[2024-01-24 13:27:40,712] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:40,714] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:40,714] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8c93190-123c-4d31-8aa5-618f7e609956/dqc_reference
[2024-01-24 13:27:41,942] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:41,943] [INFO] Task started: Prodigal
[2024-01-24 13:27:41,943] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd5bf023-b8dc-4396-85ee-efb3f25a0ec0/GCF_009184635.1_ASM918463v1_genomic.fna.gz | prodigal -d GCF_009184635.1_ASM918463v1_genomic.fna/cds.fna -a GCF_009184635.1_ASM918463v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:18,082] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:18,083] [INFO] Task started: HMMsearch
[2024-01-24 13:28:18,083] [INFO] Running command: hmmsearch --tblout GCF_009184635.1_ASM918463v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8c93190-123c-4d31-8aa5-618f7e609956/dqc_reference/reference_markers.hmm GCF_009184635.1_ASM918463v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:18,411] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:18,413] [INFO] Found 6/6 markers.
[2024-01-24 13:28:18,465] [INFO] Query marker FASTA was written to GCF_009184635.1_ASM918463v1_genomic.fna/markers.fasta
[2024-01-24 13:28:18,466] [INFO] Task started: Blastn
[2024-01-24 13:28:18,466] [INFO] Running command: blastn -query GCF_009184635.1_ASM918463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8c93190-123c-4d31-8aa5-618f7e609956/dqc_reference/reference_markers.fasta -out GCF_009184635.1_ASM918463v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:19,065] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:19,069] [INFO] Selected 19 target genomes.
[2024-01-24 13:28:19,070] [INFO] Target genome list was writen to GCF_009184635.1_ASM918463v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:19,109] [INFO] Task started: fastANI
[2024-01-24 13:28:19,110] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd5bf023-b8dc-4396-85ee-efb3f25a0ec0/GCF_009184635.1_ASM918463v1_genomic.fna.gz --refList GCF_009184635.1_ASM918463v1_genomic.fna/target_genomes.txt --output GCF_009184635.1_ASM918463v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:44,973] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:44,974] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8c93190-123c-4d31-8aa5-618f7e609956/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:44,975] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8c93190-123c-4d31-8aa5-618f7e609956/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:44,989] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:44,990] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:44,990] [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
Rudanella paleaurantiibacter	strain=HX-22-17	GCA_009184635.1	2614655	2614655	type	True	100.0	2223	2225	95	conclusive
Rudanella lutea	strain=DSM 19387	GCA_000383955.1	451374	451374	type	True	90.4025	1916	2225	95	below_threshold
Spirosoma sordidisoli	strain=TY50	GCA_004138325.1	2502893	2502893	type	True	77.079	388	2225	95	below_threshold
Fibrisoma montanum	strain=HYT19	GCA_003583365.1	2305895	2305895	type	True	76.8931	348	2225	95	below_threshold
Fibrella aestuarina	strain=BUZ 2	GCA_000331105.1	651143	651143	type	True	76.8171	379	2225	95	below_threshold
Fibrisoma limi	strain=BUZ 3	GCA_000296815.2	663275	663275	type	True	76.688	334	2225	95	below_threshold
Fibrella rubiginis	strain=HMF5335	GCA_017353185.1	2817060	2817060	type	True	76.6507	304	2225	95	below_threshold
Spirosoma rigui	strain=KCTC 12531	GCA_002067135.1	564064	564064	type	True	76.5802	303	2225	95	below_threshold
Fibrella aquatilis	strain=HMF5036	GCA_017353255.1	2817059	2817059	type	True	76.5716	335	2225	95	below_threshold
Spirosoma aureum	strain=BT328	GCA_011604685.1	2692134	2692134	type	True	76.4633	181	2225	95	below_threshold
Spirosoma aerolatum	strain=KACC 17939	GCA_002056795.1	1211326	1211326	type	True	76.4475	236	2225	95	below_threshold
Larkinella soli	strain=MIMbqt9	GCA_003703975.1	1770527	1770527	type	True	76.3549	231	2225	95	below_threshold
Spirosoma endbachense	strain=I-24	GCA_010233585.1	2666025	2666025	type	True	76.2079	202	2225	95	below_threshold
Spirosoma pollinicola	strain=Ha7	GCA_002831565.1	2057025	2057025	type	True	76.1762	204	2225	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	75.7893	70	2225	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	75.4206	58	2225	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:44,992] [INFO] DFAST Taxonomy check result was written to GCF_009184635.1_ASM918463v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:44,992] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:44,993] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:44,993] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8c93190-123c-4d31-8aa5-618f7e609956/dqc_reference/checkm_data
[2024-01-24 13:28:44,994] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:45,062] [INFO] Task started: CheckM
[2024-01-24 13:28:45,062] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009184635.1_ASM918463v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009184635.1_ASM918463v1_genomic.fna/checkm_input GCF_009184635.1_ASM918463v1_genomic.fna/checkm_result
[2024-01-24 13:30:22,131] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:22,133] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:22,159] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:22,160] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:22,160] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009184635.1_ASM918463v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:22,161] [INFO] Task started: Blastn
[2024-01-24 13:30:22,161] [INFO] Running command: blastn -query GCF_009184635.1_ASM918463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8c93190-123c-4d31-8aa5-618f7e609956/dqc_reference/reference_markers_gtdb.fasta -out GCF_009184635.1_ASM918463v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:23,142] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:23,147] [INFO] Selected 15 target genomes.
[2024-01-24 13:30:23,147] [INFO] Target genome list was writen to GCF_009184635.1_ASM918463v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:23,160] [INFO] Task started: fastANI
[2024-01-24 13:30:23,161] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd5bf023-b8dc-4396-85ee-efb3f25a0ec0/GCF_009184635.1_ASM918463v1_genomic.fna.gz --refList GCF_009184635.1_ASM918463v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009184635.1_ASM918463v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:42,332] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:42,365] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:42,365] [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_009184635.1	s__Rudanella paleaurantiibacter	100.0	2223	2225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Rudanella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000383955.1	s__Rudanella lutea	90.4025	1916	2225	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	77.9271	667	2225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Rudanella	95.0	98.31	98.31	0.91	0.91	2	-
GCF_004138325.1	s__Spirosoma sordidisoli	77.0854	387	2225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	98.69	98.69	0.94	0.94	2	-
GCF_003583365.1	s__Fibrisoma montanum	76.8931	348	2225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012849055.1	s__Spirosoma sp012849055	76.8817	326	2225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331105.1	s__Fibrella aestuarina	76.8228	378	2225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000296815.2	s__Fibrisoma limi	76.695	333	2225	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	76.5802	303	2225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017353175.1	s__Fibrella sp017353175	76.4683	266	2225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011604685.1	s__Spirosoma aureum	76.4518	182	2225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366505.1	s__Larkinella sp004366505	76.4122	284	2225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006149005.1	s__Larkinella sp006149005	76.3769	234	2225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831565.1	s__Spirosoma pollinicola	76.1777	205	2225	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 13:30:42,368] [INFO] GTDB search result was written to GCF_009184635.1_ASM918463v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:42,368] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:42,375] [INFO] DFAST_QC result json was written to GCF_009184635.1_ASM918463v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:42,376] [INFO] DFAST_QC completed!
[2024-01-24 13:30:42,376] [INFO] Total running time: 0h3m2s