[2024-01-24 11:05:26,708] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:26,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:26,710] [INFO] DQC Reference Directory: /var/lib/cwl/stg92f0b9a4-9c4e-49e5-9986-4e4aff0e6fbe/dqc_reference
[2024-01-24 11:05:28,056] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:28,057] [INFO] Task started: Prodigal
[2024-01-24 11:05:28,057] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8e28f3e-3e0b-40e8-b263-8bb127558396/GCF_024171695.1_ASM2417169v1_genomic.fna.gz | prodigal -d GCF_024171695.1_ASM2417169v1_genomic.fna/cds.fna -a GCF_024171695.1_ASM2417169v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:06:01,006] [INFO] Task succeeded: Prodigal
[2024-01-24 11:06:01,007] [INFO] Task started: HMMsearch
[2024-01-24 11:06:01,007] [INFO] Running command: hmmsearch --tblout GCF_024171695.1_ASM2417169v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92f0b9a4-9c4e-49e5-9986-4e4aff0e6fbe/dqc_reference/reference_markers.hmm GCF_024171695.1_ASM2417169v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:06:01,489] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:06:01,491] [INFO] Found 6/6 markers.
[2024-01-24 11:06:01,570] [INFO] Query marker FASTA was written to GCF_024171695.1_ASM2417169v1_genomic.fna/markers.fasta
[2024-01-24 11:06:01,570] [INFO] Task started: Blastn
[2024-01-24 11:06:01,571] [INFO] Running command: blastn -query GCF_024171695.1_ASM2417169v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92f0b9a4-9c4e-49e5-9986-4e4aff0e6fbe/dqc_reference/reference_markers.fasta -out GCF_024171695.1_ASM2417169v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:02,975] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:02,978] [INFO] Selected 18 target genomes.
[2024-01-24 11:06:02,978] [INFO] Target genome list was writen to GCF_024171695.1_ASM2417169v1_genomic.fna/target_genomes.txt
[2024-01-24 11:06:02,985] [INFO] Task started: fastANI
[2024-01-24 11:06:02,985] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8e28f3e-3e0b-40e8-b263-8bb127558396/GCF_024171695.1_ASM2417169v1_genomic.fna.gz --refList GCF_024171695.1_ASM2417169v1_genomic.fna/target_genomes.txt --output GCF_024171695.1_ASM2417169v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:46,832] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:46,833] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92f0b9a4-9c4e-49e5-9986-4e4aff0e6fbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:46,833] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92f0b9a4-9c4e-49e5-9986-4e4aff0e6fbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:46,855] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:06:46,855] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:06:46,855] [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
Actinosynnema mirum	strain=DSM 43827	GCA_000023245.1	40567	40567	type	True	94.496	2477	3094	95	below_threshold
Saccharothrix coeruleofusca	strain=JCM 3313	GCA_014648515.1	33919	33919	type	True	82.4673	1536	3094	95	below_threshold
Saccharothrix coeruleofusca	strain=DSM 43679	GCA_017876325.1	33919	33919	type	True	82.4154	1550	3094	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	81.6319	1763	3094	95	below_threshold
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	81.6023	1619	3094	95	below_threshold
Saccharothrix carnea	strain=CGMCC 4.7097	GCA_003014735.1	1280637	1280637	type	True	81.5727	1534	3094	95	below_threshold
Saccharothrix saharensis	strain=DSM 45456	GCA_006716745.1	571190	571190	type	True	81.5392	1586	3094	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	81.5269	1749	3094	95	below_threshold
Saccharothrix espanaensis	strain=type strain: DSM 44229	GCA_000328705.1	103731	103731	type	True	81.348	1501	3094	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	81.3394	1489	3094	95	below_threshold
Saccharothrix deserti	strain=BMP B8144	GCA_009769385.1	2593674	2593674	type	True	81.2726	1558	3094	95	below_threshold
Saccharothrix variisporea	strain=DSM 43911	GCA_003634995.1	543527	543527	type	True	81.1913	1530	3094	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	81.1639	1388	3094	95	below_threshold
Saccharothrix violaceirubra	strain=DSM 45084	GCA_014203755.1	413306	413306	type	True	80.9663	1250	3094	95	below_threshold
Lentzea flava	strain=DSM 43885	GCA_024171845.1	103732	103732	type	True	79.3277	1220	3094	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.5163	1064	3094	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	78.3955	1009	3094	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	78.1737	974	3094	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:46,857] [INFO] DFAST Taxonomy check result was written to GCF_024171695.1_ASM2417169v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:46,858] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:46,858] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:46,858] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92f0b9a4-9c4e-49e5-9986-4e4aff0e6fbe/dqc_reference/checkm_data
[2024-01-24 11:06:46,859] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:46,961] [INFO] Task started: CheckM
[2024-01-24 11:06:46,961] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024171695.1_ASM2417169v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024171695.1_ASM2417169v1_genomic.fna/checkm_input GCF_024171695.1_ASM2417169v1_genomic.fna/checkm_result
[2024-01-24 11:08:48,913] [INFO] Task succeeded: CheckM
[2024-01-24 11:08:48,915] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:08:48,938] [INFO] ===== Completeness check finished =====
[2024-01-24 11:08:48,939] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:08:48,939] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024171695.1_ASM2417169v1_genomic.fna/markers.fasta)
[2024-01-24 11:08:48,940] [INFO] Task started: Blastn
[2024-01-24 11:08:48,940] [INFO] Running command: blastn -query GCF_024171695.1_ASM2417169v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92f0b9a4-9c4e-49e5-9986-4e4aff0e6fbe/dqc_reference/reference_markers_gtdb.fasta -out GCF_024171695.1_ASM2417169v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:08:51,095] [INFO] Task succeeded: Blastn
[2024-01-24 11:08:51,102] [INFO] Selected 17 target genomes.
[2024-01-24 11:08:51,102] [INFO] Target genome list was writen to GCF_024171695.1_ASM2417169v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:08:51,146] [INFO] Task started: fastANI
[2024-01-24 11:08:51,147] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8e28f3e-3e0b-40e8-b263-8bb127558396/GCF_024171695.1_ASM2417169v1_genomic.fna.gz --refList GCF_024171695.1_ASM2417169v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024171695.1_ASM2417169v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:09:31,622] [INFO] Task succeeded: fastANI
[2024-01-24 11:09:31,649] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:09:31,650] [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_000023245.1	s__Actinosynnema mirum	94.5051	2476	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	96.4703	99.51	99.51	0.95	0.95	3	-
GCF_002354875.1	s__Actinosynnema auranticum	94.4638	2428	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	96.4703	100.00	100.00	1.00	1.00	2	-
GCF_014648515.1	s__Actinosynnema coeruleofuscum	82.5543	1520	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.37	99.37	0.97	0.97	2	-
GCF_016907655.1	s__Actinosynnema algeriensis	81.6945	1392	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752005.1	s__Actinosynnema texasense	81.6256	1614	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	98.51	98.51	0.92	0.92	2	-
GCF_006716745.1	s__Actinosynnema saharense	81.5925	1575	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009498035.1	s__Actinosynnema syringae	81.5726	1779	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003014735.1	s__Actinosynnema carneum	81.5592	1538	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	95.10	95.10	0.83	0.83	2	-
GCF_000328705.1	s__Actinosynnema espanaense	81.3487	1501	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634935.1	s__Actinosynnema australiense	81.3376	1493	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280085.1	s__Actinosynnema sp001280085	81.3081	1627	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009769385.1	s__Actinosynnema deserti	81.2512	1564	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634995.1	s__Actinosynnema variisporeum	81.1711	1536	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203755.1	s__Actinosynnema violaceirubrum	80.9022	1266	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016464305.1	s__REN6 sp016464305	80.7423	1248	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__REN6	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101685.1	s__Actinokineospora iranica	78.5838	972	3094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003448965.1	s__Paroceanicella sp003448965	74.9064	396	3094	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:09:31,652] [INFO] GTDB search result was written to GCF_024171695.1_ASM2417169v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:09:31,652] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:09:31,656] [INFO] DFAST_QC result json was written to GCF_024171695.1_ASM2417169v1_genomic.fna/dqc_result.json
[2024-01-24 11:09:31,656] [INFO] DFAST_QC completed!
[2024-01-24 11:09:31,656] [INFO] Total running time: 0h4m5s