[2023-03-18 07:06:19,989] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:06:19,989] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:06:19,989] [INFO] DQC Reference Directory: /var/lib/cwl/stg520e7a24-232c-4c43-96f3-0b6fd3195a67/dqc_reference
[2023-03-18 07:06:21,123] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:06:21,123] [INFO] Task started: Prodigal
[2023-03-18 07:06:21,123] [INFO] Running command: cat /var/lib/cwl/stg287a6c5a-4b74-4ba5-a0ef-c801a42ea614/OceanDNA-b6211.fa | prodigal -d OceanDNA-b6211/cds.fna -a OceanDNA-b6211/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:06:30,826] [INFO] Task succeeded: Prodigal
[2023-03-18 07:06:30,827] [INFO] Task started: HMMsearch
[2023-03-18 07:06:30,827] [INFO] Running command: hmmsearch --tblout OceanDNA-b6211/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg520e7a24-232c-4c43-96f3-0b6fd3195a67/dqc_reference/reference_markers.hmm OceanDNA-b6211/protein.faa > /dev/null
[2023-03-18 07:06:31,024] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:06:31,025] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg287a6c5a-4b74-4ba5-a0ef-c801a42ea614/OceanDNA-b6211.fa]
[2023-03-18 07:06:31,039] [INFO] Query marker FASTA was written to OceanDNA-b6211/markers.fasta
[2023-03-18 07:06:31,039] [INFO] Task started: Blastn
[2023-03-18 07:06:31,039] [INFO] Running command: blastn -query OceanDNA-b6211/markers.fasta -db /var/lib/cwl/stg520e7a24-232c-4c43-96f3-0b6fd3195a67/dqc_reference/reference_markers.fasta -out OceanDNA-b6211/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:06:31,597] [INFO] Task succeeded: Blastn
[2023-03-18 07:06:31,597] [INFO] Selected 23 target genomes.
[2023-03-18 07:06:31,598] [INFO] Target genome list was writen to OceanDNA-b6211/target_genomes.txt
[2023-03-18 07:06:31,610] [INFO] Task started: fastANI
[2023-03-18 07:06:31,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg287a6c5a-4b74-4ba5-a0ef-c801a42ea614/OceanDNA-b6211.fa --refList OceanDNA-b6211/target_genomes.txt --output OceanDNA-b6211/fastani_result.tsv --threads 1
[2023-03-18 07:06:43,475] [INFO] Task succeeded: fastANI
[2023-03-18 07:06:43,476] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg520e7a24-232c-4c43-96f3-0b6fd3195a67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:06:43,476] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg520e7a24-232c-4c43-96f3-0b6fd3195a67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:06:43,484] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:06:43,484] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 07:06:43,484] [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
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	75.9923	65	472	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	75.9906	51	472	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	75.9678	61	472	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	75.9284	69	472	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	75.9284	69	472	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	75.9061	64	472	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	75.8516	54	472	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	75.7519	55	472	95	below_threshold
Seonamhaeicola aphaedonensis	strain=CECT 8487	GCA_003386195.1	1461338	1461338	type	True	75.7106	65	472	95	below_threshold
Lutibacter oceani	strain=325-5	GCA_003384935.1	1853311	1853311	type	True	75.6169	50	472	95	below_threshold
Mangrovimonas spongiae	strain=HN-E26	GCA_003944795.1	2494697	2494697	type	True	75.5733	52	472	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	75.375	53	472	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:06:43,484] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6211/tc_result.tsv
[2023-03-18 07:06:43,484] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:06:43,484] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:06:43,485] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg520e7a24-232c-4c43-96f3-0b6fd3195a67/dqc_reference/checkm_data
[2023-03-18 07:06:43,485] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:06:43,489] [INFO] Task started: CheckM
[2023-03-18 07:06:43,489] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6211/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6211/checkm_input OceanDNA-b6211/checkm_result
[2023-03-18 07:07:12,368] [INFO] Task succeeded: CheckM
[2023-03-18 07:07:12,369] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:07:12,387] [INFO] ===== Completeness check finished =====
[2023-03-18 07:07:12,387] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:07:12,387] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6211/markers.fasta)
[2023-03-18 07:07:12,387] [INFO] Task started: Blastn
[2023-03-18 07:07:12,387] [INFO] Running command: blastn -query OceanDNA-b6211/markers.fasta -db /var/lib/cwl/stg520e7a24-232c-4c43-96f3-0b6fd3195a67/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6211/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:07:13,131] [INFO] Task succeeded: Blastn
[2023-03-18 07:07:13,132] [INFO] Selected 20 target genomes.
[2023-03-18 07:07:13,132] [INFO] Target genome list was writen to OceanDNA-b6211/target_genomes_gtdb.txt
[2023-03-18 07:07:13,240] [INFO] Task started: fastANI
[2023-03-18 07:07:13,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg287a6c5a-4b74-4ba5-a0ef-c801a42ea614/OceanDNA-b6211.fa --refList OceanDNA-b6211/target_genomes_gtdb.txt --output OceanDNA-b6211/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:07:24,155] [INFO] Task succeeded: fastANI
[2023-03-18 07:07:24,161] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:07:24,161] [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_000422365.1	s__Mesoflavibacter zeaxanthinifaciens	76.487	56	472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	97.07	97.05	0.91	0.91	3	-
GCF_008084905.1	s__Xanthomarina maritima	76.3256	57	472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	76.2847	74	472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001874335.1	s__MedPE-SWsnd-G2 sp001874335	76.2566	66	472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MedPE-SWsnd-G2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403865.1	s__Winogradskyella costae	76.0076	50	472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997385.1	s__Seonamhaeicola algicola	75.9439	65	472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	75.9061	64	472	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_008056315.1	s__Seonamhaeicola maritimus	75.7995	53	472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944795.1	s__Mangrovimonas spongiae	75.5137	51	472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mangrovimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:07:24,162] [INFO] GTDB search result was written to OceanDNA-b6211/result_gtdb.tsv
[2023-03-18 07:07:24,162] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:07:24,163] [INFO] DFAST_QC result json was written to OceanDNA-b6211/dqc_result.json
[2023-03-18 07:07:24,163] [INFO] DFAST_QC completed!
[2023-03-18 07:07:24,163] [INFO] Total running time: 0h1m4s