[2023-03-16 04:54:07,037] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:54:07,037] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:54:07,038] [INFO] DQC Reference Directory: /var/lib/cwl/stg4dd863d0-e9f5-4df3-ad52-a299d118b928/dqc_reference
[2023-03-16 04:54:08,370] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:54:08,371] [INFO] Task started: Prodigal
[2023-03-16 04:54:08,371] [INFO] Running command: cat /var/lib/cwl/stgf9444dee-6b30-4ea8-879c-8c320c9853e1/OceanDNA-b9689.fa | prodigal -d OceanDNA-b9689/cds.fna -a OceanDNA-b9689/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:54:35,869] [INFO] Task succeeded: Prodigal
[2023-03-16 04:54:35,869] [INFO] Task started: HMMsearch
[2023-03-16 04:54:35,869] [INFO] Running command: hmmsearch --tblout OceanDNA-b9689/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4dd863d0-e9f5-4df3-ad52-a299d118b928/dqc_reference/reference_markers.hmm OceanDNA-b9689/protein.faa > /dev/null
[2023-03-16 04:54:36,188] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:54:36,188] [INFO] Found 6/6 markers.
[2023-03-16 04:54:36,214] [INFO] Query marker FASTA was written to OceanDNA-b9689/markers.fasta
[2023-03-16 04:54:36,215] [INFO] Task started: Blastn
[2023-03-16 04:54:36,215] [INFO] Running command: blastn -query OceanDNA-b9689/markers.fasta -db /var/lib/cwl/stg4dd863d0-e9f5-4df3-ad52-a299d118b928/dqc_reference/reference_markers.fasta -out OceanDNA-b9689/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:54:36,861] [INFO] Task succeeded: Blastn
[2023-03-16 04:54:36,861] [INFO] Selected 13 target genomes.
[2023-03-16 04:54:36,862] [INFO] Target genome list was writen to OceanDNA-b9689/target_genomes.txt
[2023-03-16 04:54:36,870] [INFO] Task started: fastANI
[2023-03-16 04:54:36,870] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9444dee-6b30-4ea8-879c-8c320c9853e1/OceanDNA-b9689.fa --refList OceanDNA-b9689/target_genomes.txt --output OceanDNA-b9689/fastani_result.tsv --threads 1
[2023-03-16 04:54:48,289] [INFO] Task succeeded: fastANI
[2023-03-16 04:54:48,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4dd863d0-e9f5-4df3-ad52-a299d118b928/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:54:48,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4dd863d0-e9f5-4df3-ad52-a299d118b928/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:54:48,297] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 04:54:48,298] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 04:54:48,298] [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
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	98.1135	1298	1412	95	conclusive
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	86.0385	1045	1412	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	83.139	962	1412	95	below_threshold
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	82.8434	963	1412	95	below_threshold
Maribacter forsetii	strain=DSM 18668	GCA_000744105.1	444515	444515	type	True	82.7129	971	1412	95	below_threshold
Maribacter ulvicola	strain=DSM 15366	GCA_900155985.1	228959	228959	type	True	81.7202	870	1412	95	below_threshold
Maribacter litoralis	strain=SDRB-Phe2	GCA_003075045.1	2059726	2059726	type	True	81.2817	898	1412	95	below_threshold
Maribacter sedimenticola	strain=DSM 19840	GCA_900188415.1	228956	228956	type	True	79.4304	556	1412	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.2694	77	1412	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	75.9006	112	1412	95	below_threshold
Muricauda hymeniacidonis	strain=176CP4-71	GCA_004296335.1	2517819	2517819	type	True	75.5765	69	1412	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	75.489	67	1412	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:54:48,298] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9689/tc_result.tsv
[2023-03-16 04:54:48,298] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:54:48,299] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:54:48,299] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4dd863d0-e9f5-4df3-ad52-a299d118b928/dqc_reference/checkm_data
[2023-03-16 04:54:48,299] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:54:48,400] [INFO] Task started: CheckM
[2023-03-16 04:54:48,400] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9689/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9689/checkm_input OceanDNA-b9689/checkm_result
[2023-03-16 04:55:54,153] [INFO] Task succeeded: CheckM
[2023-03-16 04:55:54,153] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:55:54,156] [INFO] ===== Completeness check finished =====
[2023-03-16 04:55:54,156] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:55:54,156] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9689/markers.fasta)
[2023-03-16 04:55:54,157] [INFO] Task started: Blastn
[2023-03-16 04:55:54,157] [INFO] Running command: blastn -query OceanDNA-b9689/markers.fasta -db /var/lib/cwl/stg4dd863d0-e9f5-4df3-ad52-a299d118b928/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9689/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:55:55,034] [INFO] Task succeeded: Blastn
[2023-03-16 04:55:55,035] [INFO] Selected 9 target genomes.
[2023-03-16 04:55:55,035] [INFO] Target genome list was writen to OceanDNA-b9689/target_genomes_gtdb.txt
[2023-03-16 04:55:55,044] [INFO] Task started: fastANI
[2023-03-16 04:55:55,044] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9444dee-6b30-4ea8-879c-8c320c9853e1/OceanDNA-b9689.fa --refList OceanDNA-b9689/target_genomes_gtdb.txt --output OceanDNA-b9689/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:56:03,891] [INFO] Task succeeded: fastANI
[2023-03-16 04:56:03,897] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:56:03,897] [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_900112245.1	s__Maribacter stanieri	98.1135	1298	1412	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	conclusive
GCA_011050675.1	s__Maribacter sp011050675	90.2857	1192	1412	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900142175.1	s__Maribacter aquivivus	86.0277	1046	1412	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364165.1	s__Maribacter spongiicola	83.1365	962	1412	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364175.1	s__Maribacter caenipelagi	82.8434	963	1412	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744105.1	s__Maribacter forsetii	82.7207	969	1412	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155985.1	s__Maribacter ulvicola	81.7202	870	1412	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001913155.1	s__Maribacter hydrothermalis	80.7739	809	1412	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900188415.1	s__Maribacter sedimenticola	79.4215	557	1412	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.95	97.95	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-16 04:56:03,897] [INFO] GTDB search result was written to OceanDNA-b9689/result_gtdb.tsv
[2023-03-16 04:56:03,897] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:56:03,899] [INFO] DFAST_QC result json was written to OceanDNA-b9689/dqc_result.json
[2023-03-16 04:56:03,899] [INFO] DFAST_QC completed!
[2023-03-16 04:56:03,899] [INFO] Total running time: 0h1m57s