[2024-01-24 13:28:12,626] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:12,631] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:12,631] [INFO] DQC Reference Directory: /var/lib/cwl/stg93fb5d29-ab59-418a-9d68-95fa1d21d6db/dqc_reference
[2024-01-24 13:28:13,960] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:13,961] [INFO] Task started: Prodigal
[2024-01-24 13:28:13,961] [INFO] Running command: gunzip -c /var/lib/cwl/stg34fc5194-ab47-458f-b1a6-44401761224b/GCF_009725985.1_ASM972598v1_genomic.fna.gz | prodigal -d GCF_009725985.1_ASM972598v1_genomic.fna/cds.fna -a GCF_009725985.1_ASM972598v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:33,606] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:33,607] [INFO] Task started: HMMsearch
[2024-01-24 13:28:33,607] [INFO] Running command: hmmsearch --tblout GCF_009725985.1_ASM972598v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93fb5d29-ab59-418a-9d68-95fa1d21d6db/dqc_reference/reference_markers.hmm GCF_009725985.1_ASM972598v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:33,975] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:33,976] [INFO] Found 6/6 markers.
[2024-01-24 13:28:34,018] [INFO] Query marker FASTA was written to GCF_009725985.1_ASM972598v1_genomic.fna/markers.fasta
[2024-01-24 13:28:34,018] [INFO] Task started: Blastn
[2024-01-24 13:28:34,019] [INFO] Running command: blastn -query GCF_009725985.1_ASM972598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93fb5d29-ab59-418a-9d68-95fa1d21d6db/dqc_reference/reference_markers.fasta -out GCF_009725985.1_ASM972598v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:34,696] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:34,699] [INFO] Selected 11 target genomes.
[2024-01-24 13:28:34,699] [INFO] Target genome list was writen to GCF_009725985.1_ASM972598v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:34,705] [INFO] Task started: fastANI
[2024-01-24 13:28:34,705] [INFO] Running command: fastANI --query /var/lib/cwl/stg34fc5194-ab47-458f-b1a6-44401761224b/GCF_009725985.1_ASM972598v1_genomic.fna.gz --refList GCF_009725985.1_ASM972598v1_genomic.fna/target_genomes.txt --output GCF_009725985.1_ASM972598v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:46,630] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:46,630] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93fb5d29-ab59-418a-9d68-95fa1d21d6db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:46,631] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93fb5d29-ab59-418a-9d68-95fa1d21d6db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:46,640] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:46,640] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:46,640] [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
Zobellia amurskyensis	strain=KMM 3526	GCA_009725985.1	248905	248905	type	True	100.0	1650	1657	95	conclusive
Zobellia laminariae	strain=KMM 3676	GCA_009725995.1	248906	248906	type	True	85.5961	1190	1657	95	below_threshold
Zobellia russellii	strain=KMM 3677	GCA_018728565.1	248907	248907	type	True	85.0832	1253	1657	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	84.5108	1148	1657	95	below_threshold
Zobellia nedashkovskayae	strain=Asnod2-B07-B	GCA_015330125.1	2779510	2779510	type	True	83.7082	1100	1657	95	below_threshold
Zobellia roscoffensis	strain=Asnod1-F08	GCA_015330165.1	2779508	2779508	type	True	82.8093	1103	1657	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.6254	92	1657	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	76.1834	95	1657	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	76.048	54	1657	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	75.7929	58	1657	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:46,641] [INFO] DFAST Taxonomy check result was written to GCF_009725985.1_ASM972598v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:46,642] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:46,642] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:46,642] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93fb5d29-ab59-418a-9d68-95fa1d21d6db/dqc_reference/checkm_data
[2024-01-24 13:28:46,643] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:46,695] [INFO] Task started: CheckM
[2024-01-24 13:28:46,695] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009725985.1_ASM972598v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009725985.1_ASM972598v1_genomic.fna/checkm_input GCF_009725985.1_ASM972598v1_genomic.fna/checkm_result
[2024-01-24 13:29:42,738] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:42,739] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:42,755] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:42,755] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:42,755] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009725985.1_ASM972598v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:42,756] [INFO] Task started: Blastn
[2024-01-24 13:29:42,756] [INFO] Running command: blastn -query GCF_009725985.1_ASM972598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93fb5d29-ab59-418a-9d68-95fa1d21d6db/dqc_reference/reference_markers_gtdb.fasta -out GCF_009725985.1_ASM972598v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:43,618] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:43,623] [INFO] Selected 8 target genomes.
[2024-01-24 13:29:43,623] [INFO] Target genome list was writen to GCF_009725985.1_ASM972598v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:43,633] [INFO] Task started: fastANI
[2024-01-24 13:29:43,633] [INFO] Running command: fastANI --query /var/lib/cwl/stg34fc5194-ab47-458f-b1a6-44401761224b/GCF_009725985.1_ASM972598v1_genomic.fna.gz --refList GCF_009725985.1_ASM972598v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009725985.1_ASM972598v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:52,229] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:52,241] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:52,241] [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_009725985.1	s__Zobellia amurskyensis	100.0	1650	1657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.14	98.14	0.91	0.91	2	conclusive
GCF_009725995.1	s__Zobellia laminariae	85.596	1190	1657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018728565.1	s__Zobellia russellii	85.0665	1255	1657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	97.51	97.51	0.91	0.91	2	-
GCF_018603515.1	s__Zobellia sp018603515	84.5087	1148	1657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015330125.1	s__Zobellia sp015330125	83.7166	1099	1657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.14	98.14	0.92	0.92	2	-
GCF_015330165.1	s__Zobellia sp015330165	82.8093	1103	1657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.41	98.41	0.92	0.92	2	-
GCF_018860745.1	s__Zobellia uliginosa_B	81.7632	948	1657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993815.1	s__Muricauda sp010993815	76.4767	113	1657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:52,243] [INFO] GTDB search result was written to GCF_009725985.1_ASM972598v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:52,244] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:52,247] [INFO] DFAST_QC result json was written to GCF_009725985.1_ASM972598v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:52,247] [INFO] DFAST_QC completed!
[2024-01-24 13:29:52,247] [INFO] Total running time: 0h1m40s