[2024-01-25 19:11:05,659] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:11:05,661] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:11:05,661] [INFO] DQC Reference Directory: /var/lib/cwl/stg04f47a98-4ac3-4c50-ba17-20ba27b6a3ef/dqc_reference
[2024-01-25 19:11:06,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:11:06,787] [INFO] Task started: Prodigal
[2024-01-25 19:11:06,787] [INFO] Running command: gunzip -c /var/lib/cwl/stg3cd22374-f73b-4ba7-9ab1-c2cda618b3b4/GCF_009932475.1_ASM993247v1_genomic.fna.gz | prodigal -d GCF_009932475.1_ASM993247v1_genomic.fna/cds.fna -a GCF_009932475.1_ASM993247v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:11:19,519] [INFO] Task succeeded: Prodigal
[2024-01-25 19:11:19,520] [INFO] Task started: HMMsearch
[2024-01-25 19:11:19,520] [INFO] Running command: hmmsearch --tblout GCF_009932475.1_ASM993247v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04f47a98-4ac3-4c50-ba17-20ba27b6a3ef/dqc_reference/reference_markers.hmm GCF_009932475.1_ASM993247v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:11:19,823] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:11:19,828] [INFO] Found 6/6 markers.
[2024-01-25 19:11:19,869] [INFO] Query marker FASTA was written to GCF_009932475.1_ASM993247v1_genomic.fna/markers.fasta
[2024-01-25 19:11:19,869] [INFO] Task started: Blastn
[2024-01-25 19:11:19,869] [INFO] Running command: blastn -query GCF_009932475.1_ASM993247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04f47a98-4ac3-4c50-ba17-20ba27b6a3ef/dqc_reference/reference_markers.fasta -out GCF_009932475.1_ASM993247v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:21,093] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:21,096] [INFO] Selected 9 target genomes.
[2024-01-25 19:11:21,096] [INFO] Target genome list was writen to GCF_009932475.1_ASM993247v1_genomic.fna/target_genomes.txt
[2024-01-25 19:11:21,102] [INFO] Task started: fastANI
[2024-01-25 19:11:21,102] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cd22374-f73b-4ba7-9ab1-c2cda618b3b4/GCF_009932475.1_ASM993247v1_genomic.fna.gz --refList GCF_009932475.1_ASM993247v1_genomic.fna/target_genomes.txt --output GCF_009932475.1_ASM993247v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:11:31,107] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:31,108] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04f47a98-4ac3-4c50-ba17-20ba27b6a3ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:11:31,108] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04f47a98-4ac3-4c50-ba17-20ba27b6a3ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:11:31,115] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:11:31,115] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:11:31,115] [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 spumicola	strain=NBRC 107696	GCA_009932475.1	589161	589161	type	True	100.0	1598	1624	95	conclusive
Gordonia malaquae	strain=DSM 45064	GCA_900105435.1	410332	410332	type	True	84.7584	1111	1624	95	below_threshold
Gordonia malaquae	strain=NBRC 108250	GCA_000344135.1	410332	410332	type	True	84.4862	1087	1624	95	below_threshold
Gordonia humi	strain=DSM 45298	GCA_014197435.1	686429	686429	type	True	81.566	914	1624	95	below_threshold
Gordonia phthalatica	strain=QH-11	GCA_001305675.1	1136941	1136941	type	True	81.0372	806	1624	95	below_threshold
Gordonia neofelifaecis	strain=NRRL B-59395	GCA_000192435.2	945692	945692	type	True	81.009	804	1624	95	below_threshold
Gordonia zhaorongruii	strain=HY186	GCA_007559005.1	2597659	2597659	type	True	80.7164	706	1624	95	below_threshold
Gordonia hydrophobica	strain=NBRC 16057	GCA_001592365.1	40516	40516	type	True	80.3426	744	1624	95	below_threshold
Gordonia pseudamarae	strain=CON9	GCA_025273675.1	2831662	2831662	type	True	78.6368	503	1624	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:11:31,117] [INFO] DFAST Taxonomy check result was written to GCF_009932475.1_ASM993247v1_genomic.fna/tc_result.tsv
[2024-01-25 19:11:31,117] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:11:31,117] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:11:31,117] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04f47a98-4ac3-4c50-ba17-20ba27b6a3ef/dqc_reference/checkm_data
[2024-01-25 19:11:31,118] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:11:31,164] [INFO] Task started: CheckM
[2024-01-25 19:11:31,164] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009932475.1_ASM993247v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009932475.1_ASM993247v1_genomic.fna/checkm_input GCF_009932475.1_ASM993247v1_genomic.fna/checkm_result
[2024-01-25 19:12:21,018] [INFO] Task succeeded: CheckM
[2024-01-25 19:12:21,019] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:12:21,037] [INFO] ===== Completeness check finished =====
[2024-01-25 19:12:21,037] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:12:21,038] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009932475.1_ASM993247v1_genomic.fna/markers.fasta)
[2024-01-25 19:12:21,038] [INFO] Task started: Blastn
[2024-01-25 19:12:21,038] [INFO] Running command: blastn -query GCF_009932475.1_ASM993247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04f47a98-4ac3-4c50-ba17-20ba27b6a3ef/dqc_reference/reference_markers_gtdb.fasta -out GCF_009932475.1_ASM993247v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:22,915] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:22,917] [INFO] Selected 9 target genomes.
[2024-01-25 19:12:22,917] [INFO] Target genome list was writen to GCF_009932475.1_ASM993247v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:12:22,924] [INFO] Task started: fastANI
[2024-01-25 19:12:22,924] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cd22374-f73b-4ba7-9ab1-c2cda618b3b4/GCF_009932475.1_ASM993247v1_genomic.fna.gz --refList GCF_009932475.1_ASM993247v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009932475.1_ASM993247v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:12:32,528] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:32,534] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:12:32,534] [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_009932475.1	s__Gordonia spumicola	100.0	1600	1624	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_000344135.1	s__Gordonia malaquae	84.4865	1087	1624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016919385.1	s__Gordonia sp016919385	83.6895	1046	1624	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	81.5839	912	1624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305675.1	s__Gordonia phthalatica	81.0182	808	1624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007559005.1	s__Gordonia sp004353055	80.699	708	1624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.65	99.65	0.97	0.97	2	-
GCA_012515855.1	s__Gordonia sp012515855	80.4009	640	1624	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	80.3044	749	1624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002993285.1	s__Gordonia iterans	79.6636	654	1624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:12:32,536] [INFO] GTDB search result was written to GCF_009932475.1_ASM993247v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:12:32,537] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:12:32,539] [INFO] DFAST_QC result json was written to GCF_009932475.1_ASM993247v1_genomic.fna/dqc_result.json
[2024-01-25 19:12:32,539] [INFO] DFAST_QC completed!
[2024-01-25 19:12:32,539] [INFO] Total running time: 0h1m27s