[2024-01-24 10:57:13,073] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:13,076] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:13,076] [INFO] DQC Reference Directory: /var/lib/cwl/stge5dd6f57-3292-4ec4-8cca-bc15d1a34b98/dqc_reference
[2024-01-24 10:57:14,601] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:14,602] [INFO] Task started: Prodigal
[2024-01-24 10:57:14,602] [INFO] Running command: gunzip -c /var/lib/cwl/stgec5ba5d0-9ff6-480a-ae9d-709c213c9213/GCF_019891545.1_ASM1989154v1_genomic.fna.gz | prodigal -d GCF_019891545.1_ASM1989154v1_genomic.fna/cds.fna -a GCF_019891545.1_ASM1989154v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:27,431] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:27,431] [INFO] Task started: HMMsearch
[2024-01-24 10:57:27,431] [INFO] Running command: hmmsearch --tblout GCF_019891545.1_ASM1989154v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5dd6f57-3292-4ec4-8cca-bc15d1a34b98/dqc_reference/reference_markers.hmm GCF_019891545.1_ASM1989154v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:27,715] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:27,716] [INFO] Found 6/6 markers.
[2024-01-24 10:57:27,747] [INFO] Query marker FASTA was written to GCF_019891545.1_ASM1989154v1_genomic.fna/markers.fasta
[2024-01-24 10:57:27,747] [INFO] Task started: Blastn
[2024-01-24 10:57:27,748] [INFO] Running command: blastn -query GCF_019891545.1_ASM1989154v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5dd6f57-3292-4ec4-8cca-bc15d1a34b98/dqc_reference/reference_markers.fasta -out GCF_019891545.1_ASM1989154v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:28,402] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:28,405] [INFO] Selected 16 target genomes.
[2024-01-24 10:57:28,406] [INFO] Target genome list was writen to GCF_019891545.1_ASM1989154v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:28,427] [INFO] Task started: fastANI
[2024-01-24 10:57:28,428] [INFO] Running command: fastANI --query /var/lib/cwl/stgec5ba5d0-9ff6-480a-ae9d-709c213c9213/GCF_019891545.1_ASM1989154v1_genomic.fna.gz --refList GCF_019891545.1_ASM1989154v1_genomic.fna/target_genomes.txt --output GCF_019891545.1_ASM1989154v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:40,584] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:40,584] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5dd6f57-3292-4ec4-8cca-bc15d1a34b98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:40,585] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5dd6f57-3292-4ec4-8cca-bc15d1a34b98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:40,596] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:40,596] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:40,596] [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
Flavobacterium coralii	strain=D11R37	GCA_019891545.1	2838017	2838017	type	True	100.0	1053	1053	95	conclusive
Flavobacterium salilacus subsp. salilacus	strain=SaA2.12	GCA_004634195.1	2545633	2898423	type	True	78.4715	433	1053	95	below_threshold
Flavobacterium salilacus subsp. altitudinum	strain=LaA7.5	GCA_010078225.1	2691899	2898423	type	True	78.3441	454	1053	95	below_threshold
Flavobacterium suaedae	strain=CGMCC 1.15461	GCA_014642915.1	1767027	1767027	type	True	78.1298	344	1053	95	below_threshold
Flavobacterium zepuense	strain=ZT4R6	GCA_007097145.1	2593302	2593302	type	True	78.0152	338	1053	95	below_threshold
Flavobacterium akiainvivens	strain=IK-1	GCA_001278115.1	1202724	1202724	type	True	77.8891	316	1053	95	below_threshold
Flavobacterium akiainvivens	strain=DSM 25510	GCA_900115875.1	1202724	1202724	type	True	77.8868	312	1053	95	below_threshold
Flavobacterium album	strain=HYN0059	GCA_003096035.1	2175091	2175091	type	True	77.8672	261	1053	95	below_threshold
Flavobacterium alkalisoli	strain=XS-5	GCA_008000935.1	2602769	2602769	type	True	77.8652	298	1053	95	below_threshold
Flavobacterium arcticum	strain=KCTC 42668	GCA_004634185.1	1784713	1784713	type	True	77.8174	319	1053	95	below_threshold
Flavobacterium litorale	strain=WSW3-B6	GCA_019613795.1	2856519	2856519	type	True	77.7418	265	1053	95	below_threshold
Flavobacterium rivuli	strain=WB 3.3-2	GCA_000769825.1	498301	498301	type	True	77.6919	293	1053	95	below_threshold
Flavobacterium cyanobacteriorum	strain=TH021	GCA_002251835.1	2022802	2022802	type	True	77.6495	275	1053	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:40,598] [INFO] DFAST Taxonomy check result was written to GCF_019891545.1_ASM1989154v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:40,598] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:40,598] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:40,599] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5dd6f57-3292-4ec4-8cca-bc15d1a34b98/dqc_reference/checkm_data
[2024-01-24 10:57:40,600] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:40,634] [INFO] Task started: CheckM
[2024-01-24 10:57:40,635] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019891545.1_ASM1989154v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019891545.1_ASM1989154v1_genomic.fna/checkm_input GCF_019891545.1_ASM1989154v1_genomic.fna/checkm_result
[2024-01-24 10:58:20,462] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:20,463] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:20,506] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:20,507] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:20,507] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019891545.1_ASM1989154v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:20,508] [INFO] Task started: Blastn
[2024-01-24 10:58:20,508] [INFO] Running command: blastn -query GCF_019891545.1_ASM1989154v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5dd6f57-3292-4ec4-8cca-bc15d1a34b98/dqc_reference/reference_markers_gtdb.fasta -out GCF_019891545.1_ASM1989154v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:21,513] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:21,517] [INFO] Selected 17 target genomes.
[2024-01-24 10:58:21,517] [INFO] Target genome list was writen to GCF_019891545.1_ASM1989154v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:21,530] [INFO] Task started: fastANI
[2024-01-24 10:58:21,530] [INFO] Running command: fastANI --query /var/lib/cwl/stgec5ba5d0-9ff6-480a-ae9d-709c213c9213/GCF_019891545.1_ASM1989154v1_genomic.fna.gz --refList GCF_019891545.1_ASM1989154v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019891545.1_ASM1989154v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:33,844] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:33,871] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:33,871] [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
GCA_002714575.1	s__Flavobacterium sp002714575	95.4781	965	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004634195.1	s__Flavobacterium sp004634195	78.4536	435	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.56	97.13	0.95	0.91	3	-
GCF_009848495.1	s__Flavobacterium sp009848495	78.3643	385	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270005.1	s__Flavobacterium sp012270005	78.1929	210	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642915.1	s__Flavobacterium suaedae	78.1298	344	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097145.1	s__Flavobacterium sp007097145	78.009	338	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001278115.1	s__Flavobacterium akiainvivens	77.8989	315	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003096035.1	s__Flavobacterium album	77.8574	262	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008000935.1	s__Flavobacterium alkalisoli	77.8564	297	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350375.1	s__Flavobacterium sp003350375	77.7589	228	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344925.1	s__Flavobacterium arcticum	77.7568	317	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003403075.1	s__Flavobacterium sp003403075	77.7456	287	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000769915.1	s__Flavobacterium beibuense	77.7314	261	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378485.1	s__Flavobacterium rivuli	77.7051	299	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002251835.1	s__Flavobacterium cyanobacteriorum	77.678	272	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004151245.1	s__Flavobacterium beibuense_A	77.6584	297	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009826935.1	s__Flavobacterium sp009826935	77.6399	275	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:33,873] [INFO] GTDB search result was written to GCF_019891545.1_ASM1989154v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:33,873] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:33,877] [INFO] DFAST_QC result json was written to GCF_019891545.1_ASM1989154v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:33,877] [INFO] DFAST_QC completed!
[2024-01-24 10:58:33,877] [INFO] Total running time: 0h1m21s