[2023-03-19 02:29:22,749] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:29:22,749] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:29:22,749] [INFO] DQC Reference Directory: /var/lib/cwl/stga10f4db6-6517-4e35-b665-c1434c17f945/dqc_reference
[2023-03-19 02:29:23,823] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:29:23,823] [INFO] Task started: Prodigal
[2023-03-19 02:29:23,823] [INFO] Running command: cat /var/lib/cwl/stgc88d487b-b685-48b7-bb84-e1fbfa6ec3b6/OceanDNA-b7584.fa | prodigal -d OceanDNA-b7584/cds.fna -a OceanDNA-b7584/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:29:36,915] [INFO] Task succeeded: Prodigal
[2023-03-19 02:29:36,915] [INFO] Task started: HMMsearch
[2023-03-19 02:29:36,915] [INFO] Running command: hmmsearch --tblout OceanDNA-b7584/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga10f4db6-6517-4e35-b665-c1434c17f945/dqc_reference/reference_markers.hmm OceanDNA-b7584/protein.faa > /dev/null
[2023-03-19 02:29:37,098] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:29:37,099] [INFO] Found 6/6 markers.
[2023-03-19 02:29:37,118] [INFO] Query marker FASTA was written to OceanDNA-b7584/markers.fasta
[2023-03-19 02:29:37,119] [INFO] Task started: Blastn
[2023-03-19 02:29:37,119] [INFO] Running command: blastn -query OceanDNA-b7584/markers.fasta -db /var/lib/cwl/stga10f4db6-6517-4e35-b665-c1434c17f945/dqc_reference/reference_markers.fasta -out OceanDNA-b7584/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:29:37,696] [INFO] Task succeeded: Blastn
[2023-03-19 02:29:37,700] [INFO] Selected 31 target genomes.
[2023-03-19 02:29:37,700] [INFO] Target genome list was writen to OceanDNA-b7584/target_genomes.txt
[2023-03-19 02:29:37,720] [INFO] Task started: fastANI
[2023-03-19 02:29:37,720] [INFO] Running command: fastANI --query /var/lib/cwl/stgc88d487b-b685-48b7-bb84-e1fbfa6ec3b6/OceanDNA-b7584.fa --refList OceanDNA-b7584/target_genomes.txt --output OceanDNA-b7584/fastani_result.tsv --threads 1
[2023-03-19 02:29:56,911] [INFO] Task succeeded: fastANI
[2023-03-19 02:29:56,912] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga10f4db6-6517-4e35-b665-c1434c17f945/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:29:56,912] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga10f4db6-6517-4e35-b665-c1434c17f945/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:29:56,920] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:29:56,920] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:29:56,920] [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
Cellulophaga lytica	strain=DSM 7489	GCA_000190595.1	979	979	type	True	76.9374	84	619	95	below_threshold
Cellulophaga algicola	strain=DSM 14237	GCA_000186265.1	59600	59600	type	True	76.8678	64	619	95	below_threshold
Cellulophaga omnivescoria	strain=W5C	GCA_001999725.1	1888890	1888890	type	True	76.798	91	619	95	below_threshold
Maribacter vaceletii	strain=DSM 25230	GCA_003634105.1	1206816	1206816	type	True	76.7829	91	619	95	below_threshold
Cellulophaga fucicola	strain=DSM 24786	GCA_900119145.1	76595	76595	type	True	76.7115	81	619	95	below_threshold
Maribacter algarum	strain=RZ26	GCA_005885635.1	2578118	2578118	type	True	76.6219	50	619	95	below_threshold
Maribacter dokdonensis	strain=DSW-8	GCA_001447995.1	320912	320912	type	True	76.4736	70	619	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001673755.1	1836467	1836467	type	True	76.4685	80	619	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	76.4351	80	619	95	below_threshold
Zobellia amurskyensis	strain=KMM 3526	GCA_009725985.1	248905	248905	type	True	76.4313	58	619	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	76.3184	74	619	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:29:56,921] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7584/tc_result.tsv
[2023-03-19 02:29:56,922] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:29:56,922] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:29:56,922] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga10f4db6-6517-4e35-b665-c1434c17f945/dqc_reference/checkm_data
[2023-03-19 02:29:56,922] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:29:56,927] [INFO] Task started: CheckM
[2023-03-19 02:29:56,927] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7584/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7584/checkm_input OceanDNA-b7584/checkm_result
[2023-03-19 02:30:33,083] [INFO] Task succeeded: CheckM
[2023-03-19 02:30:33,084] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:30:33,126] [INFO] ===== Completeness check finished =====
[2023-03-19 02:30:33,126] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:30:33,126] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7584/markers.fasta)
[2023-03-19 02:30:33,127] [INFO] Task started: Blastn
[2023-03-19 02:30:33,127] [INFO] Running command: blastn -query OceanDNA-b7584/markers.fasta -db /var/lib/cwl/stga10f4db6-6517-4e35-b665-c1434c17f945/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7584/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:30:33,940] [INFO] Task succeeded: Blastn
[2023-03-19 02:30:33,943] [INFO] Selected 20 target genomes.
[2023-03-19 02:30:33,943] [INFO] Target genome list was writen to OceanDNA-b7584/target_genomes_gtdb.txt
[2023-03-19 02:30:33,957] [INFO] Task started: fastANI
[2023-03-19 02:30:33,957] [INFO] Running command: fastANI --query /var/lib/cwl/stgc88d487b-b685-48b7-bb84-e1fbfa6ec3b6/OceanDNA-b7584.fa --refList OceanDNA-b7584/target_genomes_gtdb.txt --output OceanDNA-b7584/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:30:44,625] [INFO] Task succeeded: fastANI
[2023-03-19 02:30:44,634] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 02:30:44,634] [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_000173115.1	s__MAG-120531 sp000173115	98.6657	433	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-120531	95.0	99.02	98.72	0.73	0.67	33	conclusive
GCA_905182295.1	s__MAG-120531 sp905182295	91.2803	398	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-120531	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401115.1	s__MAG-120531 sp018401115	86.8295	564	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-120531	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018500065.1	s__MAG-120531 sp018500065	78.6787	204	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-120531	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373635.1	s__MAG-120531 sp013373635	76.9705	62	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-120531	95.0	99.93	99.93	0.99	0.99	2	-
GCF_000190595.1	s__Cellulophaga lytica	76.9374	84	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	99.01	98.71	0.94	0.93	6	-
GCF_009797025.1	s__Cellulophaga sp009797025	76.8931	76	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186265.1	s__Cellulophaga algicola	76.8678	64	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	98.35	98.34	0.88	0.87	3	-
GCA_016744255.1	s__Maribacter_B sp016744255	76.8537	66	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999725.1	s__Cellulophaga omnivescoria	76.798	91	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634105.1	s__Maribacter_B vaceletii	76.7829	91	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813425.1	s__Cellulophaga sp002813425	76.7579	86	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003957295.1	s__Arenibacter aquaticus	76.6779	58	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149745.1	s__Muricauda koreensis	76.3921	53	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:30:44,636] [INFO] GTDB search result was written to OceanDNA-b7584/result_gtdb.tsv
[2023-03-19 02:30:44,637] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:30:44,640] [INFO] DFAST_QC result json was written to OceanDNA-b7584/dqc_result.json
[2023-03-19 02:30:44,640] [INFO] DFAST_QC completed!
[2023-03-19 02:30:44,640] [INFO] Total running time: 0h1m22s