[2024-01-24 13:40:33,455] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:33,458] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:33,459] [INFO] DQC Reference Directory: /var/lib/cwl/stgad1f3f7e-545f-4d6d-8c5d-82264a9bc918/dqc_reference
[2024-01-24 13:40:34,711] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:34,711] [INFO] Task started: Prodigal
[2024-01-24 13:40:34,712] [INFO] Running command: gunzip -c /var/lib/cwl/stg139bbfe9-84f5-4c21-9d97-92078e0412cc/GCF_000281085.1_ASM28108v1_genomic.fna.gz | prodigal -d GCF_000281085.1_ASM28108v1_genomic.fna/cds.fna -a GCF_000281085.1_ASM28108v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:46,068] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:46,069] [INFO] Task started: HMMsearch
[2024-01-24 13:40:46,069] [INFO] Running command: hmmsearch --tblout GCF_000281085.1_ASM28108v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad1f3f7e-545f-4d6d-8c5d-82264a9bc918/dqc_reference/reference_markers.hmm GCF_000281085.1_ASM28108v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:46,426] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:46,427] [INFO] Found 6/6 markers.
[2024-01-24 13:40:46,472] [INFO] Query marker FASTA was written to GCF_000281085.1_ASM28108v1_genomic.fna/markers.fasta
[2024-01-24 13:40:46,473] [INFO] Task started: Blastn
[2024-01-24 13:40:46,473] [INFO] Running command: blastn -query GCF_000281085.1_ASM28108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad1f3f7e-545f-4d6d-8c5d-82264a9bc918/dqc_reference/reference_markers.fasta -out GCF_000281085.1_ASM28108v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:47,242] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:47,246] [INFO] Selected 22 target genomes.
[2024-01-24 13:40:47,246] [INFO] Target genome list was writen to GCF_000281085.1_ASM28108v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:47,255] [INFO] Task started: fastANI
[2024-01-24 13:40:47,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg139bbfe9-84f5-4c21-9d97-92078e0412cc/GCF_000281085.1_ASM28108v1_genomic.fna.gz --refList GCF_000281085.1_ASM28108v1_genomic.fna/target_genomes.txt --output GCF_000281085.1_ASM28108v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:05,772] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:05,773] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad1f3f7e-545f-4d6d-8c5d-82264a9bc918/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:05,773] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad1f3f7e-545f-4d6d-8c5d-82264a9bc918/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:05,795] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:05,795] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:05,795] [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
Catenovulum agarivorans	strain=YM01	GCA_000281085.1	1172192	1172192	type	True	100.0	1642	1645	95	conclusive
Catenovulum maritimum	strain=Q1	GCA_001050375.1	1513271	1513271	type	True	78.8808	272	1645	95	below_threshold
Saccharobesus litoralis	strain=CCB-QB4	GCA_003063625.1	2172099	2172099	type	True	78.1962	184	1645	95	below_threshold
Gayadomonas joobiniege	strain=G7	GCA_000300815.1	1234606	1234606	type	True	78.0571	208	1645	95	below_threshold
Marinifaba aquimaris	strain=SM1970	GCA_013328345.1	2741323	2741323	type	True	77.779	125	1645	95	below_threshold
Pseudoalteromonas shioyasakiensis	strain=JCM 18891	GCA_001550135.1	1190813	1190813	suspected-type	True	77.2179	90	1645	95	below_threshold
Pseudoalteromonas gelatinilytica	strain=NH153	GCA_001641615.1	1703256	1703256	type	True	77.1381	91	1645	95	below_threshold
Pseudoalteromonas undina	strain=DSM 6065	GCA_000238275.4	43660	43660	type	True	76.9909	88	1645	95	below_threshold
Psychrosphaera ytuae	strain=MTZ26	GCA_017638545.1	2820710	2820710	type	True	76.9588	75	1645	95	below_threshold
Pseudoalteromonas piratica	strain=OCN003	GCA_000788395.1	1348114	1348114	type	True	76.9267	74	1645	95	below_threshold
Pseudoalteromonas ulvae	strain=UL12	GCA_014925405.1	107327	107327	type	True	76.8418	67	1645	95	below_threshold
Agarivorans litoreus	strain=NBRC 110444	GCA_019649015.1	1510455	1510455	type	True	76.6483	72	1645	95	below_threshold
Pseudoalteromonas ostreae	strain=hOe-66	GCA_018069805.1	2774154	2774154	type	True	76.6467	72	1645	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	76.4552	102	1645	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	76.4142	68	1645	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	76.3569	62	1645	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	76.3471	55	1645	95	below_threshold
Rheinheimera salexigens	strain=KH87	GCA_001752395.1	1628148	1628148	type	True	76.1878	61	1645	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:05,800] [INFO] DFAST Taxonomy check result was written to GCF_000281085.1_ASM28108v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:05,801] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:05,801] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:05,801] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad1f3f7e-545f-4d6d-8c5d-82264a9bc918/dqc_reference/checkm_data
[2024-01-24 13:41:05,803] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:05,855] [INFO] Task started: CheckM
[2024-01-24 13:41:05,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000281085.1_ASM28108v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000281085.1_ASM28108v1_genomic.fna/checkm_input GCF_000281085.1_ASM28108v1_genomic.fna/checkm_result
[2024-01-24 13:41:45,098] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:45,099] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:45,122] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:45,122] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:45,123] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000281085.1_ASM28108v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:45,123] [INFO] Task started: Blastn
[2024-01-24 13:41:45,123] [INFO] Running command: blastn -query GCF_000281085.1_ASM28108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad1f3f7e-545f-4d6d-8c5d-82264a9bc918/dqc_reference/reference_markers_gtdb.fasta -out GCF_000281085.1_ASM28108v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:46,356] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:46,361] [INFO] Selected 15 target genomes.
[2024-01-24 13:41:46,361] [INFO] Target genome list was writen to GCF_000281085.1_ASM28108v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:46,387] [INFO] Task started: fastANI
[2024-01-24 13:41:46,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg139bbfe9-84f5-4c21-9d97-92078e0412cc/GCF_000281085.1_ASM28108v1_genomic.fna.gz --refList GCF_000281085.1_ASM28108v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000281085.1_ASM28108v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:58,404] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:58,419] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:58,419] [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_000281085.1	s__Catenovulum agarivorans	100.0	1642	1645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Catenovulum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000568405.1	s__Catenovulum agarivorans_A	83.2756	914	1645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Catenovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050375.1	s__Catenovulum maritimum	78.9178	272	1645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Catenovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007289895.1	s__Catenovulum sediminis	78.367	337	1645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Catenovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300815.1	s__Catenovulum joobiniege	78.0401	209	1645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Catenovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013328345.1	s__Marinifaba aquimaris	77.779	125	1645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Marinifaba	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077505.1	s__Cognaticolwellia sp014077505	77.0381	69	1645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238275.3	s__Pseudoalteromonas undina	76.9909	88	1645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	96.09	0.91	0.86	14	-
GCF_000788395.1	s__Pseudoalteromonas piratica	76.9267	74	1645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019134595.1	s__Pseudoalteromonas shioyasakiensis_A	76.9264	89	1645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.6918	N/A	N/A	N/A	N/A	1	-
GCF_002000025.1	s__Cognaticolwellia aestuarii	76.747	73	1645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003545765.1	s__Litorilituus sp003545765	76.7276	79	1645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000414175.1	s__Agarivorans albus	76.4646	64	1645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Agarivorans	95.0	96.96	96.96	0.93	0.93	2	-
GCF_002843355.2	s__Colwellia echini	76.4552	102	1645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001752395.1	s__Rheinheimera salexigens	76.1878	61	1645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:58,421] [INFO] GTDB search result was written to GCF_000281085.1_ASM28108v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:58,422] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:58,426] [INFO] DFAST_QC result json was written to GCF_000281085.1_ASM28108v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:58,426] [INFO] DFAST_QC completed!
[2024-01-24 13:41:58,426] [INFO] Total running time: 0h1m25s