[2023-03-16 04:54:07,040] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:54:07,041] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:54:07,041] [INFO] DQC Reference Directory: /var/lib/cwl/stg7adddae4-c7f9-4175-b8c7-984bb960b2f9/dqc_reference
[2023-03-16 04:54:08,330] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:54:08,331] [INFO] Task started: Prodigal
[2023-03-16 04:54:08,331] [INFO] Running command: cat /var/lib/cwl/stg10213f8d-7be5-4fc6-80db-3b973c81ca1c/OceanDNA-b34744.fa | prodigal -d OceanDNA-b34744/cds.fna -a OceanDNA-b34744/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:54:26,598] [INFO] Task succeeded: Prodigal
[2023-03-16 04:54:26,598] [INFO] Task started: HMMsearch
[2023-03-16 04:54:26,598] [INFO] Running command: hmmsearch --tblout OceanDNA-b34744/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7adddae4-c7f9-4175-b8c7-984bb960b2f9/dqc_reference/reference_markers.hmm OceanDNA-b34744/protein.faa > /dev/null
[2023-03-16 04:54:26,853] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:54:26,854] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg10213f8d-7be5-4fc6-80db-3b973c81ca1c/OceanDNA-b34744.fa]
[2023-03-16 04:54:26,882] [INFO] Query marker FASTA was written to OceanDNA-b34744/markers.fasta
[2023-03-16 04:54:26,882] [INFO] Task started: Blastn
[2023-03-16 04:54:26,882] [INFO] Running command: blastn -query OceanDNA-b34744/markers.fasta -db /var/lib/cwl/stg7adddae4-c7f9-4175-b8c7-984bb960b2f9/dqc_reference/reference_markers.fasta -out OceanDNA-b34744/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:54:27,444] [INFO] Task succeeded: Blastn
[2023-03-16 04:54:27,445] [INFO] Selected 19 target genomes.
[2023-03-16 04:54:27,445] [INFO] Target genome list was writen to OceanDNA-b34744/target_genomes.txt
[2023-03-16 04:54:27,457] [INFO] Task started: fastANI
[2023-03-16 04:54:27,458] [INFO] Running command: fastANI --query /var/lib/cwl/stg10213f8d-7be5-4fc6-80db-3b973c81ca1c/OceanDNA-b34744.fa --refList OceanDNA-b34744/target_genomes.txt --output OceanDNA-b34744/fastani_result.tsv --threads 1
[2023-03-16 04:54:43,388] [INFO] Task succeeded: fastANI
[2023-03-16 04:54:43,388] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7adddae4-c7f9-4175-b8c7-984bb960b2f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:54:43,389] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7adddae4-c7f9-4175-b8c7-984bb960b2f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:54:43,396] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:54:43,396] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:54:43,396] [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	79.1293	424	1182	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	78.315	359	1182	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_900109795.1	641665	641665	type	True	78.3072	355	1182	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	77.3546	221	1182	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	77.3498	169	1182	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	77.3213	240	1182	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	77.3166	195	1182	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	77.1479	151	1182	95	below_threshold
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	77.0988	178	1182	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	76.8511	122	1182	95	below_threshold
Thalassomonas viridans	strain=XOM25	GCA_000948985.1	137584	137584	type	True	76.5986	65	1182	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:54:43,397] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34744/tc_result.tsv
[2023-03-16 04:54:43,397] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:54:43,398] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:54:43,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7adddae4-c7f9-4175-b8c7-984bb960b2f9/dqc_reference/checkm_data
[2023-03-16 04:54:43,398] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:54:43,453] [INFO] Task started: CheckM
[2023-03-16 04:54:43,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34744/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34744/checkm_input OceanDNA-b34744/checkm_result
[2023-03-16 04:55:30,435] [INFO] Task succeeded: CheckM
[2023-03-16 04:55:30,435] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:55:30,438] [INFO] ===== Completeness check finished =====
[2023-03-16 04:55:30,438] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:55:30,439] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34744/markers.fasta)
[2023-03-16 04:55:30,440] [INFO] Task started: Blastn
[2023-03-16 04:55:30,440] [INFO] Running command: blastn -query OceanDNA-b34744/markers.fasta -db /var/lib/cwl/stg7adddae4-c7f9-4175-b8c7-984bb960b2f9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34744/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:55:31,085] [INFO] Task succeeded: Blastn
[2023-03-16 04:55:31,086] [INFO] Selected 10 target genomes.
[2023-03-16 04:55:31,086] [INFO] Target genome list was writen to OceanDNA-b34744/target_genomes_gtdb.txt
[2023-03-16 04:55:31,097] [INFO] Task started: fastANI
[2023-03-16 04:55:31,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg10213f8d-7be5-4fc6-80db-3b973c81ca1c/OceanDNA-b34744.fa --refList OceanDNA-b34744/target_genomes_gtdb.txt --output OceanDNA-b34744/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:55:40,667] [INFO] Task succeeded: fastANI
[2023-03-16 04:55:40,673] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:55:40,674] [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_002104515.1	s__Cognaticolwellia polaris	99.4683	1103	1182	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_003061515.1	s__Cognaticolwellia sp003061515	83.0587	838	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.05	98.05	0.90	0.90	2	-
GCF_002077175.1	s__Cognaticolwellia sp002077175	81.7238	763	1182	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	81.0879	720	1182	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	80.8974	683	1182	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	80.0892	591	1182	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	80.0846	539	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014077005.1	s__Cognaticolwellia sp014077005	79.94	561	1182	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	79.8072	554	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077095.1	s__Cognaticolwellia sp014077095	79.7928	550	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:55:40,674] [INFO] GTDB search result was written to OceanDNA-b34744/result_gtdb.tsv
[2023-03-16 04:55:40,674] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:55:40,675] [INFO] DFAST_QC result json was written to OceanDNA-b34744/dqc_result.json
[2023-03-16 04:55:40,675] [INFO] DFAST_QC completed!
[2023-03-16 04:55:40,675] [INFO] Total running time: 0h1m34s