[2024-01-24 14:06:29,547] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:29,549] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:29,549] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b8c7842-a392-4b52-90ab-43b1051e6b9f/dqc_reference
[2024-01-24 14:06:30,890] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:30,890] [INFO] Task started: Prodigal
[2024-01-24 14:06:30,891] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c12c62f-e619-42c3-adcb-90251b07c176/GCF_014645795.1_ASM1464579v1_genomic.fna.gz | prodigal -d GCF_014645795.1_ASM1464579v1_genomic.fna/cds.fna -a GCF_014645795.1_ASM1464579v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:52,659] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:52,659] [INFO] Task started: HMMsearch
[2024-01-24 14:06:52,659] [INFO] Running command: hmmsearch --tblout GCF_014645795.1_ASM1464579v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b8c7842-a392-4b52-90ab-43b1051e6b9f/dqc_reference/reference_markers.hmm GCF_014645795.1_ASM1464579v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:53,008] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:53,011] [INFO] Found 6/6 markers.
[2024-01-24 14:06:53,106] [INFO] Query marker FASTA was written to GCF_014645795.1_ASM1464579v1_genomic.fna/markers.fasta
[2024-01-24 14:06:53,107] [INFO] Task started: Blastn
[2024-01-24 14:06:53,107] [INFO] Running command: blastn -query GCF_014645795.1_ASM1464579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b8c7842-a392-4b52-90ab-43b1051e6b9f/dqc_reference/reference_markers.fasta -out GCF_014645795.1_ASM1464579v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:54,440] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:54,446] [INFO] Selected 18 target genomes.
[2024-01-24 14:06:54,447] [INFO] Target genome list was writen to GCF_014645795.1_ASM1464579v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:54,456] [INFO] Task started: fastANI
[2024-01-24 14:06:54,456] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c12c62f-e619-42c3-adcb-90251b07c176/GCF_014645795.1_ASM1464579v1_genomic.fna.gz --refList GCF_014645795.1_ASM1464579v1_genomic.fna/target_genomes.txt --output GCF_014645795.1_ASM1464579v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:17,570] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:17,571] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b8c7842-a392-4b52-90ab-43b1051e6b9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:17,572] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b8c7842-a392-4b52-90ab-43b1051e6b9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:17,589] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:07:17,590] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:07:17,590] [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
Streptoalloteichus tenebrarius	strain=DSM 40477	GCA_024171885.1	1933	1933	type	True	81.2348	990	2220	95	below_threshold
Streptoalloteichus hindustanus	strain=DSM 44523	GCA_900129375.1	2017	2017	type	True	81.2316	997	2220	95	below_threshold
Saccharothrix coeruleofusca	strain=JCM 3313	GCA_014648515.1	33919	33919	type	True	79.2959	793	2220	95	below_threshold
Saccharothrix coeruleofusca	strain=DSM 43679	GCA_017876325.1	33919	33919	type	True	79.2309	816	2220	95	below_threshold
Saccharopolyspora subtropica	strain=CGMCC 4.7206	GCA_014646075.1	1530170	1530170	type	True	79.0835	624	2220	95	below_threshold
Saccharopolyspora hordei	strain=DSM 44065	GCA_013410345.1	1838	1838	type	True	79.0813	668	2220	95	below_threshold
Saccharopolyspora kobensis	strain=ATCC 20501	GCA_900108315.1	146035	146035	type	True	79.0592	688	2220	95	below_threshold
Allokutzneria albata	strain=NRRL B-24461	GCA_000720955.1	211114	211114	type	True	78.9794	763	2220	95	below_threshold
Saccharopolyspora hirsuta	strain=VKM Ac-666	GCA_008630535.1	1837	1837	type	True	78.8884	736	2220	95	below_threshold
Kutzneria kofuensis	strain=DSM 43851	GCA_014203355.1	103725	103725	type	True	78.7786	785	2220	95	below_threshold
Crossiella equi	strain=NRRL B-24104	GCA_002155995.1	130796	130796	type	True	78.6226	785	2220	95	below_threshold
Crossiella equi	strain=DSM 44580	GCA_017876755.1	130796	130796	type	True	78.5842	833	2220	95	below_threshold
Actinokineospora inagensis	strain=DSM 44258	GCA_000482865.1	103730	103730	type	True	78.5039	586	2220	95	below_threshold
Pseudonocardia nigra	strain=DSM 104088	GCA_019396355.1	1921578	1921578	type	True	77.5969	564	2220	95	below_threshold
Nocardia amamiensis	strain=NBRC 102102	GCA_001612745.1	404578	404578	type	True	77.301	352	2220	95	below_threshold
Nocardia farcinica	strain=NBRC 15532	GCA_001612925.1	37329	37329	type	True	77.2386	443	2220	95	below_threshold
Nocardia farcinica	strain=NCTC11134	GCA_001182745.2	37329	37329	type	True	77.2345	444	2220	95	below_threshold
Nocardia farcinica	strain=DSM 43257	GCA_900156775.1	37329	37329	type	True	77.2336	446	2220	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:17,592] [INFO] DFAST Taxonomy check result was written to GCF_014645795.1_ASM1464579v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:17,592] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:17,592] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:17,593] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b8c7842-a392-4b52-90ab-43b1051e6b9f/dqc_reference/checkm_data
[2024-01-24 14:07:17,593] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:17,661] [INFO] Task started: CheckM
[2024-01-24 14:07:17,661] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645795.1_ASM1464579v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645795.1_ASM1464579v1_genomic.fna/checkm_input GCF_014645795.1_ASM1464579v1_genomic.fna/checkm_result
[2024-01-24 14:08:25,329] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:25,330] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:25,347] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:25,347] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:25,348] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645795.1_ASM1464579v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:25,348] [INFO] Task started: Blastn
[2024-01-24 14:08:25,348] [INFO] Running command: blastn -query GCF_014645795.1_ASM1464579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b8c7842-a392-4b52-90ab-43b1051e6b9f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645795.1_ASM1464579v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:27,271] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:27,274] [INFO] Selected 14 target genomes.
[2024-01-24 14:08:27,274] [INFO] Target genome list was writen to GCF_014645795.1_ASM1464579v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:27,296] [INFO] Task started: fastANI
[2024-01-24 14:08:27,297] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c12c62f-e619-42c3-adcb-90251b07c176/GCF_014645795.1_ASM1464579v1_genomic.fna.gz --refList GCF_014645795.1_ASM1464579v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645795.1_ASM1464579v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:49,350] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:49,363] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:49,363] [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_014645795.1	s__Longimycelium tulufanense	100.0	2216	2220	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Longimycelium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900129375.1	s__Streptoalloteichus hindustanus	81.2735	990	2220	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Streptoalloteichus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405885.1	s__Gandjariella thermophila	79.6282	731	2220	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Gandjariella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000715825.1	s__Goodfellowiella coeruleoviolacea	79.3158	807	2220	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Goodfellowiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410345.1	s__Saccharopolyspora hordei	79.0349	674	2220	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014138725.1	s__Kutzneria viridogrisea	78.958	764	2220	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	99.33	99.33	0.95	0.95	2	-
GCF_008630535.1	s__Saccharopolyspora hirsuta	78.8872	735	2220	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203355.1	s__Kutzneria kofuensis	78.7408	791	2220	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634995.1	s__Actinosynnema variisporeum	78.6562	777	2220	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018141105.1	s__Saccharopolyspora_D erythraea_A	78.6457	738	2220	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386585.1	s__AN110305 sp008386585	78.6105	824	2220	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__AN110305	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876755.1	s__Crossiella equi	78.582	834	2220	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Crossiella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001612745.1	s__Nocardia amamiensis	77.3015	352	2220	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	77.2164	447	2220	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.16	98.59	0.93	0.88	42	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:49,365] [INFO] GTDB search result was written to GCF_014645795.1_ASM1464579v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:49,366] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:49,370] [INFO] DFAST_QC result json was written to GCF_014645795.1_ASM1464579v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:49,370] [INFO] DFAST_QC completed!
[2024-01-24 14:08:49,370] [INFO] Total running time: 0h2m20s