[2023-03-16 23:05:03,458] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:05:03,458] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:05:03,458] [INFO] DQC Reference Directory: /var/lib/cwl/stg82b7c847-e508-440e-b3e1-b8daa1fb8642/dqc_reference
[2023-03-16 23:05:04,689] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:05:04,690] [INFO] Task started: Prodigal
[2023-03-16 23:05:04,690] [INFO] Running command: cat /var/lib/cwl/stgfdf240cc-2a40-4a73-9ff7-14c8b0e2fd80/OceanDNA-b34674.fa | prodigal -d OceanDNA-b34674/cds.fna -a OceanDNA-b34674/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:05:22,298] [INFO] Task succeeded: Prodigal
[2023-03-16 23:05:22,298] [INFO] Task started: HMMsearch
[2023-03-16 23:05:22,298] [INFO] Running command: hmmsearch --tblout OceanDNA-b34674/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82b7c847-e508-440e-b3e1-b8daa1fb8642/dqc_reference/reference_markers.hmm OceanDNA-b34674/protein.faa > /dev/null
[2023-03-16 23:05:22,488] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:05:22,488] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgfdf240cc-2a40-4a73-9ff7-14c8b0e2fd80/OceanDNA-b34674.fa]
[2023-03-16 23:05:22,508] [INFO] Query marker FASTA was written to OceanDNA-b34674/markers.fasta
[2023-03-16 23:05:22,508] [INFO] Task started: Blastn
[2023-03-16 23:05:22,508] [INFO] Running command: blastn -query OceanDNA-b34674/markers.fasta -db /var/lib/cwl/stg82b7c847-e508-440e-b3e1-b8daa1fb8642/dqc_reference/reference_markers.fasta -out OceanDNA-b34674/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:05:23,015] [INFO] Task succeeded: Blastn
[2023-03-16 23:05:23,016] [INFO] Selected 23 target genomes.
[2023-03-16 23:05:23,016] [INFO] Target genome list was writen to OceanDNA-b34674/target_genomes.txt
[2023-03-16 23:05:23,029] [INFO] Task started: fastANI
[2023-03-16 23:05:23,029] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdf240cc-2a40-4a73-9ff7-14c8b0e2fd80/OceanDNA-b34674.fa --refList OceanDNA-b34674/target_genomes.txt --output OceanDNA-b34674/fastani_result.tsv --threads 1
[2023-03-16 23:05:37,629] [INFO] Task succeeded: fastANI
[2023-03-16 23:05:37,630] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82b7c847-e508-440e-b3e1-b8daa1fb8642/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:05:37,630] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82b7c847-e508-440e-b3e1-b8daa1fb8642/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:05:37,638] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:05:37,638] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 23:05:37,638] [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	79.1067	474	1141	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	78.4236	355	1141	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_900109795.1	641665	641665	type	True	78.42	346	1141	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	77.7368	183	1141	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	77.557	257	1141	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	77.4685	199	1141	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	77.4524	202	1141	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	77.3526	222	1141	95	below_threshold
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	77.2543	195	1141	95	below_threshold
Thalassotalea crassostreae	strain=LPB0090	GCA_001652445.1	1763536	1763536	type	True	77.1619	112	1141	95	below_threshold
Thalassotalea crassostreae	strain=LPB0090	GCA_001831495.1	1763536	1763536	type	True	77.1529	114	1141	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	77.091	135	1141	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 23:05:37,639] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34674/tc_result.tsv
[2023-03-16 23:05:37,639] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:05:37,639] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:05:37,639] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82b7c847-e508-440e-b3e1-b8daa1fb8642/dqc_reference/checkm_data
[2023-03-16 23:05:37,640] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:05:37,644] [INFO] Task started: CheckM
[2023-03-16 23:05:37,644] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34674/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34674/checkm_input OceanDNA-b34674/checkm_result
[2023-03-16 23:06:22,557] [INFO] Task succeeded: CheckM
[2023-03-16 23:06:22,557] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.62%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 23:06:22,560] [INFO] ===== Completeness check finished =====
[2023-03-16 23:06:22,560] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:06:22,560] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34674/markers.fasta)
[2023-03-16 23:06:22,561] [INFO] Task started: Blastn
[2023-03-16 23:06:22,561] [INFO] Running command: blastn -query OceanDNA-b34674/markers.fasta -db /var/lib/cwl/stg82b7c847-e508-440e-b3e1-b8daa1fb8642/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34674/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:06:23,234] [INFO] Task succeeded: Blastn
[2023-03-16 23:06:23,234] [INFO] Selected 9 target genomes.
[2023-03-16 23:06:23,234] [INFO] Target genome list was writen to OceanDNA-b34674/target_genomes_gtdb.txt
[2023-03-16 23:06:23,456] [INFO] Task started: fastANI
[2023-03-16 23:06:23,456] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdf240cc-2a40-4a73-9ff7-14c8b0e2fd80/OceanDNA-b34674.fa --refList OceanDNA-b34674/target_genomes_gtdb.txt --output OceanDNA-b34674/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:06:31,678] [INFO] Task succeeded: fastANI
[2023-03-16 23:06:31,684] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 23:06:31,684] [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	87.9365	947	1141	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	83.3806	830	1141	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	82.1385	747	1141	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	81.5429	718	1141	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	81.4913	680	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003354085.1	s__Cognaticolwellia sp003354085	80.5505	540	1141	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	80.2873	584	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.22	95.22	0.95	0.87	11	-
GCF_002000025.1	s__Cognaticolwellia aestuarii	79.8896	565	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002104475.1	s__Cognaticolwellia mytili	79.1026	473	1141	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 23:06:31,684] [INFO] GTDB search result was written to OceanDNA-b34674/result_gtdb.tsv
[2023-03-16 23:06:31,685] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:06:31,686] [INFO] DFAST_QC result json was written to OceanDNA-b34674/dqc_result.json
[2023-03-16 23:06:31,686] [INFO] DFAST_QC completed!
[2023-03-16 23:06:31,686] [INFO] Total running time: 0h1m28s