[2024-01-24 13:57:56,272] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:56,274] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:56,274] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d85be67-647b-450c-9c66-e463f6a4d0fc/dqc_reference
[2024-01-24 13:57:57,563] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:57,564] [INFO] Task started: Prodigal
[2024-01-24 13:57:57,564] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ab7984c-2fd1-48e4-90cf-8365cd5e65c9/GCF_000423025.1_ASM42302v1_genomic.fna.gz | prodigal -d GCF_000423025.1_ASM42302v1_genomic.fna/cds.fna -a GCF_000423025.1_ASM42302v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:07,857] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:07,857] [INFO] Task started: HMMsearch
[2024-01-24 13:58:07,858] [INFO] Running command: hmmsearch --tblout GCF_000423025.1_ASM42302v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d85be67-647b-450c-9c66-e463f6a4d0fc/dqc_reference/reference_markers.hmm GCF_000423025.1_ASM42302v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:08,155] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:08,156] [INFO] Found 6/6 markers.
[2024-01-24 13:58:08,188] [INFO] Query marker FASTA was written to GCF_000423025.1_ASM42302v1_genomic.fna/markers.fasta
[2024-01-24 13:58:08,188] [INFO] Task started: Blastn
[2024-01-24 13:58:08,189] [INFO] Running command: blastn -query GCF_000423025.1_ASM42302v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d85be67-647b-450c-9c66-e463f6a4d0fc/dqc_reference/reference_markers.fasta -out GCF_000423025.1_ASM42302v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:09,409] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:09,412] [INFO] Selected 9 target genomes.
[2024-01-24 13:58:09,412] [INFO] Target genome list was writen to GCF_000423025.1_ASM42302v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:09,418] [INFO] Task started: fastANI
[2024-01-24 13:58:09,419] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ab7984c-2fd1-48e4-90cf-8365cd5e65c9/GCF_000423025.1_ASM42302v1_genomic.fna.gz --refList GCF_000423025.1_ASM42302v1_genomic.fna/target_genomes.txt --output GCF_000423025.1_ASM42302v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:18,128] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:18,129] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d85be67-647b-450c-9c66-e463f6a4d0fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:18,129] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d85be67-647b-450c-9c66-e463f6a4d0fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:18,138] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:18,138] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:18,139] [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
Gordonia shandongensis	strain=DSM 45094	GCA_000423025.1	376351	376351	type	True	100.0	1088	1094	95	conclusive
Gordonia phthalatica	strain=QH-11	GCA_001305675.1	1136941	1136941	type	True	81.1676	751	1094	95	below_threshold
Gordonia sihwensis	strain=NBRC 108236	GCA_000333035.1	173559	173559	type	True	80.9799	702	1094	95	below_threshold
Gordonia neofelifaecis	strain=NRRL B-59395	GCA_000192435.2	945692	945692	type	True	80.7953	748	1094	95	below_threshold
Gordonia hydrophobica	strain=NBRC 16057	GCA_001592365.1	40516	40516	type	True	80.6841	725	1094	95	below_threshold
Gordonia spumicola	strain=NBRC 107696	GCA_009932475.1	589161	589161	type	True	80.027	655	1094	95	below_threshold
Gordonia humi	strain=DSM 45298	GCA_014197435.1	686429	686429	type	True	79.9528	641	1094	95	below_threshold
Gordonia malaquae	strain=DSM 45064	GCA_900105435.1	410332	410332	type	True	79.4794	620	1094	95	below_threshold
Gordonia paraffinivorans	strain=NBRC 108238	GCA_000344155.1	175628	175628	type	True	79.0102	529	1094	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:18,140] [INFO] DFAST Taxonomy check result was written to GCF_000423025.1_ASM42302v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:18,141] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:18,141] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:18,142] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d85be67-647b-450c-9c66-e463f6a4d0fc/dqc_reference/checkm_data
[2024-01-24 13:58:18,143] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:18,181] [INFO] Task started: CheckM
[2024-01-24 13:58:18,181] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000423025.1_ASM42302v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000423025.1_ASM42302v1_genomic.fna/checkm_input GCF_000423025.1_ASM42302v1_genomic.fna/checkm_result
[2024-01-24 13:59:10,356] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:10,357] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:10,379] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:10,379] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:10,380] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000423025.1_ASM42302v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:10,380] [INFO] Task started: Blastn
[2024-01-24 13:59:10,380] [INFO] Running command: blastn -query GCF_000423025.1_ASM42302v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d85be67-647b-450c-9c66-e463f6a4d0fc/dqc_reference/reference_markers_gtdb.fasta -out GCF_000423025.1_ASM42302v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:12,144] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:12,147] [INFO] Selected 9 target genomes.
[2024-01-24 13:59:12,148] [INFO] Target genome list was writen to GCF_000423025.1_ASM42302v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:12,156] [INFO] Task started: fastANI
[2024-01-24 13:59:12,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ab7984c-2fd1-48e4-90cf-8365cd5e65c9/GCF_000423025.1_ASM42302v1_genomic.fna.gz --refList GCF_000423025.1_ASM42302v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000423025.1_ASM42302v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:20,500] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:20,509] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:20,509] [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_000423025.1	s__Gordonia shandongensis	100.0	1088	1094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001305675.1	s__Gordonia phthalatica	81.1615	753	1094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000333035.1	s__Gordonia sihwensis	80.9705	703	1094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.38	98.97	0.93	0.88	4	-
GCF_000192435.1	s__Gordonia neofelifaecis	80.8072	747	1094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592365.1	s__Gordonia hydrophobica	80.689	724	1094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009932475.1	s__Gordonia spumicola	80.0055	658	1094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197435.1	s__Gordonia humi	79.9611	640	1094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000344135.1	s__Gordonia malaquae	79.453	609	1094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000344155.1	s__Gordonia paraffinivorans	79.0538	524	1094	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.97	98.74	0.93	0.90	12	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:20,511] [INFO] GTDB search result was written to GCF_000423025.1_ASM42302v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:20,511] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:20,514] [INFO] DFAST_QC result json was written to GCF_000423025.1_ASM42302v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:20,514] [INFO] DFAST_QC completed!
[2024-01-24 13:59:20,514] [INFO] Total running time: 0h1m24s