[2024-01-24 14:14:06,260] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:06,262] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:06,263] [INFO] DQC Reference Directory: /var/lib/cwl/stge2a4f3c5-3c6f-453b-8c8c-a7da54791ecd/dqc_reference
[2024-01-24 14:14:07,603] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:07,604] [INFO] Task started: Prodigal
[2024-01-24 14:14:07,604] [INFO] Running command: gunzip -c /var/lib/cwl/stg41fbbc5b-8d28-41fa-9298-06b546fbcde3/GCF_012034235.1_ASM1203423v1_genomic.fna.gz | prodigal -d GCF_012034235.1_ASM1203423v1_genomic.fna/cds.fna -a GCF_012034235.1_ASM1203423v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:25,225] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:25,225] [INFO] Task started: HMMsearch
[2024-01-24 14:14:25,226] [INFO] Running command: hmmsearch --tblout GCF_012034235.1_ASM1203423v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2a4f3c5-3c6f-453b-8c8c-a7da54791ecd/dqc_reference/reference_markers.hmm GCF_012034235.1_ASM1203423v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:25,513] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:25,515] [INFO] Found 6/6 markers.
[2024-01-24 14:14:25,560] [INFO] Query marker FASTA was written to GCF_012034235.1_ASM1203423v1_genomic.fna/markers.fasta
[2024-01-24 14:14:25,560] [INFO] Task started: Blastn
[2024-01-24 14:14:25,560] [INFO] Running command: blastn -query GCF_012034235.1_ASM1203423v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2a4f3c5-3c6f-453b-8c8c-a7da54791ecd/dqc_reference/reference_markers.fasta -out GCF_012034235.1_ASM1203423v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:26,914] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:26,917] [INFO] Selected 9 target genomes.
[2024-01-24 14:14:26,918] [INFO] Target genome list was writen to GCF_012034235.1_ASM1203423v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:26,926] [INFO] Task started: fastANI
[2024-01-24 14:14:26,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg41fbbc5b-8d28-41fa-9298-06b546fbcde3/GCF_012034235.1_ASM1203423v1_genomic.fna.gz --refList GCF_012034235.1_ASM1203423v1_genomic.fna/target_genomes.txt --output GCF_012034235.1_ASM1203423v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:42,439] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:42,439] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2a4f3c5-3c6f-453b-8c8c-a7da54791ecd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:42,440] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2a4f3c5-3c6f-453b-8c8c-a7da54791ecd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:42,456] [INFO] Found 9 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:14:42,456] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:14:42,456] [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
Streptomyces thermoviolaceus subsp. thermoviolaceus	strain=NBRC 13905	GCA_012034235.1	66860	1952	type	True	100.0	1929	1931	95	inconclusive
Streptomyces thermoviolaceus subsp. thermoviolaceus	strain=JCM 4843	GCA_014650975.1	66860	1952	type	True	99.9977	1905	1931	95	inconclusive
Streptomyces thermoviolaceus subsp. apingens	strain=JCM 4312	GCA_014649255.1	66859	1952	type	True	99.8053	1901	1931	95	inconclusive
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	95.3552	1728	1931	95	inconclusive
Streptomyces thermodiastaticus	strain=JCM 4840	GCA_014656135.1	44061	44061	type	True	95.3519	1721	1931	95	inconclusive
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	86.1527	1403	1931	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.7423	1205	1931	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	84.5278	1381	1931	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	84.376	1395	1931	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:42,458] [INFO] DFAST Taxonomy check result was written to GCF_012034235.1_ASM1203423v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:42,458] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:42,458] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:42,458] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2a4f3c5-3c6f-453b-8c8c-a7da54791ecd/dqc_reference/checkm_data
[2024-01-24 14:14:42,459] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:42,531] [INFO] Task started: CheckM
[2024-01-24 14:14:42,531] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012034235.1_ASM1203423v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012034235.1_ASM1203423v1_genomic.fna/checkm_input GCF_012034235.1_ASM1203423v1_genomic.fna/checkm_result
[2024-01-24 14:16:17,886] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:17,887] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:17,907] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:17,907] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:17,908] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012034235.1_ASM1203423v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:17,908] [INFO] Task started: Blastn
[2024-01-24 14:16:17,908] [INFO] Running command: blastn -query GCF_012034235.1_ASM1203423v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2a4f3c5-3c6f-453b-8c8c-a7da54791ecd/dqc_reference/reference_markers_gtdb.fasta -out GCF_012034235.1_ASM1203423v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:20,265] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:20,269] [INFO] Selected 16 target genomes.
[2024-01-24 14:16:20,270] [INFO] Target genome list was writen to GCF_012034235.1_ASM1203423v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:20,282] [INFO] Task started: fastANI
[2024-01-24 14:16:20,283] [INFO] Running command: fastANI --query /var/lib/cwl/stg41fbbc5b-8d28-41fa-9298-06b546fbcde3/GCF_012034235.1_ASM1203423v1_genomic.fna.gz --refList GCF_012034235.1_ASM1203423v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012034235.1_ASM1203423v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:49,404] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:49,419] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:49,420] [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_014656135.1	s__Streptomyces thermodiastaticus	95.3564	1721	1931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.31	95.26	0.89	0.88	5	conclusive
GCF_902506575.1	s__Streptomyces mexicanus	89.4983	1584	1931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.95	96.19	0.87	0.78	3	-
GCF_014654675.1	s__Streptomyces spiralis	86.4136	1520	1931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.07	98.07	0.87	0.87	2	-
GCF_000383935.1	s__Streptomyces sp000383935	86.1398	1483	1931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.62	97.70	0.92	0.84	4	-
GCF_002154505.1	s__Streptomyces carpinensis	86.0741	1342	1931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364255.1	s__Streptomyces seoulensis_A	85.9234	1483	1931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720185.1	s__Streptomyces sp000720185	85.8718	1499	1931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650655.1	s__Streptomyces anandii	85.7541	1453	1931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650575.1	s__Streptomyces naganishii	85.6783	1450	1931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155915.1	s__Streptomyces thermovulgaris	85.55	1147	1931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.61	99.61	0.95	0.95	2	-
GCF_014651135.1	s__Streptomyces echinoruber	84.9106	1357	1931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001013905.1	s__Streptomyces leeuwenhoekii	84.5444	1364	1931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.603	99.67	99.36	0.97	0.94	3	-
GCF_002155905.1	s__Streptomyces tricolor	84.4962	1189	1931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	98.00	0.86	0.72	5	-
GCF_000761215.1	s__Streptomyces glaucescens	84.2932	1330	1931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905845.1	s__Streptomyces sp001905845	84.156	1364	1931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014656015.1	s__Streptomyces griseoaurantiacus	83.4199	1278	1931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.09	98.94	0.94	0.90	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:49,422] [INFO] GTDB search result was written to GCF_012034235.1_ASM1203423v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:49,422] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:49,428] [INFO] DFAST_QC result json was written to GCF_012034235.1_ASM1203423v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:49,429] [INFO] DFAST_QC completed!
[2024-01-24 14:16:49,429] [INFO] Total running time: 0h2m43s