[2023-03-19 04:11:06,926] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:11:06,926] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:11:06,926] [INFO] DQC Reference Directory: /var/lib/cwl/stgbfb1cc32-0a45-4aa1-af7d-6281c78e849d/dqc_reference
[2023-03-19 04:11:08,645] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:11:08,645] [INFO] Task started: Prodigal
[2023-03-19 04:11:08,645] [INFO] Running command: cat /var/lib/cwl/stgb5ba65d3-e2ce-4350-838d-70d49faabee2/OceanDNA-b34734.fa | prodigal -d OceanDNA-b34734/cds.fna -a OceanDNA-b34734/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:11:20,796] [INFO] Task succeeded: Prodigal
[2023-03-19 04:11:20,797] [INFO] Task started: HMMsearch
[2023-03-19 04:11:20,797] [INFO] Running command: hmmsearch --tblout OceanDNA-b34734/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbfb1cc32-0a45-4aa1-af7d-6281c78e849d/dqc_reference/reference_markers.hmm OceanDNA-b34734/protein.faa > /dev/null
[2023-03-19 04:11:20,989] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:11:20,989] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb5ba65d3-e2ce-4350-838d-70d49faabee2/OceanDNA-b34734.fa]
[2023-03-19 04:11:21,006] [INFO] Query marker FASTA was written to OceanDNA-b34734/markers.fasta
[2023-03-19 04:11:21,006] [INFO] Task started: Blastn
[2023-03-19 04:11:21,006] [INFO] Running command: blastn -query OceanDNA-b34734/markers.fasta -db /var/lib/cwl/stgbfb1cc32-0a45-4aa1-af7d-6281c78e849d/dqc_reference/reference_markers.fasta -out OceanDNA-b34734/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:21,533] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:21,534] [INFO] Selected 19 target genomes.
[2023-03-19 04:11:21,534] [INFO] Target genome list was writen to OceanDNA-b34734/target_genomes.txt
[2023-03-19 04:11:21,546] [INFO] Task started: fastANI
[2023-03-19 04:11:21,547] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5ba65d3-e2ce-4350-838d-70d49faabee2/OceanDNA-b34734.fa --refList OceanDNA-b34734/target_genomes.txt --output OceanDNA-b34734/fastani_result.tsv --threads 1
[2023-03-19 04:11:34,194] [INFO] Task succeeded: fastANI
[2023-03-19 04:11:34,194] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbfb1cc32-0a45-4aa1-af7d-6281c78e849d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:11:34,194] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbfb1cc32-0a45-4aa1-af7d-6281c78e849d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:11:34,202] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:11:34,202] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:11:34,202] [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 echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	77.8626	160	791	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	77.6297	154	791	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	77.497	163	791	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_900109795.1	641665	641665	type	True	77.2641	140	791	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	77.2531	123	791	95	below_threshold
Thalassotalea algicola	strain=M1531	GCA_012932965.1	2716224	2716224	type	True	77.2419	127	791	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	77.2362	150	791	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	77.2092	157	791	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	77.1978	142	791	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	77.193	139	791	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	77.1713	135	791	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	77.0795	134	791	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:11:34,203] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34734/tc_result.tsv
[2023-03-19 04:11:34,203] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:11:34,203] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:11:34,203] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbfb1cc32-0a45-4aa1-af7d-6281c78e849d/dqc_reference/checkm_data
[2023-03-19 04:11:34,204] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:11:34,208] [INFO] Task started: CheckM
[2023-03-19 04:11:34,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34734/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34734/checkm_input OceanDNA-b34734/checkm_result
[2023-03-19 04:12:08,405] [INFO] Task succeeded: CheckM
[2023-03-19 04:12:08,406] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:12:08,408] [INFO] ===== Completeness check finished =====
[2023-03-19 04:12:08,408] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:12:08,408] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34734/markers.fasta)
[2023-03-19 04:12:08,409] [INFO] Task started: Blastn
[2023-03-19 04:12:08,409] [INFO] Running command: blastn -query OceanDNA-b34734/markers.fasta -db /var/lib/cwl/stgbfb1cc32-0a45-4aa1-af7d-6281c78e849d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34734/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:12:09,100] [INFO] Task succeeded: Blastn
[2023-03-19 04:12:09,101] [INFO] Selected 20 target genomes.
[2023-03-19 04:12:09,101] [INFO] Target genome list was writen to OceanDNA-b34734/target_genomes_gtdb.txt
[2023-03-19 04:12:09,340] [INFO] Task started: fastANI
[2023-03-19 04:12:09,340] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5ba65d3-e2ce-4350-838d-70d49faabee2/OceanDNA-b34734.fa --refList OceanDNA-b34734/target_genomes_gtdb.txt --output OceanDNA-b34734/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:12:22,605] [INFO] Task succeeded: fastANI
[2023-03-19 04:12:22,617] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:12:22,617] [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	77.9283	160	791	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002843355.2	s__Colwellia echini	77.8631	160	791	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002104535.1	s__Cognaticolwellia sediminilitoris	77.6771	141	791	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	77.663	148	791	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860755.1	s__Colwellia sp018860755	77.5981	160	791	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004295665.1	s__Litorilituus sediminis	77.5442	140	791	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007954355.1	s__Colwellia_A hornerae	77.497	163	791	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	100.00	100.00	0.99	0.99	3	-
GCF_018860585.1	s__Colwellia sp018860585	77.4923	169	791	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003061515.1	s__Cognaticolwellia sp003061515	77.4457	141	791	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.05	98.05	0.90	0.90	2	-
GCF_009832865.1	s__Colwellia sp009832865	77.4249	140	791	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097525.1	s__Thalassotalea_A sp007097525	77.4053	112	791	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014076845.1	s__Colwellia_A sp014076845	77.3417	140	791	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	99.15	95.49	0.95	0.86	8	-
GCA_013215655.1	s__Colwellia_A sp013215655	77.3286	148	791	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390395.1	s__Thalassotalea euphylliae_C	77.2362	108	791	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016745015.1	s__Colwellia sp016745015	77.2351	130	791	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003354085.1	s__Cognaticolwellia sp003354085	77.2106	156	791	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653195.1	s__Thalassotalea_B profundi	77.2092	157	791	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_006439335.1	s__Litorilituus lipolyticus	77.0987	133	791	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390375.1	s__Thalassotalea euphylliae_A	77.0555	113	791	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401725.1	s__GCA-2401725 sp002401725	76.7242	125	791	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__GCA-2401725	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:12:22,617] [INFO] GTDB search result was written to OceanDNA-b34734/result_gtdb.tsv
[2023-03-19 04:12:22,617] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:12:22,619] [INFO] DFAST_QC result json was written to OceanDNA-b34734/dqc_result.json
[2023-03-19 04:12:22,619] [INFO] DFAST_QC completed!
[2023-03-19 04:12:22,619] [INFO] Total running time: 0h1m16s