[2024-01-24 10:58:06,469] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:06,472] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:06,472] [INFO] DQC Reference Directory: /var/lib/cwl/stg4408e7d5-32fd-4fd3-b01a-767be92d3f94/dqc_reference
[2024-01-24 10:58:09,632] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:09,633] [INFO] Task started: Prodigal
[2024-01-24 10:58:09,633] [INFO] Running command: gunzip -c /var/lib/cwl/stg5db61136-11c4-4d08-8d36-e455438e3298/GCF_002155995.1_ASM215599v1_genomic.fna.gz | prodigal -d GCF_002155995.1_ASM215599v1_genomic.fna/cds.fna -a GCF_002155995.1_ASM215599v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:39,914] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:39,915] [INFO] Task started: HMMsearch
[2024-01-24 10:58:39,915] [INFO] Running command: hmmsearch --tblout GCF_002155995.1_ASM215599v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4408e7d5-32fd-4fd3-b01a-767be92d3f94/dqc_reference/reference_markers.hmm GCF_002155995.1_ASM215599v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:40,426] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:40,427] [INFO] Found 6/6 markers.
[2024-01-24 10:58:40,500] [INFO] Query marker FASTA was written to GCF_002155995.1_ASM215599v1_genomic.fna/markers.fasta
[2024-01-24 10:58:40,500] [INFO] Task started: Blastn
[2024-01-24 10:58:40,500] [INFO] Running command: blastn -query GCF_002155995.1_ASM215599v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4408e7d5-32fd-4fd3-b01a-767be92d3f94/dqc_reference/reference_markers.fasta -out GCF_002155995.1_ASM215599v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:41,842] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:41,846] [INFO] Selected 16 target genomes.
[2024-01-24 10:58:41,846] [INFO] Target genome list was writen to GCF_002155995.1_ASM215599v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:41,855] [INFO] Task started: fastANI
[2024-01-24 10:58:41,856] [INFO] Running command: fastANI --query /var/lib/cwl/stg5db61136-11c4-4d08-8d36-e455438e3298/GCF_002155995.1_ASM215599v1_genomic.fna.gz --refList GCF_002155995.1_ASM215599v1_genomic.fna/target_genomes.txt --output GCF_002155995.1_ASM215599v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:59:12,585] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:12,586] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4408e7d5-32fd-4fd3-b01a-767be92d3f94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:59:12,587] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4408e7d5-32fd-4fd3-b01a-767be92d3f94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:59:12,602] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:59:12,602] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:59:12,603] [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
Crossiella equi	strain=NRRL B-24104	GCA_002155995.1	130796	130796	type	True	100.0	2691	2716	95	conclusive
Crossiella equi	strain=DSM 44580	GCA_017876755.1	130796	130796	type	True	99.9886	2713	2716	95	conclusive
Crossiella cryophila	strain=DSM 44230	GCA_014204915.1	43355	43355	type	True	84.6765	1865	2716	95	below_threshold
Allokutzneria albata	strain=DSM 44149	GCA_900103775.1	211114	211114	type	True	79.501	1164	2716	95	below_threshold
Allokutzneria albata	strain=NRRL B-24461	GCA_000720955.1	211114	211114	type	True	79.4538	1166	2716	95	below_threshold
Streptoalloteichus hindustanus	strain=DSM 44523	GCA_900129375.1	2017	2017	type	True	78.9875	936	2716	95	below_threshold
Streptoalloteichus tenebrarius	strain=DSM 40477	GCA_024171885.1	1933	1933	type	True	78.916	931	2716	95	below_threshold
Saccharothrix variisporea	strain=DSM 43911	GCA_003634995.1	543527	543527	type	True	78.719	1146	2716	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.4595	884	2716	95	below_threshold
Actinokineospora bangkokensis	strain=44EHW	GCA_001940455.1	1193682	1193682	type	True	78.3773	1102	2716	95	below_threshold
Lentzea flava	strain=JCM 3296	GCA_014648475.1	103732	103732	type	True	78.2459	973	2716	95	below_threshold
Lentzea terrae	strain=NEAU-LZS 42	GCA_003265345.1	2200761	2200761	type	True	78.2134	979	2716	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	78.1881	897	2716	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	78.0358	910	2716	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	77.6359	800	2716	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	77.5078	1046	2716	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:59:12,605] [INFO] DFAST Taxonomy check result was written to GCF_002155995.1_ASM215599v1_genomic.fna/tc_result.tsv
[2024-01-24 10:59:12,605] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:59:12,605] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:59:12,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4408e7d5-32fd-4fd3-b01a-767be92d3f94/dqc_reference/checkm_data
[2024-01-24 10:59:12,607] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:59:12,702] [INFO] Task started: CheckM
[2024-01-24 10:59:12,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002155995.1_ASM215599v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002155995.1_ASM215599v1_genomic.fna/checkm_input GCF_002155995.1_ASM215599v1_genomic.fna/checkm_result
[2024-01-24 11:01:09,691] [INFO] Task succeeded: CheckM
[2024-01-24 11:01:09,693] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 11:01:09,720] [INFO] ===== Completeness check finished =====
[2024-01-24 11:01:09,721] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:01:09,721] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002155995.1_ASM215599v1_genomic.fna/markers.fasta)
[2024-01-24 11:01:09,722] [INFO] Task started: Blastn
[2024-01-24 11:01:09,722] [INFO] Running command: blastn -query GCF_002155995.1_ASM215599v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4408e7d5-32fd-4fd3-b01a-767be92d3f94/dqc_reference/reference_markers_gtdb.fasta -out GCF_002155995.1_ASM215599v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:01:11,814] [INFO] Task succeeded: Blastn
[2024-01-24 11:01:11,819] [INFO] Selected 17 target genomes.
[2024-01-24 11:01:11,819] [INFO] Target genome list was writen to GCF_002155995.1_ASM215599v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:01:11,832] [INFO] Task started: fastANI
[2024-01-24 11:01:11,833] [INFO] Running command: fastANI --query /var/lib/cwl/stg5db61136-11c4-4d08-8d36-e455438e3298/GCF_002155995.1_ASM215599v1_genomic.fna.gz --refList GCF_002155995.1_ASM215599v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002155995.1_ASM215599v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:01:44,068] [INFO] Task succeeded: fastANI
[2024-01-24 11:01:44,095] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:01:44,095] [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_017876755.1	s__Crossiella equi	99.9886	2713	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Crossiella	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_014204915.1	s__Crossiella cryophila	84.6838	1865	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Crossiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103775.1	s__Allokutzneria albata	79.5228	1158	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Allokutzneria	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002155965.1	s__Allokutzneria sp002155965	79.5137	1082	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Allokutzneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129375.1	s__Streptoalloteichus hindustanus	79.0014	932	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Streptoalloteichus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634995.1	s__Actinosynnema variisporeum	78.7442	1138	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645795.1	s__Longimycelium tulufanense	78.7257	754	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Longimycelium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907655.1	s__Actinosynnema algeriensis	78.7183	1031	2716	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	78.5031	1155	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Goodfellowiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001940455.1	s__Actinokineospora bangkokensis	78.4262	1088	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011067745.1	s__Lentzea alba	78.2603	967	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648475.1	s__Lentzea flava	78.2419	974	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003265345.1	s__Lentzea terrae	78.2067	980	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934265.1	s__Actinokineospora auranticolor	78.1975	974	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000955955.1	s__Lentzea aerocolonigenes_A	78.1393	903	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654205.1	s__Amycolatopsis bullii	77.7262	1000	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009379765.1	s__Actinophytocola sp009379765	77.6536	875	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:01:44,097] [INFO] GTDB search result was written to GCF_002155995.1_ASM215599v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:01:44,098] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:01:44,101] [INFO] DFAST_QC result json was written to GCF_002155995.1_ASM215599v1_genomic.fna/dqc_result.json
[2024-01-24 11:01:44,102] [INFO] DFAST_QC completed!
[2024-01-24 11:01:44,102] [INFO] Total running time: 0h3m38s