[2024-01-24 12:21:43,536] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:43,540] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:43,540] [INFO] DQC Reference Directory: /var/lib/cwl/stg11399a01-4039-4b0f-99c9-a622538f945a/dqc_reference
[2024-01-24 12:21:44,950] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:44,950] [INFO] Task started: Prodigal
[2024-01-24 12:21:44,951] [INFO] Running command: gunzip -c /var/lib/cwl/stgda0c31b5-8788-4429-9804-0f9b67a16d27/GCF_001552855.1_ASM155285v1_genomic.fna.gz | prodigal -d GCF_001552855.1_ASM155285v1_genomic.fna/cds.fna -a GCF_001552855.1_ASM155285v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:58,111] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:58,111] [INFO] Task started: HMMsearch
[2024-01-24 12:21:58,111] [INFO] Running command: hmmsearch --tblout GCF_001552855.1_ASM155285v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11399a01-4039-4b0f-99c9-a622538f945a/dqc_reference/reference_markers.hmm GCF_001552855.1_ASM155285v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:58,440] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:58,442] [INFO] Found 6/6 markers.
[2024-01-24 12:21:58,489] [INFO] Query marker FASTA was written to GCF_001552855.1_ASM155285v1_genomic.fna/markers.fasta
[2024-01-24 12:21:58,490] [INFO] Task started: Blastn
[2024-01-24 12:21:58,490] [INFO] Running command: blastn -query GCF_001552855.1_ASM155285v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11399a01-4039-4b0f-99c9-a622538f945a/dqc_reference/reference_markers.fasta -out GCF_001552855.1_ASM155285v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:59,637] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:59,640] [INFO] Selected 18 target genomes.
[2024-01-24 12:21:59,640] [INFO] Target genome list was writen to GCF_001552855.1_ASM155285v1_genomic.fna/target_genomes.txt
[2024-01-24 12:21:59,647] [INFO] Task started: fastANI
[2024-01-24 12:21:59,647] [INFO] Running command: fastANI --query /var/lib/cwl/stgda0c31b5-8788-4429-9804-0f9b67a16d27/GCF_001552855.1_ASM155285v1_genomic.fna.gz --refList GCF_001552855.1_ASM155285v1_genomic.fna/target_genomes.txt --output GCF_001552855.1_ASM155285v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:20,541] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:20,541] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11399a01-4039-4b0f-99c9-a622538f945a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:20,541] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11399a01-4039-4b0f-99c9-a622538f945a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:20,556] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:22:20,557] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:20,557] [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=NBRC 15059	GCA_001552855.1	39122	39122	type	True	100.0	1381	1382	95	conclusive
Skermania piniformis	strain=DSM 43998	GCA_019285775.1	39122	39122	type	True	99.9999	1381	1382	95	conclusive
Nocardia farcinica	strain=NCTC11134	GCA_001182745.2	37329	37329	type	True	78.1952	512	1382	95	below_threshold
Nocardia pneumoniae	strain=NBRC 100136	GCA_000308755.1	228601	228601	type	True	78.1546	481	1382	95	below_threshold
Nocardia farcinica	strain=NBRC 15532	GCA_001612925.1	37329	37329	type	True	78.1167	500	1382	95	below_threshold
Nocardia farcinica	strain=DSM 43257	GCA_900156775.1	37329	37329	type	True	78.0926	513	1382	95	below_threshold
Nocardia harenae	strain=NBRC 108248	GCA_001612885.1	358707	358707	type	True	78.0732	551	1382	95	below_threshold
Nocardia niwae	strain=NBRC 108934	GCA_001613465.1	626084	626084	type	True	77.9304	491	1382	95	below_threshold
Nocardia puris	strain=DSM 44599	GCA_003315035.1	208602	208602	type	True	77.8139	509	1382	95	below_threshold
Nocardia caishijiensis	strain=DSM 44831	GCA_009858255.1	184756	184756	type	True	77.7783	437	1382	95	below_threshold
Nocardia caishijiensis	strain=NBRC 108228	GCA_001612825.1	184756	184756	type	True	77.7673	439	1382	95	below_threshold
Nocardia albiluteola	strain=NEAU-G5	GCA_018860155.1	2842303	2842303	type	True	77.6564	466	1382	95	below_threshold
Nocardia sienata	strain=NBRC 100364	GCA_001613205.1	248552	248552	type	True	77.653	387	1382	95	below_threshold
Rhodococcus aetherivorans	strain=DSM 44752	GCA_011058165.1	191292	191292	type	True	77.6108	440	1382	95	below_threshold
Aldersonia kunmingensis	strain=DSM 45001	GCA_001646865.1	408066	408066	type	True	77.582	400	1382	95	below_threshold
Nocardia mangyaensis	strain=Y48	GCA_001886715.1	2213200	2213200	type	True	77.5571	515	1382	95	below_threshold
Rhodococcus aetherivorans	strain=JCM 14343	GCA_009176285.1	191292	191292	type	True	77.5235	443	1382	95	below_threshold
Nocardia testacea	strain=NBRC 100365	GCA_000308775.1	248551	248551	type	True	77.4299	415	1382	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:20,559] [INFO] DFAST Taxonomy check result was written to GCF_001552855.1_ASM155285v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:20,559] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:20,560] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:20,560] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11399a01-4039-4b0f-99c9-a622538f945a/dqc_reference/checkm_data
[2024-01-24 12:22:20,561] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:20,606] [INFO] Task started: CheckM
[2024-01-24 12:22:20,606] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001552855.1_ASM155285v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001552855.1_ASM155285v1_genomic.fna/checkm_input GCF_001552855.1_ASM155285v1_genomic.fna/checkm_result
[2024-01-24 12:23:02,148] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:02,149] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:02,170] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:02,171] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:02,171] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001552855.1_ASM155285v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:02,171] [INFO] Task started: Blastn
[2024-01-24 12:23:02,172] [INFO] Running command: blastn -query GCF_001552855.1_ASM155285v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11399a01-4039-4b0f-99c9-a622538f945a/dqc_reference/reference_markers_gtdb.fasta -out GCF_001552855.1_ASM155285v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:04,041] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:04,044] [INFO] Selected 20 target genomes.
[2024-01-24 12:23:04,045] [INFO] Target genome list was writen to GCF_001552855.1_ASM155285v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:04,068] [INFO] Task started: fastANI
[2024-01-24 12:23:04,069] [INFO] Running command: fastANI --query /var/lib/cwl/stgda0c31b5-8788-4429-9804-0f9b67a16d27/GCF_001552855.1_ASM155285v1_genomic.fna.gz --refList GCF_001552855.1_ASM155285v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001552855.1_ASM155285v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:28,520] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:28,542] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:28,542] [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	100.0	1381	1382	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_001182745.1	s__Nocardia farcinica	78.2024	511	1382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.16	98.59	0.93	0.88	42	-
GCF_000308755.1	s__Nocardia pneumoniae	78.149	480	1382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612885.1	s__Nocardia harenae	78.0611	552	1382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900269665.1	s__Nocardia suismassiliense	78.0171	499	1382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	95.20	95.20	0.87	0.87	2	-
GCF_000308575.1	s__Nocardia exalbida	77.9982	504	1382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.7192	N/A	N/A	N/A	N/A	1	-
GCF_015477605.1	s__Nocardia amamiensis_A	77.9492	480	1382	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	77.9355	489	1382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182135.1	s__Nocardia neocaledoniensis	77.8605	533	1382	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	77.8088	509	1382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.66	99.46	0.95	0.92	4	-
GCF_001612825.1	s__Nocardia caishijiensis	77.7817	437	1382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018860155.1	s__Nocardia sp018860155	77.6645	465	1382	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	77.6317	356	1382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.01	98.63	0.96	0.88	61	-
GCF_001613205.1	s__Nocardia sienata	77.6288	390	1382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613505.1	s__Nocardia mikamii	77.5931	454	1382	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	77.5916	398	1382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Aldersonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886715.1	s__Nocardia mangyaensis	77.5915	508	1382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011058165.1	s__Rhodococcus aetherivorans	77.5913	442	1382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.92	95.74	0.88	0.78	18	-
GCF_000308775.1	s__Nocardia testacea	77.4696	408	1382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727125.1	s__Mycobacterium terrae	77.3738	308	1382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:28,545] [INFO] GTDB search result was written to GCF_001552855.1_ASM155285v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:28,546] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:28,551] [INFO] DFAST_QC result json was written to GCF_001552855.1_ASM155285v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:28,551] [INFO] DFAST_QC completed!
[2024-01-24 12:23:28,551] [INFO] Total running time: 0h1m45s