[2024-01-24 13:57:00,997] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:00,999] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:00,999] [INFO] DQC Reference Directory: /var/lib/cwl/stg26885d2c-8f27-48c3-b0ef-4e61e930f50f/dqc_reference
[2024-01-24 13:57:02,463] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:02,463] [INFO] Task started: Prodigal
[2024-01-24 13:57:02,464] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc8ee99f-f5cc-4fe4-9208-4a0cdba63f1b/GCF_002234535.1_ASM223453v1_genomic.fna.gz | prodigal -d GCF_002234535.1_ASM223453v1_genomic.fna/cds.fna -a GCF_002234535.1_ASM223453v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:29,139] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:29,140] [INFO] Task started: HMMsearch
[2024-01-24 13:57:29,140] [INFO] Running command: hmmsearch --tblout GCF_002234535.1_ASM223453v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26885d2c-8f27-48c3-b0ef-4e61e930f50f/dqc_reference/reference_markers.hmm GCF_002234535.1_ASM223453v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:29,526] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:29,528] [INFO] Found 6/6 markers.
[2024-01-24 13:57:29,589] [INFO] Query marker FASTA was written to GCF_002234535.1_ASM223453v1_genomic.fna/markers.fasta
[2024-01-24 13:57:29,589] [INFO] Task started: Blastn
[2024-01-24 13:57:29,589] [INFO] Running command: blastn -query GCF_002234535.1_ASM223453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26885d2c-8f27-48c3-b0ef-4e61e930f50f/dqc_reference/reference_markers.fasta -out GCF_002234535.1_ASM223453v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:30,939] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:30,943] [INFO] Selected 5 target genomes.
[2024-01-24 13:57:30,943] [INFO] Target genome list was writen to GCF_002234535.1_ASM223453v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:30,947] [INFO] Task started: fastANI
[2024-01-24 13:57:30,947] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc8ee99f-f5cc-4fe4-9208-4a0cdba63f1b/GCF_002234535.1_ASM223453v1_genomic.fna.gz --refList GCF_002234535.1_ASM223453v1_genomic.fna/target_genomes.txt --output GCF_002234535.1_ASM223453v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:39,585] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:39,586] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26885d2c-8f27-48c3-b0ef-4e61e930f50f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:39,586] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26885d2c-8f27-48c3-b0ef-4e61e930f50f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:39,594] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:57:39,595] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:39,595] [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
Actinoalloteichus hoggarensis	strain=DSM 45943	GCA_002234535.1	1470176	1470176	type	True	100.0	2201	2202	95	conclusive
Actinoalloteichus hoggarensis	strain=CECT 8639	GCA_014203625.1	1470176	1470176	type	True	99.9898	2184	2202	95	conclusive
Actinoalloteichus fjordicus	strain=ADI127-7	GCA_001941625.1	1612552	1612552	type	True	87.1119	1827	2202	95	below_threshold
Actinoalloteichus hymeniacidonis	strain=HPA177(T) (=DSM 45092(T))	GCA_001747425.1	340345	340345	type	True	81.8319	1275	2202	95	below_threshold
Actinoalloteichus hymeniacidonis	strain=DSM 45092	GCA_014203365.1	340345	340345	type	True	81.8103	1276	2202	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:39,597] [INFO] DFAST Taxonomy check result was written to GCF_002234535.1_ASM223453v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:39,598] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:39,598] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:39,598] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26885d2c-8f27-48c3-b0ef-4e61e930f50f/dqc_reference/checkm_data
[2024-01-24 13:57:39,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:39,660] [INFO] Task started: CheckM
[2024-01-24 13:57:39,660] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002234535.1_ASM223453v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002234535.1_ASM223453v1_genomic.fna/checkm_input GCF_002234535.1_ASM223453v1_genomic.fna/checkm_result
[2024-01-24 13:59:27,133] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:27,135] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 46.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:27,158] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:27,159] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:27,159] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002234535.1_ASM223453v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:27,159] [INFO] Task started: Blastn
[2024-01-24 13:59:27,160] [INFO] Running command: blastn -query GCF_002234535.1_ASM223453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26885d2c-8f27-48c3-b0ef-4e61e930f50f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002234535.1_ASM223453v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:29,208] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:29,212] [INFO] Selected 11 target genomes.
[2024-01-24 13:59:29,213] [INFO] Target genome list was writen to GCF_002234535.1_ASM223453v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:29,225] [INFO] Task started: fastANI
[2024-01-24 13:59:29,225] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc8ee99f-f5cc-4fe4-9208-4a0cdba63f1b/GCF_002234535.1_ASM223453v1_genomic.fna.gz --refList GCF_002234535.1_ASM223453v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002234535.1_ASM223453v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:47,016] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:47,036] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:47,037] [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_002234535.1	s__Actinoalloteichus hoggarensis	100.0	2202	2202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinoalloteichus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001941625.1	s__Actinoalloteichus fjordicus	87.09	1828	2202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinoalloteichus	95.0	99.71	99.71	0.98	0.98	2	-
GCF_001747425.1	s__Actinoalloteichus hymeniacidonis	81.8567	1272	2202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinoalloteichus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000239155.1	s__Actinoalloteichus spitiensis	78.3084	592	2202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinoalloteichus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429185.1	s__Actinoalloteichus cyanogriseus	78.2131	700	2202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinoalloteichus	95.0	99.50	99.47	0.98	0.97	3	-
GCA_000715825.1	s__Goodfellowiella coeruleoviolacea	77.8437	714	2202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Goodfellowiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129375.1	s__Streptoalloteichus hindustanus	77.7577	665	2202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Streptoalloteichus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014138725.1	s__Kutzneria viridogrisea	77.7559	677	2202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	99.33	99.33	0.95	0.95	2	-
GCF_008386585.1	s__AN110305 sp008386585	77.4914	717	2202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__AN110305	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001940455.1	s__Actinokineospora bangkokensis	77.3441	688	2202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752005.1	s__Actinosynnema texasense	77.3352	794	2202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	98.51	98.51	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:47,039] [INFO] GTDB search result was written to GCF_002234535.1_ASM223453v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:47,040] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:47,043] [INFO] DFAST_QC result json was written to GCF_002234535.1_ASM223453v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:47,043] [INFO] DFAST_QC completed!
[2024-01-24 13:59:47,043] [INFO] Total running time: 0h2m46s