[2024-01-24 12:15:18,935] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:18,937] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:18,937] [INFO] DQC Reference Directory: /var/lib/cwl/stg623f5f18-27e2-40d1-9856-8a992f7a834e/dqc_reference
[2024-01-24 12:15:20,306] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:20,307] [INFO] Task started: Prodigal
[2024-01-24 12:15:20,307] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c66900c-1f1c-42f6-97a4-e05f74ec7c72/GCF_021738805.1_ASM2173880v1_genomic.fna.gz | prodigal -d GCF_021738805.1_ASM2173880v1_genomic.fna/cds.fna -a GCF_021738805.1_ASM2173880v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:32,546] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:32,547] [INFO] Task started: HMMsearch
[2024-01-24 12:15:32,547] [INFO] Running command: hmmsearch --tblout GCF_021738805.1_ASM2173880v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg623f5f18-27e2-40d1-9856-8a992f7a834e/dqc_reference/reference_markers.hmm GCF_021738805.1_ASM2173880v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:32,823] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:32,825] [INFO] Found 6/6 markers.
[2024-01-24 12:15:32,869] [INFO] Query marker FASTA was written to GCF_021738805.1_ASM2173880v1_genomic.fna/markers.fasta
[2024-01-24 12:15:32,869] [INFO] Task started: Blastn
[2024-01-24 12:15:32,869] [INFO] Running command: blastn -query GCF_021738805.1_ASM2173880v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg623f5f18-27e2-40d1-9856-8a992f7a834e/dqc_reference/reference_markers.fasta -out GCF_021738805.1_ASM2173880v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:34,004] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:34,008] [INFO] Selected 13 target genomes.
[2024-01-24 12:15:34,009] [INFO] Target genome list was writen to GCF_021738805.1_ASM2173880v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:34,015] [INFO] Task started: fastANI
[2024-01-24 12:15:34,015] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c66900c-1f1c-42f6-97a4-e05f74ec7c72/GCF_021738805.1_ASM2173880v1_genomic.fna.gz --refList GCF_021738805.1_ASM2173880v1_genomic.fna/target_genomes.txt --output GCF_021738805.1_ASM2173880v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:46,789] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:46,790] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg623f5f18-27e2-40d1-9856-8a992f7a834e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:46,791] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg623f5f18-27e2-40d1-9856-8a992f7a834e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:46,807] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:46,807] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:46,807] [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	82.3843	962	1360	95	below_threshold
Gordonia spumicola	strain=NBRC 107696	GCA_009932475.1	589161	589161	type	True	81.2337	829	1360	95	below_threshold
Gordonia malaquae	strain=NBRC 108250	GCA_000344135.1	410332	410332	type	True	80.8043	778	1360	95	below_threshold
Gordonia malaquae	strain=DSM 45064	GCA_900105435.1	410332	410332	type	True	80.6764	796	1360	95	below_threshold
Gordonia zhaorongruii	strain=HY186	GCA_007559005.1	2597659	2597659	type	True	80.2876	702	1360	95	below_threshold
Gordonia phthalatica	strain=QH-11	GCA_001305675.1	1136941	1136941	type	True	80.007	708	1360	95	below_threshold
Gordonia paraffinivorans	strain=NBRC 108238	GCA_000344155.1	175628	175628	type	True	78.7725	531	1360	95	below_threshold
Gordonia namibiensis	strain=NBRC 108229	GCA_000298235.1	168480	168480	type	True	78.6647	526	1360	95	below_threshold
Gordonia rubripertincta	strain=NBRC 101908	GCA_000327325.1	36822	36822	type	True	78.5712	520	1360	95	below_threshold
Gordonia insulae	strain=MMS17-SY073	GCA_003855095.1	2420509	2420509	type	True	78.2043	511	1360	95	below_threshold
Gordonia lacunae	strain=BS2	GCA_002149015.1	417102	417102	type	True	78.1653	506	1360	95	below_threshold
Gordonia rhizosphera	strain=NBRC 16068	GCA_000298195.1	83341	83341	type	True	78.0463	460	1360	95	below_threshold
Nocardia neocaledoniensis	strain=NBRC 108232	GCA_007990735.1	236511	236511	type	True	77.5268	361	1360	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:46,810] [INFO] DFAST Taxonomy check result was written to GCF_021738805.1_ASM2173880v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:46,811] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:46,811] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:46,811] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg623f5f18-27e2-40d1-9856-8a992f7a834e/dqc_reference/checkm_data
[2024-01-24 12:15:46,812] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:46,853] [INFO] Task started: CheckM
[2024-01-24 12:15:46,853] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021738805.1_ASM2173880v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021738805.1_ASM2173880v1_genomic.fna/checkm_input GCF_021738805.1_ASM2173880v1_genomic.fna/checkm_result
[2024-01-24 12:16:24,308] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:24,309] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:24,333] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:24,333] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:24,333] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021738805.1_ASM2173880v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:24,334] [INFO] Task started: Blastn
[2024-01-24 12:16:24,334] [INFO] Running command: blastn -query GCF_021738805.1_ASM2173880v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg623f5f18-27e2-40d1-9856-8a992f7a834e/dqc_reference/reference_markers_gtdb.fasta -out GCF_021738805.1_ASM2173880v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:25,960] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:25,964] [INFO] Selected 14 target genomes.
[2024-01-24 12:16:25,964] [INFO] Target genome list was writen to GCF_021738805.1_ASM2173880v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:26,004] [INFO] Task started: fastANI
[2024-01-24 12:16:26,004] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c66900c-1f1c-42f6-97a4-e05f74ec7c72/GCF_021738805.1_ASM2173880v1_genomic.fna.gz --refList GCF_021738805.1_ASM2173880v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021738805.1_ASM2173880v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:38,907] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:38,931] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:16:38,931] [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	82.3761	963	1360	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	81.2742	824	1360	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000344135.1	s__Gordonia malaquae	80.7866	781	1360	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	80.6473	774	1360	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	80.2955	701	1360	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.65	99.65	0.97	0.97	2	-
GCF_001305675.1	s__Gordonia phthalatica	80.018	707	1360	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012515855.1	s__Gordonia sp012515855	79.5231	602	1360	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002993285.1	s__Gordonia iterans	79.0288	564	1360	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	78.7694	532	1360	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.97	98.74	0.93	0.90	12	-
GCF_000298235.1	s__Gordonia namibiensis	78.6476	530	1360	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.13	97.13	0.90	0.90	2	-
GCA_004193205.1	s__Gordonia sediminis	78.2131	491	1360	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003855095.1	s__Gordonia insulae	78.2112	510	1360	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001186365.1	s__Gordonia jacobaea	78.1131	450	1360	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.30	95.68	0.92	0.90	5	-
GCF_000298195.1	s__Gordonia rhizosphera	78.0624	458	1360	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:38,933] [INFO] GTDB search result was written to GCF_021738805.1_ASM2173880v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:38,934] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:38,938] [INFO] DFAST_QC result json was written to GCF_021738805.1_ASM2173880v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:38,938] [INFO] DFAST_QC completed!
[2024-01-24 12:16:38,938] [INFO] Total running time: 0h1m20s