[2024-01-24 13:31:57,746] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:57,748] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:57,748] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6350ebe-04be-4a85-9efc-236dbef6f414/dqc_reference
[2024-01-24 13:31:59,091] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:59,092] [INFO] Task started: Prodigal
[2024-01-24 13:31:59,092] [INFO] Running command: gunzip -c /var/lib/cwl/stg58880b36-38e9-480d-8284-40f2a4377490/GCF_004014855.1_ASM401485v1_genomic.fna.gz | prodigal -d GCF_004014855.1_ASM401485v1_genomic.fna/cds.fna -a GCF_004014855.1_ASM401485v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:09,128] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:09,128] [INFO] Task started: HMMsearch
[2024-01-24 13:32:09,128] [INFO] Running command: hmmsearch --tblout GCF_004014855.1_ASM401485v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6350ebe-04be-4a85-9efc-236dbef6f414/dqc_reference/reference_markers.hmm GCF_004014855.1_ASM401485v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:09,373] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:09,374] [INFO] Found 6/6 markers.
[2024-01-24 13:32:09,403] [INFO] Query marker FASTA was written to GCF_004014855.1_ASM401485v1_genomic.fna/markers.fasta
[2024-01-24 13:32:09,404] [INFO] Task started: Blastn
[2024-01-24 13:32:09,404] [INFO] Running command: blastn -query GCF_004014855.1_ASM401485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6350ebe-04be-4a85-9efc-236dbef6f414/dqc_reference/reference_markers.fasta -out GCF_004014855.1_ASM401485v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:10,129] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:10,132] [INFO] Selected 23 target genomes.
[2024-01-24 13:32:10,133] [INFO] Target genome list was writen to GCF_004014855.1_ASM401485v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:10,145] [INFO] Task started: fastANI
[2024-01-24 13:32:10,146] [INFO] Running command: fastANI --query /var/lib/cwl/stg58880b36-38e9-480d-8284-40f2a4377490/GCF_004014855.1_ASM401485v1_genomic.fna.gz --refList GCF_004014855.1_ASM401485v1_genomic.fna/target_genomes.txt --output GCF_004014855.1_ASM401485v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:22,401] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:22,402] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6350ebe-04be-4a85-9efc-236dbef6f414/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:22,402] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6350ebe-04be-4a85-9efc-236dbef6f414/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:22,412] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:22,412] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:22,412] [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
Apibacter raozihei	strain=HY041	GCA_004014855.1	2500547	2500547	type	True	100.0	1095	1097	95	conclusive
Apibacter adventoris	strain=wkB301	GCA_002964975.1	1679466	1679466	type	True	77.7267	272	1097	95	below_threshold
Apibacter mensalis	strain=R-53146	GCA_900018365.1	1586267	1586267	type	True	77.7146	196	1097	95	below_threshold
Apibacter mensalis	strain=R-53146	GCA_001418685.1	1586267	1586267	type	True	77.7146	196	1097	95	below_threshold
Apibacter muscae	strain=G8	GCA_007845635.1	2509004	2509004	type	True	77.0524	154	1097	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	76.7451	61	1097	95	below_threshold
Chryseobacterium binzhouense	strain=LM2	GCA_007474545.1	2593646	2593646	type	True	76.4385	51	1097	95	below_threshold
Chryseobacterium ureilyticum	strain=DSM 18017	GCA_900156735.1	373668	373668	type	True	76.184	53	1097	95	below_threshold
Tenacibaculum jejuense	strain=type strain: KCTC 22618	GCA_900198195.1	584609	584609	type	True	76.1153	57	1097	95	below_threshold
Chryseobacterium antibioticum	strain=RP-3-3	GCA_012927325.1	2728847	2728847	type	True	75.9604	51	1097	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:22,414] [INFO] DFAST Taxonomy check result was written to GCF_004014855.1_ASM401485v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:22,414] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:22,415] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:22,415] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6350ebe-04be-4a85-9efc-236dbef6f414/dqc_reference/checkm_data
[2024-01-24 13:32:22,416] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:22,451] [INFO] Task started: CheckM
[2024-01-24 13:32:22,452] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004014855.1_ASM401485v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004014855.1_ASM401485v1_genomic.fna/checkm_input GCF_004014855.1_ASM401485v1_genomic.fna/checkm_result
[2024-01-24 13:32:54,663] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:54,664] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:54,686] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:54,686] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:54,687] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004014855.1_ASM401485v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:54,687] [INFO] Task started: Blastn
[2024-01-24 13:32:54,687] [INFO] Running command: blastn -query GCF_004014855.1_ASM401485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6350ebe-04be-4a85-9efc-236dbef6f414/dqc_reference/reference_markers_gtdb.fasta -out GCF_004014855.1_ASM401485v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:55,853] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:55,858] [INFO] Selected 24 target genomes.
[2024-01-24 13:32:55,859] [INFO] Target genome list was writen to GCF_004014855.1_ASM401485v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:55,873] [INFO] Task started: fastANI
[2024-01-24 13:32:55,874] [INFO] Running command: fastANI --query /var/lib/cwl/stg58880b36-38e9-480d-8284-40f2a4377490/GCF_004014855.1_ASM401485v1_genomic.fna.gz --refList GCF_004014855.1_ASM401485v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004014855.1_ASM401485v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:09,995] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:10,006] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:10,006] [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_004014855.1	s__Apibacter raozihei	100.0	1091	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Apibacter	95.0	98.39	98.39	0.93	0.93	2	conclusive
GCF_011082725.1	s__Apibacter sp002964915	77.7842	203	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Apibacter	95.0	97.29	96.74	0.93	0.90	15	-
GCF_002964975.1	s__Apibacter adventoris	77.7279	272	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Apibacter	95.0	98.15	98.15	0.92	0.92	2	-
GCF_001418685.1	s__Apibacter mensalis	77.608	196	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Apibacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_903969135.1	s__Chryseobacterium sp900156935	77.3069	58	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.11	99.11	0.93	0.93	2	-
GCF_007845635.1	s__Apibacter muscae	77.0367	155	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Apibacter	95.0	97.91	97.54	0.94	0.93	3	-
GCF_007474545.1	s__Chryseobacterium binzhouense	76.4385	51	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.18	97.18	0.83	0.83	2	-
GCF_900198195.1	s__Tenacibaculum jejuense	76.3171	58	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105985.1	s__Tenacibaculum sp900105985	76.0638	66	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.69	98.69	0.93	0.93	2	-
GCF_009900745.1	s__Chryseobacterium sp009900745	76.0269	52	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425355.1	s__Chryseobacterium sp001425355	75.9949	53	1097	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:10,013] [INFO] GTDB search result was written to GCF_004014855.1_ASM401485v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:10,014] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:10,018] [INFO] DFAST_QC result json was written to GCF_004014855.1_ASM401485v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:10,018] [INFO] DFAST_QC completed!
[2024-01-24 13:33:10,018] [INFO] Total running time: 0h1m12s