[2024-01-24 10:47:22,812] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:22,814] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:22,814] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc26252c-1de7-4939-8020-74ddaddf2529/dqc_reference
[2024-01-24 10:47:26,177] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,182] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,183] [INFO] Running command: gunzip -c /var/lib/cwl/stg528cb72c-e9d0-4b6b-ad11-a038a8b226da/GCF_030161395.1_ASM3016139v1_genomic.fna.gz | prodigal -d GCF_030161395.1_ASM3016139v1_genomic.fna/cds.fna -a GCF_030161395.1_ASM3016139v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:35,089] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:35,090] [INFO] Task started: HMMsearch
[2024-01-24 10:47:35,090] [INFO] Running command: hmmsearch --tblout GCF_030161395.1_ASM3016139v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc26252c-1de7-4939-8020-74ddaddf2529/dqc_reference/reference_markers.hmm GCF_030161395.1_ASM3016139v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:35,414] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:35,416] [INFO] Found 6/6 markers.
[2024-01-24 10:47:35,469] [INFO] Query marker FASTA was written to GCF_030161395.1_ASM3016139v1_genomic.fna/markers.fasta
[2024-01-24 10:47:35,469] [INFO] Task started: Blastn
[2024-01-24 10:47:35,469] [INFO] Running command: blastn -query GCF_030161395.1_ASM3016139v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc26252c-1de7-4939-8020-74ddaddf2529/dqc_reference/reference_markers.fasta -out GCF_030161395.1_ASM3016139v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:36,184] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:36,191] [INFO] Selected 27 target genomes.
[2024-01-24 10:47:36,191] [INFO] Target genome list was writen to GCF_030161395.1_ASM3016139v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:36,202] [INFO] Task started: fastANI
[2024-01-24 10:47:36,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg528cb72c-e9d0-4b6b-ad11-a038a8b226da/GCF_030161395.1_ASM3016139v1_genomic.fna.gz --refList GCF_030161395.1_ASM3016139v1_genomic.fna/target_genomes.txt --output GCF_030161395.1_ASM3016139v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:54,629] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:54,630] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc26252c-1de7-4939-8020-74ddaddf2529/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:54,630] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc26252c-1de7-4939-8020-74ddaddf2529/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:54,656] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:47:54,656] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:47:54,656] [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
Psychrosphaera aestuarii	strain=PSC101	GCA_017948405.1	1266052	1266052	type	True	78.5015	63	1463	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	78.4863	228	1463	95	below_threshold
Thalassotalea algicola	strain=M1531	GCA_012932965.1	2716224	2716224	type	True	78.1835	202	1463	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	78.0571	240	1463	95	below_threshold
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	78.0339	214	1463	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	77.9895	253	1463	95	below_threshold
Thalassotalea agarivorans	strain=DSM 19706	GCA_900111755.1	349064	349064	type	True	77.9882	120	1463	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	77.9394	189	1463	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	77.7949	179	1463	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	77.7774	255	1463	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	77.6535	175	1463	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	77.6239	173	1463	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	77.5115	189	1463	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	77.3781	222	1463	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	76.4304	63	1463	95	below_threshold
Pseudoalteromonas denitrificans	strain=DSM 6059	GCA_900112265.1	43656	43656	type	True	76.2148	78	1463	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:54,658] [INFO] DFAST Taxonomy check result was written to GCF_030161395.1_ASM3016139v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:54,659] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:54,659] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:54,659] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc26252c-1de7-4939-8020-74ddaddf2529/dqc_reference/checkm_data
[2024-01-24 10:47:54,660] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:54,704] [INFO] Task started: CheckM
[2024-01-24 10:47:54,704] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030161395.1_ASM3016139v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030161395.1_ASM3016139v1_genomic.fna/checkm_input GCF_030161395.1_ASM3016139v1_genomic.fna/checkm_result
[2024-01-24 10:48:26,344] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:26,345] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:26,376] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:26,376] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:26,377] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030161395.1_ASM3016139v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:26,377] [INFO] Task started: Blastn
[2024-01-24 10:48:26,377] [INFO] Running command: blastn -query GCF_030161395.1_ASM3016139v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc26252c-1de7-4939-8020-74ddaddf2529/dqc_reference/reference_markers_gtdb.fasta -out GCF_030161395.1_ASM3016139v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:27,572] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:27,575] [INFO] Selected 25 target genomes.
[2024-01-24 10:48:27,576] [INFO] Target genome list was writen to GCF_030161395.1_ASM3016139v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:27,610] [INFO] Task started: fastANI
[2024-01-24 10:48:27,611] [INFO] Running command: fastANI --query /var/lib/cwl/stg528cb72c-e9d0-4b6b-ad11-a038a8b226da/GCF_030161395.1_ASM3016139v1_genomic.fna.gz --refList GCF_030161395.1_ASM3016139v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030161395.1_ASM3016139v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:46,284] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:46,306] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:48:46,307] [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_017168195.1	s__G2M2-11 sp017168195	79.4684	492	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__G2M2-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390335.1	s__Thalassotalea euphylliae_B	78.8846	163	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002077175.1	s__Cognaticolwellia sp002077175	78.5866	231	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002076895.1	s__Cognaticolwellia beringensis	78.5671	218	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390395.1	s__Thalassotalea euphylliae_C	78.4973	176	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004295665.1	s__Litorilituus sediminis	78.4815	231	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764185.1	s__Colwellia psychrerythraea_B	78.2662	175	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932965.1	s__Thalassotalea algicola	78.2346	198	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077095.1	s__Cognaticolwellia sp014077095	78.0624	182	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104475.1	s__Cognaticolwellia mytili	78.0378	239	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207645.1	s__Thalassotalea_B piscium	78.0339	214	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077005.1	s__Cognaticolwellia sp014077005	78.0049	203	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.22	95.22	0.95	0.87	11	-
GCF_001913705.1	s__Thalassotalea_C sp001913705	77.9895	259	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003545765.1	s__Litorilituus sp003545765	77.9877	183	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653195.1	s__Thalassotalea_B profundi	77.9812	253	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000025.1	s__Cognaticolwellia aestuarii	77.9798	236	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014656435.1	s__Thalassotalea_C marina	77.7905	254	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003333305.1	s__Colwellia aromaticivorans	77.751	175	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836775.1	s__Colwellia sp002836775	77.7276	179	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885605.1	s__Colwellia ponticola	77.6463	174	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000085.1	s__Pseudocolwellia agarivorans	77.514	187	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudocolwellia	95.0	95.36	95.36	0.90	0.90	2	-
GCA_013215385.1	s__Colwellia_A sp013215385	77.4678	217	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003354085.1	s__Cognaticolwellia sp003354085	77.4397	208	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:46,308] [INFO] GTDB search result was written to GCF_030161395.1_ASM3016139v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:46,309] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:46,315] [INFO] DFAST_QC result json was written to GCF_030161395.1_ASM3016139v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:46,315] [INFO] DFAST_QC completed!
[2024-01-24 10:48:46,315] [INFO] Total running time: 0h1m24s