[2024-01-25 19:48:05,454] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:48:05,456] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:48:05,456] [INFO] DQC Reference Directory: /var/lib/cwl/stg58a45f35-4ded-4d54-8b86-5722ca82eee7/dqc_reference
[2024-01-25 19:48:06,592] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:48:06,592] [INFO] Task started: Prodigal
[2024-01-25 19:48:06,593] [INFO] Running command: gunzip -c /var/lib/cwl/stg02d033e2-af14-4ad4-914a-b3c1224b211f/GCF_003387475.1_ASM338747v1_genomic.fna.gz | prodigal -d GCF_003387475.1_ASM338747v1_genomic.fna/cds.fna -a GCF_003387475.1_ASM338747v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:48:53,341] [INFO] Task succeeded: Prodigal
[2024-01-25 19:48:53,341] [INFO] Task started: HMMsearch
[2024-01-25 19:48:53,341] [INFO] Running command: hmmsearch --tblout GCF_003387475.1_ASM338747v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58a45f35-4ded-4d54-8b86-5722ca82eee7/dqc_reference/reference_markers.hmm GCF_003387475.1_ASM338747v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:48:53,959] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:48:53,960] [INFO] Found 6/6 markers.
[2024-01-25 19:48:54,074] [INFO] Query marker FASTA was written to GCF_003387475.1_ASM338747v1_genomic.fna/markers.fasta
[2024-01-25 19:48:54,074] [INFO] Task started: Blastn
[2024-01-25 19:48:54,074] [INFO] Running command: blastn -query GCF_003387475.1_ASM338747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58a45f35-4ded-4d54-8b86-5722ca82eee7/dqc_reference/reference_markers.fasta -out GCF_003387475.1_ASM338747v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:55,412] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:55,415] [INFO] Selected 22 target genomes.
[2024-01-25 19:48:55,416] [INFO] Target genome list was writen to GCF_003387475.1_ASM338747v1_genomic.fna/target_genomes.txt
[2024-01-25 19:48:55,430] [INFO] Task started: fastANI
[2024-01-25 19:48:55,430] [INFO] Running command: fastANI --query /var/lib/cwl/stg02d033e2-af14-4ad4-914a-b3c1224b211f/GCF_003387475.1_ASM338747v1_genomic.fna.gz --refList GCF_003387475.1_ASM338747v1_genomic.fna/target_genomes.txt --output GCF_003387475.1_ASM338747v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:49:41,501] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:41,502] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58a45f35-4ded-4d54-8b86-5722ca82eee7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:49:41,502] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58a45f35-4ded-4d54-8b86-5722ca82eee7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:49:41,515] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:49:41,515] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:49:41,515] [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
Kutzneria buriramensis	strain=DSM 45791	GCA_003387475.1	1045776	1045776	type	True	100.0	3955	3961	95	conclusive
Kutzneria kofuensis	strain=DSM 43851	GCA_014203355.1	103725	103725	type	True	88.1725	2556	3961	95	below_threshold
Saccharothrix tamanrassetensis	strain=CECT 8640	GCA_014203665.1	1051531	1051531	type	True	78.8308	1135	3961	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	78.7065	1167	3961	95	below_threshold
Streptoalloteichus hindustanus	strain=DSM 44523	GCA_900129375.1	2017	2017	type	True	78.6112	1012	3961	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	78.6107	1147	3961	95	below_threshold
Saccharothrix variisporea	strain=DSM 43911	GCA_003634995.1	543527	543527	type	True	78.5904	1291	3961	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	78.5848	1465	3961	95	below_threshold
Saccharothrix carnea	strain=CGMCC 4.7097	GCA_003014735.1	1280637	1280637	type	True	78.5762	1223	3961	95	below_threshold
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	78.5708	1339	3961	95	below_threshold
Saccharothrix saharensis	strain=DSM 45456	GCA_006716745.1	571190	571190	type	True	78.5668	1316	3961	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	78.5589	1485	3961	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	78.5468	1233	3961	95	below_threshold
Saccharothrix deserti	strain=BMP B8144	GCA_009769385.1	2593674	2593674	type	True	78.5349	1254	3961	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.4786	964	3961	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	78.4576	1002	3961	95	below_threshold
Saccharothrix violaceirubra	strain=DSM 45084	GCA_014203755.1	413306	413306	type	True	78.3292	1025	3961	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	78.2764	1060	3961	95	below_threshold
Actinokineospora bangkokensis	strain=44EHW	GCA_001940455.1	1193682	1193682	type	True	78.252	1155	3961	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.0604	1367	3961	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	77.8003	918	3961	95	below_threshold
Amycolatopsis anabasis	strain=EGI 650086	GCA_009765355.1	1840409	1840409	type	True	77.6141	1154	3961	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:49:41,516] [INFO] DFAST Taxonomy check result was written to GCF_003387475.1_ASM338747v1_genomic.fna/tc_result.tsv
[2024-01-25 19:49:41,517] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:49:41,517] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:49:41,517] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58a45f35-4ded-4d54-8b86-5722ca82eee7/dqc_reference/checkm_data
[2024-01-25 19:49:41,517] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:49:41,622] [INFO] Task started: CheckM
[2024-01-25 19:49:41,622] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003387475.1_ASM338747v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003387475.1_ASM338747v1_genomic.fna/checkm_input GCF_003387475.1_ASM338747v1_genomic.fna/checkm_result
[2024-01-25 19:52:53,274] [INFO] Task succeeded: CheckM
[2024-01-25 19:52:53,275] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.94%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:52:53,325] [INFO] ===== Completeness check finished =====
[2024-01-25 19:52:53,326] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:52:53,327] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003387475.1_ASM338747v1_genomic.fna/markers.fasta)
[2024-01-25 19:52:53,327] [INFO] Task started: Blastn
[2024-01-25 19:52:53,327] [INFO] Running command: blastn -query GCF_003387475.1_ASM338747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58a45f35-4ded-4d54-8b86-5722ca82eee7/dqc_reference/reference_markers_gtdb.fasta -out GCF_003387475.1_ASM338747v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:55,505] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:55,509] [INFO] Selected 15 target genomes.
[2024-01-25 19:52:55,509] [INFO] Target genome list was writen to GCF_003387475.1_ASM338747v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:52:55,533] [INFO] Task started: fastANI
[2024-01-25 19:52:55,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg02d033e2-af14-4ad4-914a-b3c1224b211f/GCF_003387475.1_ASM338747v1_genomic.fna.gz --refList GCF_003387475.1_ASM338747v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003387475.1_ASM338747v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:53:35,161] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:35,170] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:53:35,170] [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_003387475.1	s__Kutzneria buriramensis	100.0	3955	3961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014203355.1	s__Kutzneria kofuensis	88.167	2557	3961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018263855.1	s__Kutzneria sp018263855	87.5264	2606	3961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000568255.1	s__Kutzneria sp000568255	86.9597	2618	3961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014138725.1	s__Kutzneria viridogrisea	80.9851	1700	3961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	99.33	99.33	0.95	0.95	2	-
GCF_016907655.1	s__Actinosynnema algeriensis	78.7582	1153	3961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129375.1	s__Streptoalloteichus hindustanus	78.5946	1016	3961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Streptoalloteichus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009498035.1	s__Actinosynnema syringae	78.5525	1478	3961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003752005.1	s__Actinosynnema texasense	78.5378	1347	3961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	98.51	98.51	0.92	0.92	2	-
GCF_003634935.1	s__Actinosynnema australiense	78.5254	1240	3961	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	78.5214	1259	3961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000715825.1	s__Goodfellowiella coeruleoviolacea	78.5187	1269	3961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Goodfellowiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374445.1	s__Actinokineospora enzanensis	78.4395	1007	3961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280085.1	s__Actinosynnema sp001280085	78.3241	1394	3961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001940455.1	s__Actinokineospora bangkokensis	78.2266	1162	3961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:53:35,172] [INFO] GTDB search result was written to GCF_003387475.1_ASM338747v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:53:35,172] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:53:35,175] [INFO] DFAST_QC result json was written to GCF_003387475.1_ASM338747v1_genomic.fna/dqc_result.json
[2024-01-25 19:53:35,175] [INFO] DFAST_QC completed!
[2024-01-25 19:53:35,175] [INFO] Total running time: 0h5m30s