[2023-06-16 22:13:36,436] [INFO] DFAST_QC pipeline started.
[2023-06-16 22:13:36,439] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 22:13:36,439] [INFO] DQC Reference Directory: /var/lib/cwl/stgdcb0842c-0ac2-4008-9c35-854281b259a9/dqc_reference
[2023-06-16 22:13:37,693] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 22:13:37,694] [INFO] Task started: Prodigal
[2023-06-16 22:13:37,694] [INFO] Running command: gunzip -c /var/lib/cwl/stg783e5a48-ec16-46f1-8fba-d1ee5a41304d/GCA_905182925.1_FRAM18_bin208_genomic.fna.gz | prodigal -d GCA_905182925.1_FRAM18_bin208_genomic.fna/cds.fna -a GCA_905182925.1_FRAM18_bin208_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 22:13:44,828] [INFO] Task succeeded: Prodigal
[2023-06-16 22:13:44,829] [INFO] Task started: HMMsearch
[2023-06-16 22:13:44,829] [INFO] Running command: hmmsearch --tblout GCA_905182925.1_FRAM18_bin208_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdcb0842c-0ac2-4008-9c35-854281b259a9/dqc_reference/reference_markers.hmm GCA_905182925.1_FRAM18_bin208_genomic.fna/protein.faa > /dev/null
[2023-06-16 22:13:45,108] [INFO] Task succeeded: HMMsearch
[2023-06-16 22:13:45,109] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg783e5a48-ec16-46f1-8fba-d1ee5a41304d/GCA_905182925.1_FRAM18_bin208_genomic.fna.gz]
[2023-06-16 22:13:45,132] [INFO] Query marker FASTA was written to GCA_905182925.1_FRAM18_bin208_genomic.fna/markers.fasta
[2023-06-16 22:13:45,133] [INFO] Task started: Blastn
[2023-06-16 22:13:45,133] [INFO] Running command: blastn -query GCA_905182925.1_FRAM18_bin208_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcb0842c-0ac2-4008-9c35-854281b259a9/dqc_reference/reference_markers.fasta -out GCA_905182925.1_FRAM18_bin208_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:13:45,815] [INFO] Task succeeded: Blastn
[2023-06-16 22:13:45,820] [INFO] Selected 32 target genomes.
[2023-06-16 22:13:45,820] [INFO] Target genome list was writen to GCA_905182925.1_FRAM18_bin208_genomic.fna/target_genomes.txt
[2023-06-16 22:13:45,837] [INFO] Task started: fastANI
[2023-06-16 22:13:45,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg783e5a48-ec16-46f1-8fba-d1ee5a41304d/GCA_905182925.1_FRAM18_bin208_genomic.fna.gz --refList GCA_905182925.1_FRAM18_bin208_genomic.fna/target_genomes.txt --output GCA_905182925.1_FRAM18_bin208_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 22:14:06,406] [INFO] Task succeeded: fastANI
[2023-06-16 22:14:06,407] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdcb0842c-0ac2-4008-9c35-854281b259a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 22:14:06,408] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdcb0842c-0ac2-4008-9c35-854281b259a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 22:14:06,434] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 22:14:06,434] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 22:14:06,434] [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
Formosa sediminum	strain=PS13	GCA_007197735.1	2594004	2594004	type	True	77.3972	92	780	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.3175	79	780	95	below_threshold
Patiriisocius marinistellae	strain=KK4	GCA_009014635.1	2494560	2494560	type	True	77.3115	120	780	95	below_threshold
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	77.2876	106	780	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	77.2861	108	780	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	77.1922	91	780	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	77.1664	86	780	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.0838	75	780	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	77.055	96	780	95	below_threshold
Algibacter mikhailovii	strain=KCTC 12710	GCA_014651495.1	425498	425498	type	True	77.0122	77	780	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	76.9917	91	780	95	below_threshold
Lacinutrix mariniflava	strain=AKS432	GCA_001418015.1	342955	342955	type	True	76.9133	107	780	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	76.9129	103	780	95	below_threshold
Aequorivita soesokkakensis	strain=RSSK-12	GCA_001641085.1	1385699	1385699	type	True	76.9093	72	780	95	below_threshold
Aequorivita viscosa	strain=CGMCC 1.11023	GCA_900106795.1	797419	797419	type	True	76.9068	72	780	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	76.8825	122	780	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	76.8716	115	780	95	below_threshold
Lacinutrix algicola	strain=AKS293	GCA_001418085.1	342954	342954	type	True	76.8258	109	780	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	76.7947	112	780	95	below_threshold
Aequorivita viscosa	strain=DSM 26349	GCA_900141955.1	797419	797419	type	True	76.7662	72	780	95	below_threshold
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	76.7018	82	780	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	76.6908	90	780	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	76.6646	122	780	95	below_threshold
Cellulophaga algicola	strain=DSM 14237	GCA_000186265.1	59600	59600	type	True	76.6291	97	780	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	76.4619	94	780	95	below_threshold
Aquimarina aggregata	strain=RZW4-3-2	GCA_001632745.1	1642818	1642818	type	True	76.4189	98	780	95	below_threshold
Cellulophaga baltica	strain=DSM 24729	GCA_900102165.1	76594	76594	type	True	76.2249	77	780	95	below_threshold
Maribacter vaceletii	strain=DSM 25230	GCA_003634105.1	1206816	1206816	type	True	76.0865	103	780	95	below_threshold
Flavobacterium cellulosilyticum	strain=AR-3-4	GCA_004349355.1	2541731	2541731	type	True	75.7836	77	780	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 22:14:06,436] [INFO] DFAST Taxonomy check result was written to GCA_905182925.1_FRAM18_bin208_genomic.fna/tc_result.tsv
[2023-06-16 22:14:06,437] [INFO] ===== Taxonomy check completed =====
[2023-06-16 22:14:06,438] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 22:14:06,438] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdcb0842c-0ac2-4008-9c35-854281b259a9/dqc_reference/checkm_data
[2023-06-16 22:14:06,439] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 22:14:06,467] [INFO] Task started: CheckM
[2023-06-16 22:14:06,467] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905182925.1_FRAM18_bin208_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905182925.1_FRAM18_bin208_genomic.fna/checkm_input GCA_905182925.1_FRAM18_bin208_genomic.fna/checkm_result
[2023-06-16 22:14:33,024] [INFO] Task succeeded: CheckM
[2023-06-16 22:14:33,026] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 22:14:33,047] [INFO] ===== Completeness check finished =====
[2023-06-16 22:14:33,047] [INFO] ===== Start GTDB Search =====
[2023-06-16 22:14:33,048] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905182925.1_FRAM18_bin208_genomic.fna/markers.fasta)
[2023-06-16 22:14:33,048] [INFO] Task started: Blastn
[2023-06-16 22:14:33,048] [INFO] Running command: blastn -query GCA_905182925.1_FRAM18_bin208_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcb0842c-0ac2-4008-9c35-854281b259a9/dqc_reference/reference_markers_gtdb.fasta -out GCA_905182925.1_FRAM18_bin208_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:14:33,954] [INFO] Task succeeded: Blastn
[2023-06-16 22:14:33,958] [INFO] Selected 11 target genomes.
[2023-06-16 22:14:33,959] [INFO] Target genome list was writen to GCA_905182925.1_FRAM18_bin208_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 22:14:33,972] [INFO] Task started: fastANI
[2023-06-16 22:14:33,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg783e5a48-ec16-46f1-8fba-d1ee5a41304d/GCA_905182925.1_FRAM18_bin208_genomic.fna.gz --refList GCA_905182925.1_FRAM18_bin208_genomic.fna/target_genomes_gtdb.txt --output GCA_905182925.1_FRAM18_bin208_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 22:14:39,409] [INFO] Task succeeded: fastANI
[2023-06-16 22:14:39,422] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-16 22:14:39,422] [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_002713705.1	s__GCA-002733185 sp002713705	94.1668	626	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	97.32	97.11	0.93	0.92	3	-
GCA_018669795.1	s__GCA-002733185 sp018669795	91.9879	588	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	98.54	95.82	0.94	0.91	4	-
GCA_905181835.1	s__GCA-002733185 sp905181835	79.2399	335	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733185.1	s__GCA-002733185 sp002733185	78.6037	303	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213605.1	s__GCA-002733185 sp004213605	78.5191	211	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	95.79	95.79	0.89	0.89	2	-
GCA_004214175.1	s__GCA-002733185 sp004214175	78.3803	213	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	77.1556	120	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106795.1	s__Aequorivita viscosa	76.9068	72	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013285155.1	s__Winogradskyella undariae	76.8923	114	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.00	96.07	0.88	0.85	4	-
GCF_008084905.1	s__Xanthomarina maritima	76.7207	123	780	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 22:14:39,424] [INFO] GTDB search result was written to GCA_905182925.1_FRAM18_bin208_genomic.fna/result_gtdb.tsv
[2023-06-16 22:14:39,425] [INFO] ===== GTDB Search completed =====
[2023-06-16 22:14:39,429] [INFO] DFAST_QC result json was written to GCA_905182925.1_FRAM18_bin208_genomic.fna/dqc_result.json
[2023-06-16 22:14:39,430] [INFO] DFAST_QC completed!
[2023-06-16 22:14:39,430] [INFO] Total running time: 0h1m3s