[2023-03-18 23:22:48,520] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:22:48,520] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:22:48,520] [INFO] DQC Reference Directory: /var/lib/cwl/stg33433540-f92d-4e9d-88f8-65c09cba3fdc/dqc_reference
[2023-03-18 23:22:49,618] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:22:49,618] [INFO] Task started: Prodigal
[2023-03-18 23:22:49,619] [INFO] Running command: cat /var/lib/cwl/stg7c4c1664-cc09-49dd-9013-aaf1ce491675/OceanDNA-b34735.fa | prodigal -d OceanDNA-b34735/cds.fna -a OceanDNA-b34735/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:23:08,261] [INFO] Task succeeded: Prodigal
[2023-03-18 23:23:08,262] [INFO] Task started: HMMsearch
[2023-03-18 23:23:08,262] [INFO] Running command: hmmsearch --tblout OceanDNA-b34735/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33433540-f92d-4e9d-88f8-65c09cba3fdc/dqc_reference/reference_markers.hmm OceanDNA-b34735/protein.faa > /dev/null
[2023-03-18 23:23:08,494] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:23:08,495] [INFO] Found 6/6 markers.
[2023-03-18 23:23:08,517] [INFO] Query marker FASTA was written to OceanDNA-b34735/markers.fasta
[2023-03-18 23:23:08,518] [INFO] Task started: Blastn
[2023-03-18 23:23:08,518] [INFO] Running command: blastn -query OceanDNA-b34735/markers.fasta -db /var/lib/cwl/stg33433540-f92d-4e9d-88f8-65c09cba3fdc/dqc_reference/reference_markers.fasta -out OceanDNA-b34735/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:23:09,171] [INFO] Task succeeded: Blastn
[2023-03-18 23:23:09,173] [INFO] Selected 19 target genomes.
[2023-03-18 23:23:09,173] [INFO] Target genome list was writen to OceanDNA-b34735/target_genomes.txt
[2023-03-18 23:23:09,220] [INFO] Task started: fastANI
[2023-03-18 23:23:09,221] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c4c1664-cc09-49dd-9013-aaf1ce491675/OceanDNA-b34735.fa --refList OceanDNA-b34735/target_genomes.txt --output OceanDNA-b34735/fastani_result.tsv --threads 1
[2023-03-18 23:23:22,511] [INFO] Task succeeded: fastANI
[2023-03-18 23:23:22,512] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33433540-f92d-4e9d-88f8-65c09cba3fdc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:23:22,512] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33433540-f92d-4e9d-88f8-65c09cba3fdc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:23:22,520] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:23:22,520] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:23:22,520] [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
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	80.1424	550	1192	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_900109795.1	641665	641665	type	True	79.6563	431	1192	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	79.5252	441	1192	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	78.375	220	1192	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	78.314	263	1192	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	78.2357	192	1192	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	78.2319	244	1192	95	below_threshold
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	78.0889	219	1192	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	78.0252	241	1192	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	77.9398	232	1192	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	77.9127	221	1192	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	77.6486	224	1192	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:23:22,520] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34735/tc_result.tsv
[2023-03-18 23:23:22,521] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:23:22,521] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:23:22,521] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33433540-f92d-4e9d-88f8-65c09cba3fdc/dqc_reference/checkm_data
[2023-03-18 23:23:22,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:23:22,528] [INFO] Task started: CheckM
[2023-03-18 23:23:22,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34735/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34735/checkm_input OceanDNA-b34735/checkm_result
[2023-03-18 23:24:10,283] [INFO] Task succeeded: CheckM
[2023-03-18 23:24:10,283] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 23:24:10,286] [INFO] ===== Completeness check finished =====
[2023-03-18 23:24:10,286] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:24:10,286] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34735/markers.fasta)
[2023-03-18 23:24:10,287] [INFO] Task started: Blastn
[2023-03-18 23:24:10,287] [INFO] Running command: blastn -query OceanDNA-b34735/markers.fasta -db /var/lib/cwl/stg33433540-f92d-4e9d-88f8-65c09cba3fdc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34735/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:24:11,330] [INFO] Task succeeded: Blastn
[2023-03-18 23:24:11,331] [INFO] Selected 12 target genomes.
[2023-03-18 23:24:11,331] [INFO] Target genome list was writen to OceanDNA-b34735/target_genomes_gtdb.txt
[2023-03-18 23:24:11,338] [INFO] Task started: fastANI
[2023-03-18 23:24:11,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c4c1664-cc09-49dd-9013-aaf1ce491675/OceanDNA-b34735.fa --refList OceanDNA-b34735/target_genomes_gtdb.txt --output OceanDNA-b34735/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:24:21,806] [INFO] Task succeeded: fastANI
[2023-03-18 23:24:21,814] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:24:21,814] [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_002000025.1	s__Cognaticolwellia aestuarii	96.7902	1091	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_003354085.1	s__Cognaticolwellia sp003354085	82.3057	746	1192	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	81.5248	761	1192	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	80.9082	610	1192	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	80.8595	622	1192	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	80.7268	626	1192	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	80.7216	603	1192	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	80.6285	583	1192	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	80.4929	574	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.22	95.22	0.95	0.87	11	-
GCF_007954265.1	s__Cognaticolwellia sp007954265	80.3265	577	1192	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	80.3005	596	1192	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	80.0611	578	1192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:24:21,814] [INFO] GTDB search result was written to OceanDNA-b34735/result_gtdb.tsv
[2023-03-18 23:24:21,815] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:24:21,817] [INFO] DFAST_QC result json was written to OceanDNA-b34735/dqc_result.json
[2023-03-18 23:24:21,817] [INFO] DFAST_QC completed!
[2023-03-18 23:24:21,817] [INFO] Total running time: 0h1m33s