[2024-01-24 13:40:45,096] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:45,099] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:45,099] [INFO] DQC Reference Directory: /var/lib/cwl/stg82a4a869-8cef-494d-9023-7ad8a17d6ef3/dqc_reference
[2024-01-24 13:40:46,395] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:46,396] [INFO] Task started: Prodigal
[2024-01-24 13:40:46,396] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf43075d-a0f4-4819-8bde-008d20391f70/GCF_001592365.1_ASM159236v1_genomic.fna.gz | prodigal -d GCF_001592365.1_ASM159236v1_genomic.fna/cds.fna -a GCF_001592365.1_ASM159236v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:00,044] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:00,044] [INFO] Task started: HMMsearch
[2024-01-24 13:41:00,044] [INFO] Running command: hmmsearch --tblout GCF_001592365.1_ASM159236v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82a4a869-8cef-494d-9023-7ad8a17d6ef3/dqc_reference/reference_markers.hmm GCF_001592365.1_ASM159236v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:00,338] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:00,339] [INFO] Found 6/6 markers.
[2024-01-24 13:41:00,384] [INFO] Query marker FASTA was written to GCF_001592365.1_ASM159236v1_genomic.fna/markers.fasta
[2024-01-24 13:41:00,384] [INFO] Task started: Blastn
[2024-01-24 13:41:00,384] [INFO] Running command: blastn -query GCF_001592365.1_ASM159236v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82a4a869-8cef-494d-9023-7ad8a17d6ef3/dqc_reference/reference_markers.fasta -out GCF_001592365.1_ASM159236v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:01,505] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:01,515] [INFO] Selected 8 target genomes.
[2024-01-24 13:41:01,516] [INFO] Target genome list was writen to GCF_001592365.1_ASM159236v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:01,521] [INFO] Task started: fastANI
[2024-01-24 13:41:01,521] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf43075d-a0f4-4819-8bde-008d20391f70/GCF_001592365.1_ASM159236v1_genomic.fna.gz --refList GCF_001592365.1_ASM159236v1_genomic.fna/target_genomes.txt --output GCF_001592365.1_ASM159236v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:10,051] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:10,051] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82a4a869-8cef-494d-9023-7ad8a17d6ef3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:10,052] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82a4a869-8cef-494d-9023-7ad8a17d6ef3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:10,063] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:10,063] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:10,064] [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 hydrophobica	strain=NBRC 16057	GCA_001592365.1	40516	40516	type	True	100.0	1504	1506	95	conclusive
Gordonia phthalatica	strain=QH-11	GCA_001305675.1	1136941	1136941	type	True	84.6295	1047	1506	95	below_threshold
Gordonia neofelifaecis	strain=NRRL B-59395	GCA_000192435.2	945692	945692	type	True	82.0483	902	1506	95	below_threshold
Gordonia sihwensis	strain=NBRC 108236	GCA_000333035.1	173559	173559	type	True	81.5978	860	1506	95	below_threshold
Gordonia shandongensis	strain=DSM 45094	GCA_000423025.1	376351	376351	type	True	80.741	703	1506	95	below_threshold
Gordonia spumicola	strain=NBRC 107696	GCA_009932475.1	589161	589161	type	True	80.2652	753	1506	95	below_threshold
Gordonia humi	strain=DSM 45298	GCA_014197435.1	686429	686429	type	True	80.1307	794	1506	95	below_threshold
Gordonia pseudamarae	strain=CON9	GCA_025273675.1	2831662	2831662	type	True	78.033	467	1506	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:10,077] [INFO] DFAST Taxonomy check result was written to GCF_001592365.1_ASM159236v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:10,078] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:10,078] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:10,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82a4a869-8cef-494d-9023-7ad8a17d6ef3/dqc_reference/checkm_data
[2024-01-24 13:41:10,080] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:10,127] [INFO] Task started: CheckM
[2024-01-24 13:41:10,127] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001592365.1_ASM159236v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001592365.1_ASM159236v1_genomic.fna/checkm_input GCF_001592365.1_ASM159236v1_genomic.fna/checkm_result
[2024-01-24 13:41:56,165] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:56,166] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:56,187] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:56,187] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:56,188] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001592365.1_ASM159236v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:56,188] [INFO] Task started: Blastn
[2024-01-24 13:41:56,188] [INFO] Running command: blastn -query GCF_001592365.1_ASM159236v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82a4a869-8cef-494d-9023-7ad8a17d6ef3/dqc_reference/reference_markers_gtdb.fasta -out GCF_001592365.1_ASM159236v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:57,839] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:57,842] [INFO] Selected 8 target genomes.
[2024-01-24 13:41:57,842] [INFO] Target genome list was writen to GCF_001592365.1_ASM159236v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:57,864] [INFO] Task started: fastANI
[2024-01-24 13:41:57,865] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf43075d-a0f4-4819-8bde-008d20391f70/GCF_001592365.1_ASM159236v1_genomic.fna.gz --refList GCF_001592365.1_ASM159236v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001592365.1_ASM159236v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:06,179] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:06,192] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:06,192] [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_001592365.1	s__Gordonia hydrophobica	100.0	1504	1506	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001305675.1	s__Gordonia phthalatica	84.6488	1045	1506	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012515855.1	s__Gordonia sp012515855	82.6896	817	1506	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000192435.1	s__Gordonia neofelifaecis	82.0986	896	1506	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	81.5975	860	1506	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.38	98.97	0.93	0.88	4	-
GCF_000423025.1	s__Gordonia shandongensis	80.7556	701	1506	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009932475.1	s__Gordonia spumicola	80.2655	753	1506	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	80.0892	800	1506	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:06,194] [INFO] GTDB search result was written to GCF_001592365.1_ASM159236v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:06,195] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:06,198] [INFO] DFAST_QC result json was written to GCF_001592365.1_ASM159236v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:06,198] [INFO] DFAST_QC completed!
[2024-01-24 13:42:06,198] [INFO] Total running time: 0h1m21s