[2024-01-24 13:25:30,337] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:30,343] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:30,343] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3bd7a3b-8cb3-4a50-9a92-662dee798364/dqc_reference
[2024-01-24 13:25:31,750] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:31,751] [INFO] Task started: Prodigal
[2024-01-24 13:25:31,751] [INFO] Running command: gunzip -c /var/lib/cwl/stgf08c02e5-5dbf-4631-92e2-82e50652dcd6/GCF_021462265.1_ASM2146226v1_genomic.fna.gz | prodigal -d GCF_021462265.1_ASM2146226v1_genomic.fna/cds.fna -a GCF_021462265.1_ASM2146226v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:01,922] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:01,923] [INFO] Task started: HMMsearch
[2024-01-24 13:26:01,923] [INFO] Running command: hmmsearch --tblout GCF_021462265.1_ASM2146226v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3bd7a3b-8cb3-4a50-9a92-662dee798364/dqc_reference/reference_markers.hmm GCF_021462265.1_ASM2146226v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:02,365] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:02,366] [INFO] Found 6/6 markers.
[2024-01-24 13:26:02,444] [INFO] Query marker FASTA was written to GCF_021462265.1_ASM2146226v1_genomic.fna/markers.fasta
[2024-01-24 13:26:02,444] [INFO] Task started: Blastn
[2024-01-24 13:26:02,444] [INFO] Running command: blastn -query GCF_021462265.1_ASM2146226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3bd7a3b-8cb3-4a50-9a92-662dee798364/dqc_reference/reference_markers.fasta -out GCF_021462265.1_ASM2146226v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:03,743] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:03,746] [INFO] Selected 11 target genomes.
[2024-01-24 13:26:03,746] [INFO] Target genome list was writen to GCF_021462265.1_ASM2146226v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:03,754] [INFO] Task started: fastANI
[2024-01-24 13:26:03,754] [INFO] Running command: fastANI --query /var/lib/cwl/stgf08c02e5-5dbf-4631-92e2-82e50652dcd6/GCF_021462265.1_ASM2146226v1_genomic.fna.gz --refList GCF_021462265.1_ASM2146226v1_genomic.fna/target_genomes.txt --output GCF_021462265.1_ASM2146226v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:32,448] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:32,449] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3bd7a3b-8cb3-4a50-9a92-662dee798364/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:32,449] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3bd7a3b-8cb3-4a50-9a92-662dee798364/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:32,462] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:26:32,462] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:32,462] [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 shenzhenensis	strain=DSM 42034	GCA_021462265.1	943815	943815	type	True	100.0	3456	3461	95	conclusive
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	96.1617	1949	3461	95	conclusive
Streptomyces hyaluromycini	strain=NBRC 110483	GCA_002217755.1	1377993	1377993	type	True	91.6832	2436	3461	95	below_threshold
Streptomyces fuscichromogenes	strain=CGMCC 4.7110	GCA_014645815.1	1324013	1324013	type	True	91.0038	2325	3461	95	below_threshold
Streptomyces humi	strain=MUSC 119	GCA_001005085.2	1428620	1428620	type	True	89.3453	2299	3461	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	85.3474	1935	3461	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	84.9278	1951	3461	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	84.5769	2004	3461	95	below_threshold
Streptomyces davaonensis	strain=JCM 4913	GCA_000349325.1	348043	348043	type	True	84.2651	1850	3461	95	below_threshold
Streptomyces chromofuscus	strain=DSM 40273	GCA_015160875.1	42881	42881	type	True	84.2231	1695	3461	95	below_threshold
Streptomyces chromofuscus	strain=JCM 4354	GCA_014649435.1	42881	42881	type	True	84.057	1720	3461	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:32,464] [INFO] DFAST Taxonomy check result was written to GCF_021462265.1_ASM2146226v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:32,464] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:32,464] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:32,465] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3bd7a3b-8cb3-4a50-9a92-662dee798364/dqc_reference/checkm_data
[2024-01-24 13:26:32,465] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:32,559] [INFO] Task started: CheckM
[2024-01-24 13:26:32,560] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021462265.1_ASM2146226v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021462265.1_ASM2146226v1_genomic.fna/checkm_input GCF_021462265.1_ASM2146226v1_genomic.fna/checkm_result
[2024-01-24 13:28:58,970] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:58,971] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:59,001] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:59,001] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:59,002] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021462265.1_ASM2146226v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:59,002] [INFO] Task started: Blastn
[2024-01-24 13:28:59,002] [INFO] Running command: blastn -query GCF_021462265.1_ASM2146226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3bd7a3b-8cb3-4a50-9a92-662dee798364/dqc_reference/reference_markers_gtdb.fasta -out GCF_021462265.1_ASM2146226v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:01,115] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:01,118] [INFO] Selected 10 target genomes.
[2024-01-24 13:29:01,119] [INFO] Target genome list was writen to GCF_021462265.1_ASM2146226v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:01,133] [INFO] Task started: fastANI
[2024-01-24 13:29:01,134] [INFO] Running command: fastANI --query /var/lib/cwl/stgf08c02e5-5dbf-4631-92e2-82e50652dcd6/GCF_021462265.1_ASM2146226v1_genomic.fna.gz --refList GCF_021462265.1_ASM2146226v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021462265.1_ASM2146226v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:28,112] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:28,128] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:29:28,128] [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_002217755.1	s__Streptomyces hyaluromycini	91.6845	2436	3461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.22	96.22	0.84	0.84	2	-
GCF_900105755.1	s__Streptomyces sp900105755	91.1124	2401	3461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645815.1	s__Streptomyces fuscichromogenes	90.9495	2333	3461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814875.1	s__Streptomyces sp003814875	89.4488	2460	3461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001005085.2	s__Streptomyces humi	89.347	2299	3461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.38	96.38	0.85	0.85	2	-
GCF_004342105.1	s__Streptomyces sp004342105	89.3213	2230	3461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636945.1	s__Streptomyces sp001636945	85.2091	1880	3461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648635.1	s__Streptomyces cinerochromogenes	85.147	1936	3461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000349325.1	s__Streptomyces davaonensis	84.2733	1848	3461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015160875.1	s__Streptomyces chromofuscus	84.2215	1694	3461	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:28,129] [INFO] GTDB search result was written to GCF_021462265.1_ASM2146226v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:28,130] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:28,133] [INFO] DFAST_QC result json was written to GCF_021462265.1_ASM2146226v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:28,133] [INFO] DFAST_QC completed!
[2024-01-24 13:29:28,133] [INFO] Total running time: 0h3m58s