[2024-01-24 14:28:01,829] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:01,831] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:01,831] [INFO] DQC Reference Directory: /var/lib/cwl/stg9102565c-156b-4fce-8d09-1ccf865b0964/dqc_reference
[2024-01-24 14:28:03,132] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:03,133] [INFO] Task started: Prodigal
[2024-01-24 14:28:03,133] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ecd3e97-a35c-46b8-94cd-cca157c761ef/GCF_000331105.1_ASM33110v1_genomic.fna.gz | prodigal -d GCF_000331105.1_ASM33110v1_genomic.fna/cds.fna -a GCF_000331105.1_ASM33110v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:42,398] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:42,399] [INFO] Task started: HMMsearch
[2024-01-24 14:28:42,399] [INFO] Running command: hmmsearch --tblout GCF_000331105.1_ASM33110v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9102565c-156b-4fce-8d09-1ccf865b0964/dqc_reference/reference_markers.hmm GCF_000331105.1_ASM33110v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:42,783] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:42,784] [INFO] Found 6/6 markers.
[2024-01-24 14:28:42,843] [INFO] Query marker FASTA was written to GCF_000331105.1_ASM33110v1_genomic.fna/markers.fasta
[2024-01-24 14:28:42,843] [INFO] Task started: Blastn
[2024-01-24 14:28:42,843] [INFO] Running command: blastn -query GCF_000331105.1_ASM33110v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9102565c-156b-4fce-8d09-1ccf865b0964/dqc_reference/reference_markers.fasta -out GCF_000331105.1_ASM33110v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:43,543] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:43,547] [INFO] Selected 14 target genomes.
[2024-01-24 14:28:43,547] [INFO] Target genome list was writen to GCF_000331105.1_ASM33110v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:43,585] [INFO] Task started: fastANI
[2024-01-24 14:28:43,585] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ecd3e97-a35c-46b8-94cd-cca157c761ef/GCF_000331105.1_ASM33110v1_genomic.fna.gz --refList GCF_000331105.1_ASM33110v1_genomic.fna/target_genomes.txt --output GCF_000331105.1_ASM33110v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:29:01,315] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:01,315] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9102565c-156b-4fce-8d09-1ccf865b0964/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:29:01,316] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9102565c-156b-4fce-8d09-1ccf865b0964/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:29:01,327] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:29:01,327] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:29:01,328] [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
Fibrella aestuarina	strain=BUZ 2	GCA_000331105.1	651143	651143	type	True	100.0	2310	2311	95	conclusive
Fibrella aquatilis	strain=HMF5036	GCA_017353255.1	2817059	2817059	type	True	78.0876	727	2311	95	below_threshold
Fibrella rubiginis	strain=HMF5335	GCA_017353185.1	2817060	2817060	type	True	77.9311	693	2311	95	below_threshold
Fibrisoma montanum	strain=HYT19	GCA_003583365.1	2305895	2305895	type	True	77.0429	376	2311	95	below_threshold
Rudanella lutea	strain=DSM 19387	GCA_000383955.1	451374	451374	type	True	76.976	405	2311	95	below_threshold
Fibrisoma limi	strain=BUZ 3	GCA_000296815.2	663275	663275	type	True	76.9301	346	2311	95	below_threshold
Spirosoma rigui	strain=KCTC 12531	GCA_002067135.1	564064	564064	type	True	76.8315	318	2311	95	below_threshold
Rudanella paleaurantiibacter	strain=HX-22-17	GCA_009184635.1	2614655	2614655	type	True	76.7825	400	2311	95	below_threshold
Larkinella punicea	strain=ZZJ9	GCA_003334855.1	2315727	2315727	type	True	76.3158	280	2311	95	below_threshold
Spirosoma agri	strain=KCTC 52727	GCA_010747415.1	1987381	1987381	type	True	76.1822	232	2311	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	75.9067	105	2311	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	75.7792	105	2311	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	75.5586	77	2311	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:29:01,329] [INFO] DFAST Taxonomy check result was written to GCF_000331105.1_ASM33110v1_genomic.fna/tc_result.tsv
[2024-01-24 14:29:01,330] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:29:01,330] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:29:01,331] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9102565c-156b-4fce-8d09-1ccf865b0964/dqc_reference/checkm_data
[2024-01-24 14:29:01,332] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:29:01,400] [INFO] Task started: CheckM
[2024-01-24 14:29:01,400] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000331105.1_ASM33110v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000331105.1_ASM33110v1_genomic.fna/checkm_input GCF_000331105.1_ASM33110v1_genomic.fna/checkm_result
[2024-01-24 14:30:43,817] [INFO] Task succeeded: CheckM
[2024-01-24 14:30:43,819] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:30:43,844] [INFO] ===== Completeness check finished =====
[2024-01-24 14:30:43,844] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:30:43,845] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000331105.1_ASM33110v1_genomic.fna/markers.fasta)
[2024-01-24 14:30:43,845] [INFO] Task started: Blastn
[2024-01-24 14:30:43,845] [INFO] Running command: blastn -query GCF_000331105.1_ASM33110v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9102565c-156b-4fce-8d09-1ccf865b0964/dqc_reference/reference_markers_gtdb.fasta -out GCF_000331105.1_ASM33110v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:44,720] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:44,723] [INFO] Selected 16 target genomes.
[2024-01-24 14:30:44,723] [INFO] Target genome list was writen to GCF_000331105.1_ASM33110v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:30:44,755] [INFO] Task started: fastANI
[2024-01-24 14:30:44,755] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ecd3e97-a35c-46b8-94cd-cca157c761ef/GCF_000331105.1_ASM33110v1_genomic.fna.gz --refList GCF_000331105.1_ASM33110v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000331105.1_ASM33110v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:03,437] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:03,449] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:03,450] [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_000331105.1	s__Fibrella aestuarina	100.0	2310	2311	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017353255.1	s__Fibrella sp017353255	78.0873	727	2311	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002108455.1	s__Fibrella sp002108455	77.9671	631	2311	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrella	95.0	98.52	98.52	0.95	0.95	2	-
GCF_017353175.1	s__Fibrella sp017353175	77.9622	646	2311	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017353185.1	s__Fibrella sp017353185	77.9282	695	2311	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012849055.1	s__Spirosoma sp012849055	77.1481	419	2311	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583365.1	s__Fibrisoma montanum	77.0213	380	2311	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000296815.2	s__Fibrisoma limi	76.9077	346	2311	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002067135.1	s__Spirosoma rigui	76.8528	317	2311	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375035.1	s__Spirosoma sp013375035	76.8481	280	2311	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184635.1	s__Rudanella paleaurantiibacter	76.7825	400	2311	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Rudanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004292855.1	s__Rudanella sp004292855	76.4853	347	2311	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Rudanella	95.0	98.31	98.31	0.91	0.91	2	-
GCF_010747415.1	s__Spirosoma agri	76.1822	232	2311	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:03,452] [INFO] GTDB search result was written to GCF_000331105.1_ASM33110v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:03,453] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:03,457] [INFO] DFAST_QC result json was written to GCF_000331105.1_ASM33110v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:03,457] [INFO] DFAST_QC completed!
[2024-01-24 14:31:03,457] [INFO] Total running time: 0h3m2s