[2024-01-25 17:46:35,683] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:46:35,684] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:46:35,684] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ff478ef-6f8a-4695-b93f-27cbd1212b72/dqc_reference
[2024-01-25 17:46:36,859] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:46:36,860] [INFO] Task started: Prodigal
[2024-01-25 17:46:36,860] [INFO] Running command: gunzip -c /var/lib/cwl/stg38e83f73-d41b-47ae-a639-3784b187b647/GCF_014639795.1_ASM1463979v1_genomic.fna.gz | prodigal -d GCF_014639795.1_ASM1463979v1_genomic.fna/cds.fna -a GCF_014639795.1_ASM1463979v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:46:49,511] [INFO] Task succeeded: Prodigal
[2024-01-25 17:46:49,512] [INFO] Task started: HMMsearch
[2024-01-25 17:46:49,512] [INFO] Running command: hmmsearch --tblout GCF_014639795.1_ASM1463979v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ff478ef-6f8a-4695-b93f-27cbd1212b72/dqc_reference/reference_markers.hmm GCF_014639795.1_ASM1463979v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:46:49,777] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:46:49,778] [INFO] Found 6/6 markers.
[2024-01-25 17:46:49,814] [INFO] Query marker FASTA was written to GCF_014639795.1_ASM1463979v1_genomic.fna/markers.fasta
[2024-01-25 17:46:49,815] [INFO] Task started: Blastn
[2024-01-25 17:46:49,815] [INFO] Running command: blastn -query GCF_014639795.1_ASM1463979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ff478ef-6f8a-4695-b93f-27cbd1212b72/dqc_reference/reference_markers.fasta -out GCF_014639795.1_ASM1463979v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:50,920] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:50,923] [INFO] Selected 22 target genomes.
[2024-01-25 17:46:50,924] [INFO] Target genome list was writen to GCF_014639795.1_ASM1463979v1_genomic.fna/target_genomes.txt
[2024-01-25 17:46:50,939] [INFO] Task started: fastANI
[2024-01-25 17:46:50,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg38e83f73-d41b-47ae-a639-3784b187b647/GCF_014639795.1_ASM1463979v1_genomic.fna.gz --refList GCF_014639795.1_ASM1463979v1_genomic.fna/target_genomes.txt --output GCF_014639795.1_ASM1463979v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:47:11,845] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:11,846] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ff478ef-6f8a-4695-b93f-27cbd1212b72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:47:11,846] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ff478ef-6f8a-4695-b93f-27cbd1212b72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:47:11,861] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:47:11,861] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:47:11,861] [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 jinhuaensis	strain=CGMCC 1.12827	GCA_014639795.1	1517702	1517702	type	True	100.0	1423	1427	95	conclusive
Gordonia paraffinivorans	strain=NBRC 108238	GCA_000344155.1	175628	175628	type	True	79.1569	496	1427	95	below_threshold
Gordonia bronchialis	strain=DSM 43247	GCA_000024785.1	2054	2054	type	True	79.142	497	1427	95	below_threshold
Gordonia westfalica	strain=DSM 44215	GCA_900105725.1	158898	158898	type	True	79.1126	498	1427	95	below_threshold
Gordonia bronchialis	strain=FDAARGOS_1594	GCA_020731255.1	2054	2054	type	True	79.1124	488	1427	95	below_threshold
Gordonia bronchialis	strain=NCTC10667	GCA_900450805.1	2054	2054	type	True	79.1035	500	1427	95	below_threshold
Gordonia desulfuricans	strain=NBRC 100010	GCA_001485495.1	89051	89051	type	True	79.0533	526	1427	95	below_threshold
Gordonia desulfuricans	strain=213E	GCA_010119475.1	89051	89051	type	True	78.9892	536	1427	95	below_threshold
Gordonia aichiensis	strain=NBRC 108223	GCA_000332975.1	36820	36820	type	True	78.9743	467	1427	95	below_threshold
Gordonia alkanivorans	strain=NBRC 16433	GCA_000225505.1	84096	84096	type	True	78.9302	486	1427	95	below_threshold
Gordonia rubripertincta	strain=NBRC 101908	GCA_000327325.1	36822	36822	type	True	78.8249	490	1427	95	below_threshold
Gordonia jinghuaiqii	strain=zg-686	GCA_014041935.1	2758710	2758710	type	True	78.7933	471	1427	95	below_threshold
Gordonia jinghuaiqii	strain=zg-686	GCA_024701535.1	2758710	2758710	type	True	78.7602	477	1427	95	below_threshold
Gordonia namibiensis	strain=NBRC 108229	GCA_000298235.1	168480	168480	type	True	78.7186	506	1427	95	below_threshold
Gordonia polyisoprenivorans	strain=ATCC BAA-14	GCA_012396285.1	84595	84595	type	True	78.6328	528	1427	95	below_threshold
Gordonia polyisoprenivorans	strain=NBRC 16320	GCA_000241325.2	84595	84595	type	True	78.5979	542	1427	95	below_threshold
Jongsikchunia kroppenstedtii	strain=NP8-5	GCA_000380485.1	1121721	1121721	type	True	78.291	382	1427	95	below_threshold
Nocardia farcinica	strain=NBRC 15532	GCA_001612925.1	37329	37329	type	True	77.9477	391	1427	95	below_threshold
Nocardia farcinica	strain=DSM 43257	GCA_900156775.1	37329	37329	type	True	77.9156	393	1427	95	below_threshold
Nocardia farcinica	strain=NCTC11134	GCA_001182745.2	37329	37329	type	True	77.9066	405	1427	95	below_threshold
Mycolicibacterium insubricum	strain=JCM 16366	GCA_010731615.1	444597	444597	type	True	77.5508	313	1427	95	below_threshold
Nocardia yunnanensis	strain=CFH S0054	GCA_003626895.1	2382165	2382165	type	True	77.4354	357	1427	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:47:11,863] [INFO] DFAST Taxonomy check result was written to GCF_014639795.1_ASM1463979v1_genomic.fna/tc_result.tsv
[2024-01-25 17:47:11,863] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:47:11,863] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:47:11,864] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ff478ef-6f8a-4695-b93f-27cbd1212b72/dqc_reference/checkm_data
[2024-01-25 17:47:11,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:47:11,905] [INFO] Task started: CheckM
[2024-01-25 17:47:11,906] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014639795.1_ASM1463979v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014639795.1_ASM1463979v1_genomic.fna/checkm_input GCF_014639795.1_ASM1463979v1_genomic.fna/checkm_result
[2024-01-25 17:48:26,054] [INFO] Task succeeded: CheckM
[2024-01-25 17:48:26,055] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:48:26,105] [INFO] ===== Completeness check finished =====
[2024-01-25 17:48:26,105] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:48:26,106] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014639795.1_ASM1463979v1_genomic.fna/markers.fasta)
[2024-01-25 17:48:26,107] [INFO] Task started: Blastn
[2024-01-25 17:48:26,107] [INFO] Running command: blastn -query GCF_014639795.1_ASM1463979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ff478ef-6f8a-4695-b93f-27cbd1212b72/dqc_reference/reference_markers_gtdb.fasta -out GCF_014639795.1_ASM1463979v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:27,819] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:27,822] [INFO] Selected 21 target genomes.
[2024-01-25 17:48:27,822] [INFO] Target genome list was writen to GCF_014639795.1_ASM1463979v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:48:27,832] [INFO] Task started: fastANI
[2024-01-25 17:48:27,833] [INFO] Running command: fastANI --query /var/lib/cwl/stg38e83f73-d41b-47ae-a639-3784b187b647/GCF_014639795.1_ASM1463979v1_genomic.fna.gz --refList GCF_014639795.1_ASM1463979v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014639795.1_ASM1463979v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:48:48,420] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:48,436] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:48:48,436] [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_014639795.1	s__Gordonia_B jinhuaensis	100.0	1423	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000344155.1	s__Gordonia paraffinivorans	79.1578	495	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.97	98.74	0.93	0.90	12	-
GCF_000024785.1	s__Gordonia bronchialis	79.136	499	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900105725.1	s__Gordonia westfalica	79.1131	498	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011290605.1	s__Gordonia sp002009645	79.0511	485	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.70	97.37	0.91	0.88	14	-
GCF_001485495.1	s__Gordonia desulfuricans	79.0511	525	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.37	98.77	0.95	0.92	3	-
GCF_000332975.1	s__Gordonia aichiensis	78.9893	465	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000225505.1	s__Gordonia alkanivorans	78.934	485	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.26	97.87	0.90	0.88	6	-
GCF_000327325.1	s__Gordonia rubripertincta	78.8075	492	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.55	98.07	0.91	0.87	6	-
GCA_014041935.1	s__Gordonia sp014041935	78.7798	474	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.20	99.20	0.95	0.95	2	-
GCA_002700145.1	s__Gordonia sp002700145	78.7467	461	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000298235.1	s__Gordonia namibiensis	78.7185	506	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.13	97.13	0.90	0.90	2	-
GCF_003797825.1	s__Gordonia sp003797825	78.6449	474	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017654315.1	s__Gordonia polyisoprenivorans_A	78.6375	525	1427	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	78.6151	485	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000241325.1	s__Gordonia polyisoprenivorans	78.6148	539	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.60	97.62	0.90	0.79	11	-
GCF_009862785.1	s__Gordonia sp009862785	78.4532	417	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797185.1	s__Gordonia oryzae	78.3667	444	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380485.1	s__Jongsikchunia kroppenstedtii	78.3093	379	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Jongsikchunia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001182745.1	s__Nocardia farcinica	77.9247	403	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.16	98.59	0.93	0.88	42	-
GCF_003626895.1	s__Nocardia yunnanensis	77.4778	352	1427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:48:48,444] [INFO] GTDB search result was written to GCF_014639795.1_ASM1463979v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:48:48,444] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:48:48,448] [INFO] DFAST_QC result json was written to GCF_014639795.1_ASM1463979v1_genomic.fna/dqc_result.json
[2024-01-25 17:48:48,448] [INFO] DFAST_QC completed!
[2024-01-25 17:48:48,448] [INFO] Total running time: 0h2m13s