica	77.825	90	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.91	96.03	0.87	0.80	33	-
GCF_002075795.1	s__Shewanella japonica	77.7521	73	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.37	97.91	0.95	0.93	6	-
GCF_004792295.1	s__Pseudoalteromonas lipolytica_C	77.732	99	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.42	98.24	0.87	0.68	9	-
GCF_002289345.1	s__Pseudoalteromonas sp002289345	77.64	68	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.3013	N/A	N/A	N/A	N/A	1	-
GCF_002964665.1	s__Pseudoalteromonas sp002964665	77.5595	62	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001306915.1	s__Pseudoalteromonas lipolytica_A	77.5187	97	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.22	97.66	0.91	0.90	9	-
GCF_001550155.1	s__Pseudoalteromonas arabiensis	77.4537	96	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.77	95.60	0.91	0.90	4	-
GCF_005886345.1	s__Pseudoalteromonas phenolica_A	77.3677	71	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	96.97	0.91	0.89	3	-
GCA_000814675.1	s__Pseudoalteromonas distincta	77.2324	84	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	95.34	0.88	0.77	38	-
GCA_007988745.1	s__Pseudoalteromonas atlantica	77.2243	79	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.93	97.66	0.89	0.85	29	-
GCF_002723455.1	s__Pseudoalteromonas sp002723455	77.1607	77	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.50	98.50	0.93	0.93	2	-
GCF_000808575.1	s__Alteromonas marina	76.6969	53	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.44	97.44	0.91	0.91	2	-
GCF_018860585.1	s__Colwellia sp018860585	76.6696	72	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000690055.1	s__Pseudoalteromonas fuliginea	76.6395	90	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.33	97.88	0.92	0.87	9	-
GCF_900112265.1	s__Pseudoalteromonas denitrificans	76.5526	92	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:50,971] [INFO] GTDB search result was written to GCF_016469335.1_ASM1646933v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:50,972] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:50,977] [INFO] DFAST_QC result json was written to GCF_016469335.1_ASM1646933v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:50,977] [INFO] DFAST_QC completed!
[2024-01-24 13:50:50,977] [INFO] Total running time: 0h1m23s