[2024-01-25 17:48:21,007] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:48:21,009] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:48:21,009] [INFO] DQC Reference Directory: /var/lib/cwl/stgddf6f96b-9997-4be6-846b-ba46353ddca4/dqc_reference
[2024-01-25 17:48:22,157] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:48:22,158] [INFO] Task started: Prodigal
[2024-01-25 17:48:22,158] [INFO] Running command: gunzip -c /var/lib/cwl/stge7a8e5b5-37ee-4a21-96fa-c0fc616354dc/GCF_000761485.1_ASM76148v1_genomic.fna.gz | prodigal -d GCF_000761485.1_ASM76148v1_genomic.fna/cds.fna -a GCF_000761485.1_ASM76148v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:48:33,675] [INFO] Task succeeded: Prodigal
[2024-01-25 17:48:33,675] [INFO] Task started: HMMsearch
[2024-01-25 17:48:33,675] [INFO] Running command: hmmsearch --tblout GCF_000761485.1_ASM76148v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgddf6f96b-9997-4be6-846b-ba46353ddca4/dqc_reference/reference_markers.hmm GCF_000761485.1_ASM76148v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:48:33,953] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:48:33,955] [INFO] Found 6/6 markers.
[2024-01-25 17:48:34,002] [INFO] Query marker FASTA was written to GCF_000761485.1_ASM76148v1_genomic.fna/markers.fasta
[2024-01-25 17:48:34,003] [INFO] Task started: Blastn
[2024-01-25 17:48:34,003] [INFO] Running command: blastn -query GCF_000761485.1_ASM76148v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgddf6f96b-9997-4be6-846b-ba46353ddca4/dqc_reference/reference_markers.fasta -out GCF_000761485.1_ASM76148v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:35,238] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:35,243] [INFO] Selected 7 target genomes.
[2024-01-25 17:48:35,244] [INFO] Target genome list was writen to GCF_000761485.1_ASM76148v1_genomic.fna/target_genomes.txt
[2024-01-25 17:48:35,248] [INFO] Task started: fastANI
[2024-01-25 17:48:35,249] [INFO] Running command: fastANI --query /var/lib/cwl/stge7a8e5b5-37ee-4a21-96fa-c0fc616354dc/GCF_000761485.1_ASM76148v1_genomic.fna.gz --refList GCF_000761485.1_ASM76148v1_genomic.fna/target_genomes.txt --output GCF_000761485.1_ASM76148v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:48:44,959] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:44,960] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgddf6f96b-9997-4be6-846b-ba46353ddca4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:48:44,960] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgddf6f96b-9997-4be6-846b-ba46353ddca4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:48:44,966] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:48:44,967] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:48:44,967] [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
Modestobacter caceresii	strain=KNN 45-2b	GCA_000761485.1	1522368	1522368	type	True	100.0	1584	1588	95	conclusive
Modestobacter marinus	strain=DSM 45201	GCA_011758655.1	477641	477641	type	True	91.8602	1263	1588	95	below_threshold
Modestobacter marinus	strain=CGMCC 4.5581	GCA_014645755.1	477641	477641	type	True	91.7764	1278	1588	95	below_threshold
Modestobacter marinus	strain=DSM 45201	GCA_023383595.1	477641	477641	type	True	91.6226	1182	1588	95	below_threshold
Modestobacter versicolor	strain=DSM 16678	GCA_014195485.1	429133	429133	type	True	86.1222	1082	1588	95	below_threshold
Modestobacter excelsi	strain=1G6	GCA_005930495.1	2213161	2213161	type	True	85.1245	1013	1588	95	below_threshold
Modestobacter muralis	strain=DSM 100205	GCA_010682105.1	1608614	1608614	type	True	84.6562	936	1588	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:48:44,968] [INFO] DFAST Taxonomy check result was written to GCF_000761485.1_ASM76148v1_genomic.fna/tc_result.tsv
[2024-01-25 17:48:44,969] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:48:44,969] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:48:44,969] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgddf6f96b-9997-4be6-846b-ba46353ddca4/dqc_reference/checkm_data
[2024-01-25 17:48:44,970] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:48:45,017] [INFO] Task started: CheckM
[2024-01-25 17:48:45,017] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000761485.1_ASM76148v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000761485.1_ASM76148v1_genomic.fna/checkm_input GCF_000761485.1_ASM76148v1_genomic.fna/checkm_result
[2024-01-25 17:49:57,525] [INFO] Task succeeded: CheckM
[2024-01-25 17:49:57,526] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:49:57,548] [INFO] ===== Completeness check finished =====
[2024-01-25 17:49:57,548] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:49:57,549] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000761485.1_ASM76148v1_genomic.fna/markers.fasta)
[2024-01-25 17:49:57,549] [INFO] Task started: Blastn
[2024-01-25 17:49:57,549] [INFO] Running command: blastn -query GCF_000761485.1_ASM76148v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgddf6f96b-9997-4be6-846b-ba46353ddca4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000761485.1_ASM76148v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:59,514] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:59,518] [INFO] Selected 10 target genomes.
[2024-01-25 17:49:59,518] [INFO] Target genome list was writen to GCF_000761485.1_ASM76148v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:49:59,520] [INFO] Task started: fastANI
[2024-01-25 17:49:59,520] [INFO] Running command: fastANI --query /var/lib/cwl/stge7a8e5b5-37ee-4a21-96fa-c0fc616354dc/GCF_000761485.1_ASM76148v1_genomic.fna.gz --refList GCF_000761485.1_ASM76148v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000761485.1_ASM76148v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:50:12,923] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:12,932] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:50:12,932] [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_000761485.1	s__Modestobacter caceresii	100.0	1584	1588	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	98.27	98.27	0.83	0.83	2	conclusive
GCF_011758655.1	s__Modestobacter marinus	91.8877	1261	1588	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014195485.1	s__Modestobacter versicolor	86.191	1075	1588	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	99.97	99.97	1.00	1.00	2	-
GCF_007994135.1	s__Modestobacter roseus	85.5855	1056	1588	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	99.87	99.87	0.97	0.97	2	-
GCF_000306785.1	s__Modestobacter marinus_A	85.303	1101	1588	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005930495.1	s__Modestobacter excelsi	85.1382	1011	1588	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000620205.1	s__Modestobacter sp000620205	85.1216	1045	1588	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010682105.1	s__Modestobacter muralis	84.7017	931	1588	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_019112525.1	s__Modestobacter sp019112525	84.564	980	1588	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408865.1	s__Modestobacter sp013408865	83.669	983	1588	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:50:12,934] [INFO] GTDB search result was written to GCF_000761485.1_ASM76148v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:50:12,934] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:50:12,937] [INFO] DFAST_QC result json was written to GCF_000761485.1_ASM76148v1_genomic.fna/dqc_result.json
[2024-01-25 17:50:12,937] [INFO] DFAST_QC completed!
[2024-01-25 17:50:12,937] [INFO] Total running time: 0h1m52s