[2024-01-24 12:40:35,675] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:35,677] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:35,677] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b68840b-b7f5-4654-9950-acf8bbcca362/dqc_reference
[2024-01-24 12:40:36,902] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:36,903] [INFO] Task started: Prodigal
[2024-01-24 12:40:36,903] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a5b0dcd-31ab-4279-aa22-3d2defb0aba3/GCF_000176155.1_ASM17615v1_genomic.fna.gz | prodigal -d GCF_000176155.1_ASM17615v1_genomic.fna/cds.fna -a GCF_000176155.1_ASM17615v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:45,689] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:45,690] [INFO] Task started: HMMsearch
[2024-01-24 12:40:45,690] [INFO] Running command: hmmsearch --tblout GCF_000176155.1_ASM17615v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b68840b-b7f5-4654-9950-acf8bbcca362/dqc_reference/reference_markers.hmm GCF_000176155.1_ASM17615v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:45,969] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:45,970] [INFO] Found 6/6 markers.
[2024-01-24 12:40:46,008] [INFO] Query marker FASTA was written to GCF_000176155.1_ASM17615v1_genomic.fna/markers.fasta
[2024-01-24 12:40:46,009] [INFO] Task started: Blastn
[2024-01-24 12:40:46,009] [INFO] Running command: blastn -query GCF_000176155.1_ASM17615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b68840b-b7f5-4654-9950-acf8bbcca362/dqc_reference/reference_markers.fasta -out GCF_000176155.1_ASM17615v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:46,812] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:46,817] [INFO] Selected 15 target genomes.
[2024-01-24 12:40:46,818] [INFO] Target genome list was writen to GCF_000176155.1_ASM17615v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:46,828] [INFO] Task started: fastANI
[2024-01-24 12:40:46,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a5b0dcd-31ab-4279-aa22-3d2defb0aba3/GCF_000176155.1_ASM17615v1_genomic.fna.gz --refList GCF_000176155.1_ASM17615v1_genomic.fna/target_genomes.txt --output GCF_000176155.1_ASM17615v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:58,816] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:58,817] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b68840b-b7f5-4654-9950-acf8bbcca362/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:58,817] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b68840b-b7f5-4654-9950-acf8bbcca362/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:58,833] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:40:58,834] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:58,834] [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
Vibrio metschnikovii	strain=CIP 69.14	GCA_000176155.1	28172	28172	type	True	100.0	1266	1266	95	conclusive
Vibrio metschnikovii	strain=NCTC8443	GCA_900460295.1	28172	28172	type	True	99.9962	1265	1266	95	conclusive
Vibrio injensis	strain=M12-1144	GCA_001895205.1	1307414	1307414	type	True	92.8654	1046	1266	95	below_threshold
Vibrio fujianensis	strain=FJ201301	GCA_002749895.1	1974215	1974215	type	True	81.0363	564	1266	95	below_threshold
Vibrio cincinnatiensis	strain=NCTC12012	GCA_900460255.1	675	675	type	True	80.4759	555	1266	95	below_threshold
Vibrio cincinnatiensis	strain=DSM 19608	GCA_900167345.1	675	675	type	True	80.3236	519	1266	95	below_threshold
Vibrio furnissii	strain=FDAARGOS_777	GCA_006364355.1	29494	29494	type	True	79.6465	364	1266	95	below_threshold
Vibrio furnissii	strain=CIP 102972	GCA_000176175.1	29494	29494	type	True	79.5	356	1266	95	below_threshold
Vibrio zhugei	strain=KCTC 62784	GCA_024347155.1	2479546	2479546	type	True	78.9106	217	1266	95	below_threshold
Vibrio tarriae	strain=2521-89	GCA_002216685.1	2014742	2014742	type	True	78.9022	361	1266	95	below_threshold
Vibrio ziniensis	strain=ZWAL4003	GCA_011064285.1	2711221	2711221	type	True	78.8551	300	1266	95	below_threshold
Vibrio hippocampi	strain=CECT 8226	GCA_921292975.1	654686	654686	type	True	78.7628	191	1266	95	below_threshold
Vibrio nitrifigilis	strain=NFV-1	GCA_015686695.1	2789781	2789781	type	True	78.7566	273	1266	95	below_threshold
Vibrio vulnificus	strain=ATCC 27562	GCA_000299635.1	672	672	suspected-type	True	78.6516	220	1266	95	below_threshold
Vibrio algicola	strain=SM1977	GCA_009601765.2	2662262	2662262	type	True	78.5379	152	1266	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:58,836] [INFO] DFAST Taxonomy check result was written to GCF_000176155.1_ASM17615v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:58,837] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:58,837] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:58,837] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b68840b-b7f5-4654-9950-acf8bbcca362/dqc_reference/checkm_data
[2024-01-24 12:40:58,839] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:58,882] [INFO] Task started: CheckM
[2024-01-24 12:40:58,882] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000176155.1_ASM17615v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000176155.1_ASM17615v1_genomic.fna/checkm_input GCF_000176155.1_ASM17615v1_genomic.fna/checkm_result
[2024-01-24 12:41:30,575] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:30,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:30,597] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:30,597] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:30,598] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000176155.1_ASM17615v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:30,598] [INFO] Task started: Blastn
[2024-01-24 12:41:30,598] [INFO] Running command: blastn -query GCF_000176155.1_ASM17615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b68840b-b7f5-4654-9950-acf8bbcca362/dqc_reference/reference_markers_gtdb.fasta -out GCF_000176155.1_ASM17615v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:31,743] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:31,746] [INFO] Selected 9 target genomes.
[2024-01-24 12:41:31,747] [INFO] Target genome list was writen to GCF_000176155.1_ASM17615v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:31,757] [INFO] Task started: fastANI
[2024-01-24 12:41:31,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a5b0dcd-31ab-4279-aa22-3d2defb0aba3/GCF_000176155.1_ASM17615v1_genomic.fna.gz --refList GCF_000176155.1_ASM17615v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000176155.1_ASM17615v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:39,426] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:39,442] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:39,443] [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_000176155.1	s__Vibrio metschnikovii	100.0	1266	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.65	97.32	0.91	0.86	50	conclusive
GCF_001895205.1	s__Vibrio injensis	92.8563	1047	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.81	98.81	0.92	0.92	2	-
GCA_007124475.1	s__Vibrio sp007124475	82.6686	504	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.98	98.98	0.80	0.80	2	-
GCF_002749895.1	s__Vibrio fujianensis	81.0553	562	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.21	99.14	0.95	0.93	8	-
GCF_900167345.1	s__Vibrio cincinnatiensis	80.322	519	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.52	99.06	0.97	0.94	6	-
GCF_000176175.1	s__Vibrio furnissii	79.4856	358	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.58	97.97	0.95	0.91	12	-
GCF_009665255.1	s__Vibrio metoecus_B	79.05	341	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.11	98.11	0.94	0.94	2	-
GCF_011064285.1	s__Vibrio ziniensis	78.8544	298	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002849855.1	s__Vibrio azureus	78.6958	210	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:39,445] [INFO] GTDB search result was written to GCF_000176155.1_ASM17615v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:39,445] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:39,451] [INFO] DFAST_QC result json was written to GCF_000176155.1_ASM17615v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:39,451] [INFO] DFAST_QC completed!
[2024-01-24 12:41:39,451] [INFO] Total running time: 0h1m4s