[2024-01-24 10:48:09,565] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,574] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,574] [INFO] DQC Reference Directory: /var/lib/cwl/stgf36c9c8e-b69d-476e-b5f4-35a262e8f470/dqc_reference
[2024-01-24 10:48:23,956] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,959] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,960] [INFO] Running command: gunzip -c /var/lib/cwl/stg545ff17d-1811-4b35-b543-9c1883081a14/GCF_009932435.1_ASM993243v1_genomic.fna.gz | prodigal -d GCF_009932435.1_ASM993243v1_genomic.fna/cds.fna -a GCF_009932435.1_ASM993243v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:35,478] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:35,478] [INFO] Task started: HMMsearch
[2024-01-24 10:48:35,478] [INFO] Running command: hmmsearch --tblout GCF_009932435.1_ASM993243v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf36c9c8e-b69d-476e-b5f4-35a262e8f470/dqc_reference/reference_markers.hmm GCF_009932435.1_ASM993243v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:35,751] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:35,753] [INFO] Found 6/6 markers.
[2024-01-24 10:48:35,791] [INFO] Query marker FASTA was written to GCF_009932435.1_ASM993243v1_genomic.fna/markers.fasta
[2024-01-24 10:48:35,791] [INFO] Task started: Blastn
[2024-01-24 10:48:35,791] [INFO] Running command: blastn -query GCF_009932435.1_ASM993243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf36c9c8e-b69d-476e-b5f4-35a262e8f470/dqc_reference/reference_markers.fasta -out GCF_009932435.1_ASM993243v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:36,957] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:36,961] [INFO] Selected 14 target genomes.
[2024-01-24 10:48:36,961] [INFO] Target genome list was writen to GCF_009932435.1_ASM993243v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:36,986] [INFO] Task started: fastANI
[2024-01-24 10:48:36,986] [INFO] Running command: fastANI --query /var/lib/cwl/stg545ff17d-1811-4b35-b543-9c1883081a14/GCF_009932435.1_ASM993243v1_genomic.fna.gz --refList GCF_009932435.1_ASM993243v1_genomic.fna/target_genomes.txt --output GCF_009932435.1_ASM993243v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:50,621] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:50,622] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf36c9c8e-b69d-476e-b5f4-35a262e8f470/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:50,623] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf36c9c8e-b69d-476e-b5f4-35a262e8f470/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:50,635] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:50,635] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:50,636] [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
Gordonia crocea	strain=NBRC 107697	GCA_009932435.1	589162	589162	type	True	100.0	1231	1251	95	conclusive
Gordonia araii	strain=NBRC 100433	GCA_000241265.2	263909	263909	type	True	82.8792	885	1251	95	below_threshold
Gordonia araii	strain=IFM 10211	GCA_013004535.1	263909	263909	type	True	82.8433	879	1251	95	below_threshold
Gordonia paraffinivorans	strain=NBRC 108238	GCA_000344155.1	175628	175628	type	True	79.8749	576	1251	95	below_threshold
Gordonia westfalica	strain=DSM 44215	GCA_900105725.1	158898	158898	type	True	79.5384	560	1251	95	below_threshold
Gordonia amicalis	strain=NBRC 100051	GCA_000332995.1	89053	89053	type	True	79.4291	512	1251	95	below_threshold
Gordonia amicalis	strain=DSM 44461	GCA_012395955.1	89053	89053	type	True	79.3562	518	1251	95	below_threshold
Gordonia phthalatica	strain=QH-11	GCA_001305675.1	1136941	1136941	type	True	79.3053	522	1251	95	below_threshold
Gordonia alkanivorans	strain=NBRC 16433	GCA_000225505.1	84096	84096	type	True	79.2827	539	1251	95	below_threshold
Gordonia rubripertincta	strain=NBRC 101908	GCA_000327325.1	36822	36822	type	True	79.1557	543	1251	95	below_threshold
Gordonia jinghuaiqii	strain=zg-686	GCA_024701535.1	2758710	2758710	type	True	79.1479	525	1251	95	below_threshold
Williamsia serinedens	strain=DSM 45037	GCA_024171725.1	391736	391736	type	True	78.7413	479	1251	95	below_threshold
Gordonia insulae	strain=MMS17-SY073	GCA_003855095.1	2420509	2420509	type	True	78.6715	532	1251	95	below_threshold
Gordonia hankookensis	strain=ON-33	GCA_014673215.1	589403	589403	type	True	78.3415	484	1251	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:50,637] [INFO] DFAST Taxonomy check result was written to GCF_009932435.1_ASM993243v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:50,638] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:50,638] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:50,638] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf36c9c8e-b69d-476e-b5f4-35a262e8f470/dqc_reference/checkm_data
[2024-01-24 10:48:50,639] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:50,676] [INFO] Task started: CheckM
[2024-01-24 10:48:50,676] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009932435.1_ASM993243v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009932435.1_ASM993243v1_genomic.fna/checkm_input GCF_009932435.1_ASM993243v1_genomic.fna/checkm_result
[2024-01-24 10:49:37,900] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:37,902] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:37,924] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:37,925] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:37,925] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009932435.1_ASM993243v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:37,925] [INFO] Task started: Blastn
[2024-01-24 10:49:37,926] [INFO] Running command: blastn -query GCF_009932435.1_ASM993243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf36c9c8e-b69d-476e-b5f4-35a262e8f470/dqc_reference/reference_markers_gtdb.fasta -out GCF_009932435.1_ASM993243v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:39,760] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:39,764] [INFO] Selected 11 target genomes.
[2024-01-24 10:49:39,764] [INFO] Target genome list was writen to GCF_009932435.1_ASM993243v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:39,789] [INFO] Task started: fastANI
[2024-01-24 10:49:39,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg545ff17d-1811-4b35-b543-9c1883081a14/GCF_009932435.1_ASM993243v1_genomic.fna.gz --refList GCF_009932435.1_ASM993243v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009932435.1_ASM993243v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:50,659] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:50,674] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:50,674] [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_009932435.1	s__Gordonia crocea	100.0	1230	1251	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000241265.1	s__Gordonia araii	82.8723	886	1251	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013348785.1	s__Gordonia sp013348785	82.1966	830	1251	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002477755.1	s__Gordonia sp002477755	81.8273	737	1251	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.87	99.81	0.89	0.84	3	-
GCA_002414845.1	s__Gordonia sp002414845	81.1895	703	1251	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000344155.1	s__Gordonia paraffinivorans	79.8336	581	1251	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.97	98.74	0.93	0.90	12	-
GCF_900105725.1	s__Gordonia westfalica	79.5537	562	1251	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332995.1	s__Gordonia amicalis	79.4197	513	1251	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.45	97.39	0.94	0.91	7	-
GCF_000225505.1	s__Gordonia alkanivorans	79.287	538	1251	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.26	97.87	0.90	0.88	6	-
GCF_003855095.1	s__Gordonia insulae	78.6865	530	1251	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014673215.1	s__Gordonia hankookensis	78.3454	484	1251	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.33	98.32	0.95	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:50,676] [INFO] GTDB search result was written to GCF_009932435.1_ASM993243v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:50,676] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:50,679] [INFO] DFAST_QC result json was written to GCF_009932435.1_ASM993243v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:50,680] [INFO] DFAST_QC completed!
[2024-01-24 10:49:50,680] [INFO] Total running time: 0h1m41s