[2024-01-24 12:39:47,526] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:47,527] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:47,528] [INFO] DQC Reference Directory: /var/lib/cwl/stge532ea42-6b69-43b1-83df-6325acb13275/dqc_reference
[2024-01-24 12:39:48,658] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:48,659] [INFO] Task started: Prodigal
[2024-01-24 12:39:48,659] [INFO] Running command: gunzip -c /var/lib/cwl/stg44d2f045-8544-45d9-a703-afcbc3d53104/GCF_005780245.1_ASM578024v1_genomic.fna.gz | prodigal -d GCF_005780245.1_ASM578024v1_genomic.fna/cds.fna -a GCF_005780245.1_ASM578024v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:09,643] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:09,644] [INFO] Task started: HMMsearch
[2024-01-24 12:40:09,644] [INFO] Running command: hmmsearch --tblout GCF_005780245.1_ASM578024v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge532ea42-6b69-43b1-83df-6325acb13275/dqc_reference/reference_markers.hmm GCF_005780245.1_ASM578024v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:09,884] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:09,885] [INFO] Found 6/6 markers.
[2024-01-24 12:40:09,924] [INFO] Query marker FASTA was written to GCF_005780245.1_ASM578024v1_genomic.fna/markers.fasta
[2024-01-24 12:40:09,924] [INFO] Task started: Blastn
[2024-01-24 12:40:09,924] [INFO] Running command: blastn -query GCF_005780245.1_ASM578024v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge532ea42-6b69-43b1-83df-6325acb13275/dqc_reference/reference_markers.fasta -out GCF_005780245.1_ASM578024v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:10,572] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:10,577] [INFO] Selected 14 target genomes.
[2024-01-24 12:40:10,577] [INFO] Target genome list was writen to GCF_005780245.1_ASM578024v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:10,582] [INFO] Task started: fastANI
[2024-01-24 12:40:10,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg44d2f045-8544-45d9-a703-afcbc3d53104/GCF_005780245.1_ASM578024v1_genomic.fna.gz --refList GCF_005780245.1_ASM578024v1_genomic.fna/target_genomes.txt --output GCF_005780245.1_ASM578024v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:20,885] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:20,886] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge532ea42-6b69-43b1-83df-6325acb13275/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:20,886] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge532ea42-6b69-43b1-83df-6325acb13275/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:20,895] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:40:20,896] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:40:20,896] [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 aurantiacus	strain=KCTC 52409	GCA_005780245.1	1882343	1882343	type	True	100.0	1374	1374	95	inconclusive
Maribacter flavus	strain=KCTC 42508	GCA_008386635.1	1658664	1658664	type	True	96.5552	1210	1374	95	inconclusive
Maribacter algicola	strain=PoM-212	GCA_003933245.1	2498892	2498892	type	True	84.9729	987	1374	95	below_threshold
Maribacter cobaltidurans	strain=CGMCC 1.15508	GCA_014643435.1	1178778	1178778	type	True	80.5893	708	1374	95	below_threshold
Maribacter cobaltidurans	strain=B1	GCA_002269385.1	1178778	1178778	type	True	80.4942	719	1374	95	below_threshold
Zobellia uliginosa	strain=DSM 2061	GCA_900156625.1	143224	143224	type	True	76.7319	146	1374	95	below_threshold
Arenibacter troitsensis	strain=DSM 19835	GCA_900177645.1	188872	188872	type	True	76.6345	144	1374	95	below_threshold
Muricauda aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	76.56	127	1374	95	below_threshold
Muriicola soli	strain=MMS17-SY002	GCA_004139715.1	2507538	2507538	type	True	76.5292	64	1374	95	below_threshold
Pricia antarctica	strain=DSM 23421	GCA_900101815.1	641691	641691	type	True	76.2028	117	1374	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:20,898] [INFO] DFAST Taxonomy check result was written to GCF_005780245.1_ASM578024v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:20,899] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:20,899] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:20,900] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge532ea42-6b69-43b1-83df-6325acb13275/dqc_reference/checkm_data
[2024-01-24 12:40:20,901] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:20,942] [INFO] Task started: CheckM
[2024-01-24 12:40:20,942] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005780245.1_ASM578024v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005780245.1_ASM578024v1_genomic.fna/checkm_input GCF_005780245.1_ASM578024v1_genomic.fna/checkm_result
[2024-01-24 12:41:18,881] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:18,882] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:18,900] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:18,900] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:18,901] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005780245.1_ASM578024v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:18,901] [INFO] Task started: Blastn
[2024-01-24 12:41:18,901] [INFO] Running command: blastn -query GCF_005780245.1_ASM578024v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge532ea42-6b69-43b1-83df-6325acb13275/dqc_reference/reference_markers_gtdb.fasta -out GCF_005780245.1_ASM578024v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:19,676] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:19,679] [INFO] Selected 13 target genomes.
[2024-01-24 12:41:19,679] [INFO] Target genome list was writen to GCF_005780245.1_ASM578024v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:19,687] [INFO] Task started: fastANI
[2024-01-24 12:41:19,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg44d2f045-8544-45d9-a703-afcbc3d53104/GCF_005780245.1_ASM578024v1_genomic.fna.gz --refList GCF_005780245.1_ASM578024v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005780245.1_ASM578024v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:28,900] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:28,910] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:28,910] [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_008386635.1	s__Maribacter flavus	96.5658	1209	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	96.59	96.59	0.88	0.88	2	conclusive
GCF_003933245.1	s__Maribacter algicola	84.9836	986	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002742265.1	s__Maribacter sp002742265	82.7416	912	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002269385.1	s__Maribacter cobaltidurans	80.4942	719	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018100785.1	s__Maribacter sp018100785	78.1034	259	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001020565.1	s__Maribacter thermophilus	77.7548	280	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017795065.1	s__Muricauda sp017795065	77.0567	125	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001935.1	s__Maribacter_A sp013001935	76.6068	60	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	96.76	96.72	0.66	0.66	3	-
GCF_000745185.1	s__Muricauda sp000745185	76.5298	151	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813125.1	s__Muricauda sp002813125	76.4053	125	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101815.1	s__Pricia antarctica	76.2028	117	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pricia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214065.1	s__DT-32 sp013214065	76.1306	78	1374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__DT-32	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:28,912] [INFO] GTDB search result was written to GCF_005780245.1_ASM578024v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:28,912] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:28,915] [INFO] DFAST_QC result json was written to GCF_005780245.1_ASM578024v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:28,916] [INFO] DFAST_QC completed!
[2024-01-24 12:41:28,916] [INFO] Total running time: 0h1m41s