[2023-03-18 01:54:18,006] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:54:18,007] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:54:18,007] [INFO] DQC Reference Directory: /var/lib/cwl/stg4294b7b2-b270-485c-84e4-387656c67461/dqc_reference
[2023-03-18 01:54:19,123] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:54:19,123] [INFO] Task started: Prodigal
[2023-03-18 01:54:19,124] [INFO] Running command: cat /var/lib/cwl/stgd6b80f93-a83e-4a63-b52b-3ca292070eec/OceanDNA-b6362.fa | prodigal -d OceanDNA-b6362/cds.fna -a OceanDNA-b6362/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:54:27,035] [INFO] Task succeeded: Prodigal
[2023-03-18 01:54:27,035] [INFO] Task started: HMMsearch
[2023-03-18 01:54:27,035] [INFO] Running command: hmmsearch --tblout OceanDNA-b6362/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4294b7b2-b270-485c-84e4-387656c67461/dqc_reference/reference_markers.hmm OceanDNA-b6362/protein.faa > /dev/null
[2023-03-18 01:54:27,205] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:54:27,205] [INFO] Found 6/6 markers.
[2023-03-18 01:54:27,217] [INFO] Query marker FASTA was written to OceanDNA-b6362/markers.fasta
[2023-03-18 01:54:27,218] [INFO] Task started: Blastn
[2023-03-18 01:54:27,218] [INFO] Running command: blastn -query OceanDNA-b6362/markers.fasta -db /var/lib/cwl/stg4294b7b2-b270-485c-84e4-387656c67461/dqc_reference/reference_markers.fasta -out OceanDNA-b6362/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:54:27,767] [INFO] Task succeeded: Blastn
[2023-03-18 01:54:27,768] [INFO] Selected 31 target genomes.
[2023-03-18 01:54:27,768] [INFO] Target genome list was writen to OceanDNA-b6362/target_genomes.txt
[2023-03-18 01:54:27,779] [INFO] Task started: fastANI
[2023-03-18 01:54:27,779] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6b80f93-a83e-4a63-b52b-3ca292070eec/OceanDNA-b6362.fa --refList OceanDNA-b6362/target_genomes.txt --output OceanDNA-b6362/fastani_result.tsv --threads 1
[2023-03-18 01:54:43,366] [INFO] Task succeeded: fastANI
[2023-03-18 01:54:43,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4294b7b2-b270-485c-84e4-387656c67461/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:54:43,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4294b7b2-b270-485c-84e4-387656c67461/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:54:43,374] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:54:43,374] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:54:43,374] [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
Mesoflavibacter profundi	strain=YC1039	GCA_014764305.1	2708110	2708110	type	True	76.4443	55	450	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	76.2847	58	450	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	76.2339	61	450	95	below_threshold
Cellulophaga lytica	strain=DSM 7489	GCA_000190595.1	979	979	type	True	76.2019	50	450	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	76.174	63	450	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.1529	58	450	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.1127	54	450	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	76.111	62	450	95	below_threshold
Oceanihabitans sediminis	strain=DSM 28133	GCA_003315315.1	1812012	1812012	type	True	76.0712	51	450	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	76.0397	52	450	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	76.0048	53	450	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	75.9486	55	450	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:54:43,374] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6362/tc_result.tsv
[2023-03-18 01:54:43,375] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:54:43,375] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:54:43,375] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4294b7b2-b270-485c-84e4-387656c67461/dqc_reference/checkm_data
[2023-03-18 01:54:43,375] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:54:43,378] [INFO] Task started: CheckM
[2023-03-18 01:54:43,378] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6362/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6362/checkm_input OceanDNA-b6362/checkm_result
[2023-03-18 01:55:08,294] [INFO] Task succeeded: CheckM
[2023-03-18 01:55:08,294] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:55:08,296] [INFO] ===== Completeness check finished =====
[2023-03-18 01:55:08,296] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:55:08,296] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6362/markers.fasta)
[2023-03-18 01:55:08,296] [INFO] Task started: Blastn
[2023-03-18 01:55:08,296] [INFO] Running command: blastn -query OceanDNA-b6362/markers.fasta -db /var/lib/cwl/stg4294b7b2-b270-485c-84e4-387656c67461/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6362/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:55:09,058] [INFO] Task succeeded: Blastn
[2023-03-18 01:55:09,059] [INFO] Selected 20 target genomes.
[2023-03-18 01:55:09,059] [INFO] Target genome list was writen to OceanDNA-b6362/target_genomes_gtdb.txt
[2023-03-18 01:55:09,079] [INFO] Task started: fastANI
[2023-03-18 01:55:09,079] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6b80f93-a83e-4a63-b52b-3ca292070eec/OceanDNA-b6362.fa --refList OceanDNA-b6362/target_genomes_gtdb.txt --output OceanDNA-b6362/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:55:17,079] [INFO] Task succeeded: fastANI
[2023-03-18 01:55:17,086] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:55:17,086] [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
GCA_905182835.1	s__SGZJ01 sp905182835	83.25	326	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SGZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213995.1	s__SGZJ01 sp004213995	80.2491	244	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SGZJ01	95.0	95.83	95.53	0.71	0.69	3	-
GCA_902515565.1	s__SGZJ01 sp902515565	79.9517	210	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SGZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018674025.1	s__SGZJ01 sp018674025	79.5573	231	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SGZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741945.1	s__Wocania sp002741945	76.5364	57	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691265.1	s__MED-G13 sp002691265	76.4784	54	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	97.61	95.49	0.82	0.79	4	-
GCF_018860825.1	s__Oceanihabitans sp018860825	76.3149	53	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190595.1	s__Cellulophaga lytica	76.2019	50	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	99.01	98.71	0.94	0.93	6	-
GCA_902518355.1	s__MED-G13 sp902518355	76.183	53	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	96.57	96.00	0.86	0.83	4	-
GCF_003143755.1	s__Algibacter_B sp003143755	76.174	63	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249065.1	s__Winogradskyella litoriviva	76.1529	58	450	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:55:17,087] [INFO] GTDB search result was written to OceanDNA-b6362/result_gtdb.tsv
[2023-03-18 01:55:17,087] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:55:17,088] [INFO] DFAST_QC result json was written to OceanDNA-b6362/dqc_result.json
[2023-03-18 01:55:17,089] [INFO] DFAST_QC completed!
[2023-03-18 01:55:17,089] [INFO] Total running time: 0h0m59s