[2024-01-24 13:58:56,279] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:56,281] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:56,281] [INFO] DQC Reference Directory: /var/lib/cwl/stg60b052f2-0813-4fb3-9baf-ac76f55abf26/dqc_reference
[2024-01-24 13:58:57,691] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:57,692] [INFO] Task started: Prodigal
[2024-01-24 13:58:57,692] [INFO] Running command: gunzip -c /var/lib/cwl/stg916300a4-f3f4-4436-9df7-3a317461102d/GCF_002104455.1_ASM210445v1_genomic.fna.gz | prodigal -d GCF_002104455.1_ASM210445v1_genomic.fna/cds.fna -a GCF_002104455.1_ASM210445v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:59:07,026] [INFO] Task succeeded: Prodigal
[2024-01-24 13:59:07,027] [INFO] Task started: HMMsearch
[2024-01-24 13:59:07,027] [INFO] Running command: hmmsearch --tblout GCF_002104455.1_ASM210445v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60b052f2-0813-4fb3-9baf-ac76f55abf26/dqc_reference/reference_markers.hmm GCF_002104455.1_ASM210445v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:59:07,376] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:59:07,378] [INFO] Found 6/6 markers.
[2024-01-24 13:59:07,434] [INFO] Query marker FASTA was written to GCF_002104455.1_ASM210445v1_genomic.fna/markers.fasta
[2024-01-24 13:59:07,435] [INFO] Task started: Blastn
[2024-01-24 13:59:07,435] [INFO] Running command: blastn -query GCF_002104455.1_ASM210445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60b052f2-0813-4fb3-9baf-ac76f55abf26/dqc_reference/reference_markers.fasta -out GCF_002104455.1_ASM210445v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:08,221] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:08,225] [INFO] Selected 20 target genomes.
[2024-01-24 13:59:08,226] [INFO] Target genome list was writen to GCF_002104455.1_ASM210445v1_genomic.fna/target_genomes.txt
[2024-01-24 13:59:08,238] [INFO] Task started: fastANI
[2024-01-24 13:59:08,239] [INFO] Running command: fastANI --query /var/lib/cwl/stg916300a4-f3f4-4436-9df7-3a317461102d/GCF_002104455.1_ASM210445v1_genomic.fna.gz --refList GCF_002104455.1_ASM210445v1_genomic.fna/target_genomes.txt --output GCF_002104455.1_ASM210445v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:25,004] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:25,005] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60b052f2-0813-4fb3-9baf-ac76f55abf26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:25,005] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60b052f2-0813-4fb3-9baf-ac76f55abf26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:25,016] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:59:25,016] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:25,017] [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
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	100.0	1321	1322	95	conclusive
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_900109795.1	641665	641665	type	True	99.9887	1305	1322	95	conclusive
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	80.2017	229	1322	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	79.8065	211	1322	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	78.8661	429	1322	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	78.2634	177	1322	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	78.0988	166	1322	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	77.893	160	1322	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	77.8398	239	1322	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	77.7566	170	1322	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	77.7484	66	1322	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	77.6461	196	1322	95	below_threshold
Shewanella donghaensis	strain=LT17	GCA_007567505.1	238836	238836	type	True	76.3475	53	1322	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:25,018] [INFO] DFAST Taxonomy check result was written to GCF_002104455.1_ASM210445v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:25,019] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:25,019] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:25,019] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60b052f2-0813-4fb3-9baf-ac76f55abf26/dqc_reference/checkm_data
[2024-01-24 13:59:25,020] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:25,060] [INFO] Task started: CheckM
[2024-01-24 13:59:25,060] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002104455.1_ASM210445v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002104455.1_ASM210445v1_genomic.fna/checkm_input GCF_002104455.1_ASM210445v1_genomic.fna/checkm_result
[2024-01-24 13:59:56,861] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:56,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:56,889] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:56,890] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:56,890] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002104455.1_ASM210445v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:56,891] [INFO] Task started: Blastn
[2024-01-24 13:59:56,891] [INFO] Running command: blastn -query GCF_002104455.1_ASM210445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60b052f2-0813-4fb3-9baf-ac76f55abf26/dqc_reference/reference_markers_gtdb.fasta -out GCF_002104455.1_ASM210445v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:58,022] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:58,026] [INFO] Selected 14 target genomes.
[2024-01-24 13:59:58,026] [INFO] Target genome list was writen to GCF_002104455.1_ASM210445v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:58,049] [INFO] Task started: fastANI
[2024-01-24 13:59:58,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg916300a4-f3f4-4436-9df7-3a317461102d/GCF_002104455.1_ASM210445v1_genomic.fna.gz --refList GCF_002104455.1_ASM210445v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002104455.1_ASM210445v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:08,806] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:08,823] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:08,823] [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_002104455.1	s__Cognaticolwellia chukchiensis	100.0	1321	1322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_002000025.1	s__Cognaticolwellia aestuarii	79.6382	507	1322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002104535.1	s__Cognaticolwellia sediminilitoris	79.485	484	1322	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	79.2547	477	1322	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	79.2415	486	1322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003971255.1	s__Cognaticolwellia sp003971255	79.2242	481	1322	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	79.1554	472	1322	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	79.0998	461	1322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.05	98.05	0.90	0.90	2	-
GCA_003354085.1	s__Cognaticolwellia sp003354085	79.0566	497	1322	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	79.0552	512	1322	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	78.9677	460	1322	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	78.8766	429	1322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017168195.1	s__G2M2-11 sp017168195	77.8786	222	1322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__G2M2-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003521815.1	s__Colwellia sp003521815	76.9824	126	1322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:08,831] [INFO] GTDB search result was written to GCF_002104455.1_ASM210445v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:08,832] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:08,837] [INFO] DFAST_QC result json was written to GCF_002104455.1_ASM210445v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:08,838] [INFO] DFAST_QC completed!
[2024-01-24 14:00:08,838] [INFO] Total running time: 0h1m13s