[2024-01-24 11:35:11,940] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:11,949] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:11,949] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc2938c2-af9d-4e95-8d00-e756360426ba/dqc_reference
[2024-01-24 11:35:14,359] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:14,360] [INFO] Task started: Prodigal
[2024-01-24 11:35:14,360] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b07c12d-0b2a-4dbc-8e47-c563bc4bc732/GCF_024171885.1_ASM2417188v1_genomic.fna.gz | prodigal -d GCF_024171885.1_ASM2417188v1_genomic.fna/cds.fna -a GCF_024171885.1_ASM2417188v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:34,092] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:34,093] [INFO] Task started: HMMsearch
[2024-01-24 11:35:34,093] [INFO] Running command: hmmsearch --tblout GCF_024171885.1_ASM2417188v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc2938c2-af9d-4e95-8d00-e756360426ba/dqc_reference/reference_markers.hmm GCF_024171885.1_ASM2417188v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:34,441] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:34,443] [INFO] Found 6/6 markers.
[2024-01-24 11:35:34,519] [INFO] Query marker FASTA was written to GCF_024171885.1_ASM2417188v1_genomic.fna/markers.fasta
[2024-01-24 11:35:34,520] [INFO] Task started: Blastn
[2024-01-24 11:35:34,520] [INFO] Running command: blastn -query GCF_024171885.1_ASM2417188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc2938c2-af9d-4e95-8d00-e756360426ba/dqc_reference/reference_markers.fasta -out GCF_024171885.1_ASM2417188v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:35,918] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:35,922] [INFO] Selected 14 target genomes.
[2024-01-24 11:35:35,922] [INFO] Target genome list was writen to GCF_024171885.1_ASM2417188v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:35,925] [INFO] Task started: fastANI
[2024-01-24 11:35:35,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b07c12d-0b2a-4dbc-8e47-c563bc4bc732/GCF_024171885.1_ASM2417188v1_genomic.fna.gz --refList GCF_024171885.1_ASM2417188v1_genomic.fna/target_genomes.txt --output GCF_024171885.1_ASM2417188v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:36:00,058] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:00,059] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc2938c2-af9d-4e95-8d00-e756360426ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:36:00,059] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc2938c2-af9d-4e95-8d00-e756360426ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:36:00,072] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:36:00,072] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:36:00,072] [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	100.0	2309	2313	95	conclusive
Streptoalloteichus hindustanus	strain=DSM 44523	GCA_900129375.1	2017	2017	type	True	86.9261	1752	2313	95	below_threshold
Saccharothrix coeruleofusca	strain=DSM 43679	GCA_017876325.1	33919	33919	type	True	79.6169	974	2313	95	below_threshold
Saccharothrix coeruleofusca	strain=JCM 3313	GCA_014648515.1	33919	33919	type	True	79.5662	962	2313	95	below_threshold
Saccharopolyspora subtropica	strain=CGMCC 4.7206	GCA_014646075.1	1530170	1530170	type	True	79.0055	715	2313	95	below_threshold
Actinokineospora fastidiosa	strain=JCM 3276	GCA_014648415.1	1816	1816	type	True	78.8101	860	2313	95	below_threshold
Saccharopolyspora hirsuta	strain=VKM Ac-666	GCA_008630535.1	1837	1837	type	True	78.8056	864	2313	95	below_threshold
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	78.7713	989	2313	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	78.7515	1083	2313	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	78.7159	1098	2313	95	below_threshold
Saccharopolyspora antimicrobica	strain=DSM 45119	GCA_003635025.1	455193	455193	type	True	78.7026	868	2313	95	below_threshold
Actinokineospora cianjurensis	strain=DSM 45657	GCA_003663795.1	585224	585224	type	True	78.5406	767	2313	95	below_threshold
Saccharopolyspora shandongensis	strain=CGMCC 4.3530	GCA_900106995.1	418495	418495	type	True	78.488	872	2313	95	below_threshold
Amycolatopsis viridis	strain=DSM 45668	GCA_011758765.1	185678	185678	type	True	78.2261	739	2313	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:36:00,075] [INFO] DFAST Taxonomy check result was written to GCF_024171885.1_ASM2417188v1_genomic.fna/tc_result.tsv
[2024-01-24 11:36:00,077] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:36:00,077] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:36:00,079] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc2938c2-af9d-4e95-8d00-e756360426ba/dqc_reference/checkm_data
[2024-01-24 11:36:00,080] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:00,155] [INFO] Task started: CheckM
[2024-01-24 11:36:00,155] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024171885.1_ASM2417188v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024171885.1_ASM2417188v1_genomic.fna/checkm_input GCF_024171885.1_ASM2417188v1_genomic.fna/checkm_result
[2024-01-24 11:37:45,550] [INFO] Task succeeded: CheckM
[2024-01-24 11:37:45,552] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.94%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:37:45,579] [INFO] ===== Completeness check finished =====
[2024-01-24 11:37:45,579] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:37:45,579] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024171885.1_ASM2417188v1_genomic.fna/markers.fasta)
[2024-01-24 11:37:45,580] [INFO] Task started: Blastn
[2024-01-24 11:37:45,580] [INFO] Running command: blastn -query GCF_024171885.1_ASM2417188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc2938c2-af9d-4e95-8d00-e756360426ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_024171885.1_ASM2417188v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:37:47,692] [INFO] Task succeeded: Blastn
[2024-01-24 11:37:47,697] [INFO] Selected 17 target genomes.
[2024-01-24 11:37:47,697] [INFO] Target genome list was writen to GCF_024171885.1_ASM2417188v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:37:47,711] [INFO] Task started: fastANI
[2024-01-24 11:37:47,711] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b07c12d-0b2a-4dbc-8e47-c563bc4bc732/GCF_024171885.1_ASM2417188v1_genomic.fna.gz --refList GCF_024171885.1_ASM2417188v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024171885.1_ASM2417188v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:38:14,305] [INFO] Task succeeded: fastANI
[2024-01-24 11:38:14,321] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:38:14,321] [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_900129375.1	s__Streptoalloteichus hindustanus	86.9103	1754	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Streptoalloteichus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645795.1	s__Longimycelium tulufanense	81.1449	993	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Longimycelium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405885.1	s__Gandjariella thermophila	79.6722	840	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Gandjariella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648515.1	s__Actinosynnema coeruleofuscum	79.6005	954	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.37	99.37	0.97	0.97	2	-
GCA_000715825.1	s__Goodfellowiella coeruleoviolacea	79.4088	1011	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Goodfellowiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386585.1	s__AN110305 sp008386585	79.1459	998	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__AN110305	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646075.1	s__Saccharopolyspora subtropica	79.0456	708	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410345.1	s__Saccharopolyspora hordei	78.8405	821	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630535.1	s__Saccharopolyspora hirsuta	78.8013	866	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752005.1	s__Actinosynnema texasense	78.7937	982	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	98.51	98.51	0.92	0.92	2	-
GCF_014204915.1	s__Crossiella cryophila	78.754	984	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Crossiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009498035.1	s__Actinosynnema syringae	78.7394	1092	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000374445.1	s__Actinokineospora enzanensis	78.4046	780	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934265.1	s__Actinokineospora auranticolor	78.3683	832	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011758745.1	s__Amycolatopsis granulosa	78.2172	747	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.9842	N/A	N/A	N/A	N/A	1	-
GCF_011758765.1	s__Amycolatopsis viridis	78.2077	745	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.9842	N/A	N/A	N/A	N/A	1	-
GCF_000231075.2	s__Amycolatopsis sp000231075	78.1831	855	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.4849	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:38:14,323] [INFO] GTDB search result was written to GCF_024171885.1_ASM2417188v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:38:14,323] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:38:14,327] [INFO] DFAST_QC result json was written to GCF_024171885.1_ASM2417188v1_genomic.fna/dqc_result.json
[2024-01-24 11:38:14,327] [INFO] DFAST_QC completed!
[2024-01-24 11:38:14,328] [INFO] Total running time: 0h3m2s