[2024-01-24 13:32:11,936] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:11,938] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:11,939] [INFO] DQC Reference Directory: /var/lib/cwl/stg84c8abba-0a9b-4c8f-b217-bc7f7bb88adc/dqc_reference
[2024-01-24 13:32:14,742] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:14,743] [INFO] Task started: Prodigal
[2024-01-24 13:32:14,743] [INFO] Running command: gunzip -c /var/lib/cwl/stg824875b8-3da8-42a6-9933-9abd7a6255d7/GCF_019285775.1_ASM1928577v1_genomic.fna.gz | prodigal -d GCF_019285775.1_ASM1928577v1_genomic.fna/cds.fna -a GCF_019285775.1_ASM1928577v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:38,222] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:38,223] [INFO] Task started: HMMsearch
[2024-01-24 13:32:38,223] [INFO] Running command: hmmsearch --tblout GCF_019285775.1_ASM1928577v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84c8abba-0a9b-4c8f-b217-bc7f7bb88adc/dqc_reference/reference_markers.hmm GCF_019285775.1_ASM1928577v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:38,518] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:38,520] [INFO] Found 6/6 markers.
[2024-01-24 13:32:38,564] [INFO] Query marker FASTA was written to GCF_019285775.1_ASM1928577v1_genomic.fna/markers.fasta
[2024-01-24 13:32:38,565] [INFO] Task started: Blastn
[2024-01-24 13:32:38,565] [INFO] Running command: blastn -query GCF_019285775.1_ASM1928577v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84c8abba-0a9b-4c8f-b217-bc7f7bb88adc/dqc_reference/reference_markers.fasta -out GCF_019285775.1_ASM1928577v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:39,935] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:39,939] [INFO] Selected 18 target genomes.
[2024-01-24 13:32:39,940] [INFO] Target genome list was writen to GCF_019285775.1_ASM1928577v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:39,955] [INFO] Task started: fastANI
[2024-01-24 13:32:39,956] [INFO] Running command: fastANI --query /var/lib/cwl/stg824875b8-3da8-42a6-9933-9abd7a6255d7/GCF_019285775.1_ASM1928577v1_genomic.fna.gz --refList GCF_019285775.1_ASM1928577v1_genomic.fna/target_genomes.txt --output GCF_019285775.1_ASM1928577v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:59,877] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:59,878] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84c8abba-0a9b-4c8f-b217-bc7f7bb88adc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:59,878] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84c8abba-0a9b-4c8f-b217-bc7f7bb88adc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:59,896] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:59,897] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:59,897] [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
Skermania piniformis	strain=DSM 43998	GCA_019285775.1	39122	39122	type	True	100.0	1410	1410	95	conclusive
Skermania piniformis	strain=NBRC 15059	GCA_001552855.1	39122	39122	type	True	99.9856	1375	1410	95	conclusive
Nocardia harenae	strain=NBRC 108248	GCA_001612885.1	358707	358707	type	True	78.1435	560	1410	95	below_threshold
Nocardia farcinica	strain=DSM 43257	GCA_900156775.1	37329	37329	type	True	78.0599	541	1410	95	below_threshold
Nocardia pneumoniae	strain=NBRC 100136	GCA_000308755.1	228601	228601	type	True	78.0323	495	1410	95	below_threshold
Nocardia farcinica	strain=NCTC11134	GCA_001182745.2	37329	37329	type	True	78.0322	545	1410	95	below_threshold
Nocardia farcinica	strain=NBRC 15532	GCA_001612925.1	37329	37329	type	True	77.9976	526	1410	95	below_threshold
Nocardia niwae	strain=NBRC 108934	GCA_001613465.1	626084	626084	type	True	77.9913	486	1410	95	below_threshold
Nocardia mangyaensis	strain=Y48	GCA_001886715.1	2213200	2213200	type	True	77.8326	492	1410	95	below_threshold
Nocardia caishijiensis	strain=NBRC 108228	GCA_001612825.1	184756	184756	type	True	77.7683	445	1410	95	below_threshold
Nocardia caishijiensis	strain=DSM 44831	GCA_009858255.1	184756	184756	type	True	77.7526	443	1410	95	below_threshold
Nocardia puris	strain=DSM 44599	GCA_003315035.1	208602	208602	type	True	77.6823	521	1410	95	below_threshold
Nocardia albiluteola	strain=NEAU-G5	GCA_018860155.1	2842303	2842303	type	True	77.6555	463	1410	95	below_threshold
Rhodococcus aetherivorans	strain=JCM 14343	GCA_009176285.1	191292	191292	type	True	77.5246	435	1410	95	below_threshold
Rhodococcus aetherivorans	strain=DSM 44752	GCA_011058165.1	191292	191292	type	True	77.5239	445	1410	95	below_threshold
Aldersonia kunmingensis	strain=DSM 45001	GCA_001646865.1	408066	408066	type	True	77.5064	412	1410	95	below_threshold
Nocardia sienata	strain=NBRC 100364	GCA_001613205.1	248552	248552	type	True	77.4743	398	1410	95	below_threshold
Nocardia testacea	strain=NBRC 100365	GCA_000308775.1	248551	248551	type	True	77.3929	435	1410	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:59,899] [INFO] DFAST Taxonomy check result was written to GCF_019285775.1_ASM1928577v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:59,899] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:59,899] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:59,900] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84c8abba-0a9b-4c8f-b217-bc7f7bb88adc/dqc_reference/checkm_data
[2024-01-24 13:32:59,901] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:59,951] [INFO] Task started: CheckM
[2024-01-24 13:32:59,952] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019285775.1_ASM1928577v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019285775.1_ASM1928577v1_genomic.fna/checkm_input GCF_019285775.1_ASM1928577v1_genomic.fna/checkm_result
[2024-01-24 13:34:02,560] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:02,561] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:02,582] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:02,582] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:02,583] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019285775.1_ASM1928577v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:02,583] [INFO] Task started: Blastn
[2024-01-24 13:34:02,583] [INFO] Running command: blastn -query GCF_019285775.1_ASM1928577v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84c8abba-0a9b-4c8f-b217-bc7f7bb88adc/dqc_reference/reference_markers_gtdb.fasta -out GCF_019285775.1_ASM1928577v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:04,356] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:04,361] [INFO] Selected 20 target genomes.
[2024-01-24 13:34:04,361] [INFO] Target genome list was writen to GCF_019285775.1_ASM1928577v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:04,385] [INFO] Task started: fastANI
[2024-01-24 13:34:04,386] [INFO] Running command: fastANI --query /var/lib/cwl/stg824875b8-3da8-42a6-9933-9abd7a6255d7/GCF_019285775.1_ASM1928577v1_genomic.fna.gz --refList GCF_019285775.1_ASM1928577v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019285775.1_ASM1928577v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:28,036] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:28,059] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:28,060] [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_001552855.1	s__Skermania piniformis	99.9856	1375	1410	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Skermania	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001612885.1	s__Nocardia harenae	78.1387	560	1410	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001182745.1	s__Nocardia farcinica	78.0581	546	1410	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.16	98.59	0.93	0.88	42	-
GCF_900269665.1	s__Nocardia suismassiliense	78.0366	508	1410	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	95.20	95.20	0.87	0.87	2	-
GCF_000308755.1	s__Nocardia pneumoniae	78.0305	494	1410	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613465.1	s__Nocardia niwae	78.0043	484	1410	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015477605.1	s__Nocardia amamiensis_A	77.9538	481	1410	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308575.1	s__Nocardia exalbida	77.9456	520	1410	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.7192	N/A	N/A	N/A	N/A	1	-
GCF_003182135.1	s__Nocardia neocaledoniensis	77.903	534	1410	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001886715.1	s__Nocardia mangyaensis	77.8441	489	1410	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612825.1	s__Nocardia caishijiensis	77.7673	444	1410	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003315035.1	s__Nocardia puris	77.6707	523	1410	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.66	99.46	0.95	0.92	4	-
GCF_018860155.1	s__Nocardia sp018860155	77.6657	463	1410	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001646865.1	s__Aldersonia kunmingensis	77.5434	407	1410	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Aldersonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727125.1	s__Mycobacterium terrae	77.5282	314	1410	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	99.99	1.00	1.00	3	-
GCF_011058165.1	s__Rhodococcus aetherivorans	77.518	446	1410	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.92	95.74	0.88	0.78	18	-
GCF_001613505.1	s__Nocardia mikamii	77.5152	464	1410	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613205.1	s__Nocardia sienata	77.5045	394	1410	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001646645.1	s__Rhodococcus hoagii	77.4849	375	1410	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.01	98.63	0.96	0.88	61	-
GCF_000308775.1	s__Nocardia testacea	77.4278	429	1410	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:28,061] [INFO] GTDB search result was written to GCF_019285775.1_ASM1928577v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:28,062] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:28,066] [INFO] DFAST_QC result json was written to GCF_019285775.1_ASM1928577v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:28,067] [INFO] DFAST_QC completed!
[2024-01-24 13:34:28,067] [INFO] Total running time: 0h2m16s