[2024-01-25 19:02:35,660] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:02:35,661] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:02:35,661] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9cc7080-3a9e-45ca-9c8b-843f1e57ee0c/dqc_reference
[2024-01-25 19:02:36,791] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:02:36,792] [INFO] Task started: Prodigal
[2024-01-25 19:02:36,792] [INFO] Running command: gunzip -c /var/lib/cwl/stgd301d003-7b28-4351-b8ee-24c7670bf7c4/GCF_021738965.1_ASM2173896v1_genomic.fna.gz | prodigal -d GCF_021738965.1_ASM2173896v1_genomic.fna/cds.fna -a GCF_021738965.1_ASM2173896v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:02:47,784] [INFO] Task succeeded: Prodigal
[2024-01-25 19:02:47,784] [INFO] Task started: HMMsearch
[2024-01-25 19:02:47,784] [INFO] Running command: hmmsearch --tblout GCF_021738965.1_ASM2173896v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9cc7080-3a9e-45ca-9c8b-843f1e57ee0c/dqc_reference/reference_markers.hmm GCF_021738965.1_ASM2173896v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:02:48,008] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:02:48,009] [INFO] Found 6/6 markers.
[2024-01-25 19:02:48,047] [INFO] Query marker FASTA was written to GCF_021738965.1_ASM2173896v1_genomic.fna/markers.fasta
[2024-01-25 19:02:48,047] [INFO] Task started: Blastn
[2024-01-25 19:02:48,047] [INFO] Running command: blastn -query GCF_021738965.1_ASM2173896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9cc7080-3a9e-45ca-9c8b-843f1e57ee0c/dqc_reference/reference_markers.fasta -out GCF_021738965.1_ASM2173896v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:49,116] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:49,118] [INFO] Selected 11 target genomes.
[2024-01-25 19:02:49,119] [INFO] Target genome list was writen to GCF_021738965.1_ASM2173896v1_genomic.fna/target_genomes.txt
[2024-01-25 19:02:49,127] [INFO] Task started: fastANI
[2024-01-25 19:02:49,127] [INFO] Running command: fastANI --query /var/lib/cwl/stgd301d003-7b28-4351-b8ee-24c7670bf7c4/GCF_021738965.1_ASM2173896v1_genomic.fna.gz --refList GCF_021738965.1_ASM2173896v1_genomic.fna/target_genomes.txt --output GCF_021738965.1_ASM2173896v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:02:59,702] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:59,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9cc7080-3a9e-45ca-9c8b-843f1e57ee0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:02:59,702] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9cc7080-3a9e-45ca-9c8b-843f1e57ee0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:02:59,710] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:02:59,710] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:02:59,710] [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 humi	strain=DSM 45298	GCA_014197435.1	686429	686429	type	True	82.3342	941	1349	95	below_threshold
Gordonia spumicola	strain=NBRC 107696	GCA_009932475.1	589161	589161	type	True	81.2782	830	1349	95	below_threshold
Gordonia zhaorongruii	strain=HY186	GCA_007559005.1	2597659	2597659	type	True	80.9883	727	1349	95	below_threshold
Gordonia malaquae	strain=DSM 45064	GCA_900105435.1	410332	410332	type	True	80.8251	775	1349	95	below_threshold
Gordonia malaquae	strain=NBRC 108250	GCA_000344135.1	410332	410332	type	True	80.7883	775	1349	95	below_threshold
Gordonia phthalatica	strain=QH-11	GCA_001305675.1	1136941	1136941	type	True	80.2599	700	1349	95	below_threshold
Gordonia paraffinivorans	strain=NBRC 108238	GCA_000344155.1	175628	175628	type	True	78.9261	530	1349	95	below_threshold
Gordonia rubripertincta	strain=ATCC 14352	GCA_012396225.1	36822	36822	type	True	78.6702	511	1349	95	below_threshold
Gordonia rubripertincta	strain=NBRC 101908	GCA_000327325.1	36822	36822	type	True	78.5968	507	1349	95	below_threshold
Smaragdicoccus niigatensis	strain=NBRC 103563	GCA_001552795.1	359359	359359	type	True	77.1625	240	1349	95	below_threshold
Streptomyces finlayi	strain=JCM 4637	GCA_014650515.1	67296	67296	type	True	76.0191	195	1349	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:02:59,712] [INFO] DFAST Taxonomy check result was written to GCF_021738965.1_ASM2173896v1_genomic.fna/tc_result.tsv
[2024-01-25 19:02:59,712] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:02:59,712] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:02:59,713] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9cc7080-3a9e-45ca-9c8b-843f1e57ee0c/dqc_reference/checkm_data
[2024-01-25 19:02:59,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:02:59,755] [INFO] Task started: CheckM
[2024-01-25 19:02:59,755] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021738965.1_ASM2173896v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021738965.1_ASM2173896v1_genomic.fna/checkm_input GCF_021738965.1_ASM2173896v1_genomic.fna/checkm_result
[2024-01-25 19:03:35,158] [INFO] Task succeeded: CheckM
[2024-01-25 19:03:35,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:03:35,176] [INFO] ===== Completeness check finished =====
[2024-01-25 19:03:35,177] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:03:35,177] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021738965.1_ASM2173896v1_genomic.fna/markers.fasta)
[2024-01-25 19:03:35,177] [INFO] Task started: Blastn
[2024-01-25 19:03:35,177] [INFO] Running command: blastn -query GCF_021738965.1_ASM2173896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9cc7080-3a9e-45ca-9c8b-843f1e57ee0c/dqc_reference/reference_markers_gtdb.fasta -out GCF_021738965.1_ASM2173896v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:36,765] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:36,768] [INFO] Selected 11 target genomes.
[2024-01-25 19:03:36,769] [INFO] Target genome list was writen to GCF_021738965.1_ASM2173896v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:03:36,778] [INFO] Task started: fastANI
[2024-01-25 19:03:36,778] [INFO] Running command: fastANI --query /var/lib/cwl/stgd301d003-7b28-4351-b8ee-24c7670bf7c4/GCF_021738965.1_ASM2173896v1_genomic.fna.gz --refList GCF_021738965.1_ASM2173896v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021738965.1_ASM2173896v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:03:48,977] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:48,986] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:03:48,986] [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_014197435.1	s__Gordonia humi	82.3428	941	1349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009932475.1	s__Gordonia spumicola	81.2772	830	1349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007559005.1	s__Gordonia sp004353055	80.9811	726	1349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.65	99.65	0.97	0.97	2	-
GCF_000344135.1	s__Gordonia malaquae	80.7723	777	1349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016919385.1	s__Gordonia sp016919385	80.5211	776	1349	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	78.9505	527	1349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.97	98.74	0.93	0.90	12	-
GCF_000327325.1	s__Gordonia rubripertincta	78.5817	509	1349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.55	98.07	0.91	0.87	6	-
GCF_009914535.1	s__Gordonia pseudoamarae	78.1107	423	1349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.95	99.95	1.00	1.00	2	-
GCF_001186365.1	s__Gordonia jacobaea	78.0813	445	1349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.30	95.68	0.92	0.90	5	-
GCA_014650415.1	s__Streptomyces spiroverticillatus	76.0587	197	1349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001942465.1	s__Spirillospora sp001942465	75.6332	280	1349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:03:48,988] [INFO] GTDB search result was written to GCF_021738965.1_ASM2173896v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:03:48,990] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:03:48,993] [INFO] DFAST_QC result json was written to GCF_021738965.1_ASM2173896v1_genomic.fna/dqc_result.json
[2024-01-25 19:03:48,993] [INFO] DFAST_QC completed!
[2024-01-25 19:03:48,993] [INFO] Total running time: 0h1m13s