[2024-01-25 20:14:35,486] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:14:35,488] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:14:35,489] [INFO] DQC Reference Directory: /var/lib/cwl/stgb114af03-38b8-4d4a-8628-84f1444e3965/dqc_reference
[2024-01-25 20:14:36,675] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:14:36,676] [INFO] Task started: Prodigal
[2024-01-25 20:14:36,676] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e17256e-e4f4-4705-9153-af39cef78b72/GCF_002104475.1_ASM210447v1_genomic.fna.gz | prodigal -d GCF_002104475.1_ASM210447v1_genomic.fna/cds.fna -a GCF_002104475.1_ASM210447v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:14:44,391] [INFO] Task succeeded: Prodigal
[2024-01-25 20:14:44,391] [INFO] Task started: HMMsearch
[2024-01-25 20:14:44,392] [INFO] Running command: hmmsearch --tblout GCF_002104475.1_ASM210447v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb114af03-38b8-4d4a-8628-84f1444e3965/dqc_reference/reference_markers.hmm GCF_002104475.1_ASM210447v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:14:44,628] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:14:44,629] [INFO] Found 6/6 markers.
[2024-01-25 20:14:44,666] [INFO] Query marker FASTA was written to GCF_002104475.1_ASM210447v1_genomic.fna/markers.fasta
[2024-01-25 20:14:44,666] [INFO] Task started: Blastn
[2024-01-25 20:14:44,666] [INFO] Running command: blastn -query GCF_002104475.1_ASM210447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb114af03-38b8-4d4a-8628-84f1444e3965/dqc_reference/reference_markers.fasta -out GCF_002104475.1_ASM210447v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:45,347] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:45,350] [INFO] Selected 20 target genomes.
[2024-01-25 20:14:45,350] [INFO] Target genome list was writen to GCF_002104475.1_ASM210447v1_genomic.fna/target_genomes.txt
[2024-01-25 20:14:45,356] [INFO] Task started: fastANI
[2024-01-25 20:14:45,356] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e17256e-e4f4-4705-9153-af39cef78b72/GCF_002104475.1_ASM210447v1_genomic.fna.gz --refList GCF_002104475.1_ASM210447v1_genomic.fna/target_genomes.txt --output GCF_002104475.1_ASM210447v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:15:00,947] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:00,947] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb114af03-38b8-4d4a-8628-84f1444e3965/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:15:00,947] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb114af03-38b8-4d4a-8628-84f1444e3965/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:15:00,956] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:15:00,956] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:15:00,956] [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
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	100.0	1492	1493	95	conclusive
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	78.8286	428	1493	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_900109795.1	641665	641665	type	True	78.8269	424	1493	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	78.5486	295	1493	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	78.4054	243	1493	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	78.3499	215	1493	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	78.3211	323	1493	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	78.2846	244	1493	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	78.1835	229	1493	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	78.1311	250	1493	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	77.9948	247	1493	95	below_threshold
Aliivibrio fischeri	strain=DSM 507	GCA_023983475.1	668	668	suspected-type	True	76.486	51	1493	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	76.0175	73	1493	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_000949955.1	659	659	type	True	75.8057	58	1493	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:15:00,958] [INFO] DFAST Taxonomy check result was written to GCF_002104475.1_ASM210447v1_genomic.fna/tc_result.tsv
[2024-01-25 20:15:00,959] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:15:00,959] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:15:00,959] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb114af03-38b8-4d4a-8628-84f1444e3965/dqc_reference/checkm_data
[2024-01-25 20:15:00,960] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:15:01,003] [INFO] Task started: CheckM
[2024-01-25 20:15:01,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002104475.1_ASM210447v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002104475.1_ASM210447v1_genomic.fna/checkm_input GCF_002104475.1_ASM210447v1_genomic.fna/checkm_result
[2024-01-25 20:15:27,823] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:27,823] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:27,846] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:27,846] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:27,846] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002104475.1_ASM210447v1_genomic.fna/markers.fasta)
[2024-01-25 20:15:27,846] [INFO] Task started: Blastn
[2024-01-25 20:15:27,846] [INFO] Running command: blastn -query GCF_002104475.1_ASM210447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb114af03-38b8-4d4a-8628-84f1444e3965/dqc_reference/reference_markers_gtdb.fasta -out GCF_002104475.1_ASM210447v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:28,915] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:28,918] [INFO] Selected 16 target genomes.
[2024-01-25 20:15:28,918] [INFO] Target genome list was writen to GCF_002104475.1_ASM210447v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:28,944] [INFO] Task started: fastANI
[2024-01-25 20:15:28,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e17256e-e4f4-4705-9153-af39cef78b72/GCF_002104475.1_ASM210447v1_genomic.fna.gz --refList GCF_002104475.1_ASM210447v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002104475.1_ASM210447v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:15:46,023] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:46,033] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:15:46,033] [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_002104475.1	s__Cognaticolwellia mytili	100.0	1492	1493	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003971255.1	s__Cognaticolwellia sp003971255	80.3479	690	1493	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000025.1	s__Cognaticolwellia aestuarii	80.3396	653	1493	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003354085.1	s__Cognaticolwellia sp003354085	80.2501	642	1493	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077505.1	s__Cognaticolwellia sp014077505	80.0355	568	1493	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104515.1	s__Cognaticolwellia polaris	80.0111	529	1493	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	79.9969	589	1493	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002077175.1	s__Cognaticolwellia sp002077175	79.9933	566	1493	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002104535.1	s__Cognaticolwellia sediminilitoris	79.9506	520	1493	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003061515.1	s__Cognaticolwellia sp003061515	79.7884	553	1493	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.05	98.05	0.90	0.90	2	-
GCF_014077095.1	s__Cognaticolwellia sp014077095	79.7324	519	1493	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007954265.1	s__Cognaticolwellia sp007954265	79.6826	530	1493	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077005.1	s__Cognaticolwellia sp014077005	79.6666	535	1493	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.22	95.22	0.95	0.87	11	-
GCF_000764185.1	s__Colwellia psychrerythraea_B	78.504	260	1493	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007954355.1	s__Colwellia_A hornerae	78.2907	325	1493	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	100.00	100.00	0.99	0.99	3	-
GCA_013215655.1	s__Colwellia_A sp013215655	78.0484	330	1493	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:15:46,035] [INFO] GTDB search result was written to GCF_002104475.1_ASM210447v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:15:46,035] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:15:46,038] [INFO] DFAST_QC result json was written to GCF_002104475.1_ASM210447v1_genomic.fna/dqc_result.json
[2024-01-25 20:15:46,038] [INFO] DFAST_QC completed!
[2024-01-25 20:15:46,038] [INFO] Total running time: 0h1m11s