[2024-01-25 18:53:05,894] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:53:05,897] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:53:05,897] [INFO] DQC Reference Directory: /var/lib/cwl/stga783c774-c176-4bfd-9e2b-9aa3ff34d012/dqc_reference
[2024-01-25 18:53:07,084] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:53:07,087] [INFO] Task started: Prodigal
[2024-01-25 18:53:07,087] [INFO] Running command: gunzip -c /var/lib/cwl/stg53aba966-dcaa-4bd1-8537-9c36f8035a98/GCF_012396285.1_ASM1239628v1_genomic.fna.gz | prodigal -d GCF_012396285.1_ASM1239628v1_genomic.fna/cds.fna -a GCF_012396285.1_ASM1239628v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:53:34,088] [INFO] Task succeeded: Prodigal
[2024-01-25 18:53:34,089] [INFO] Task started: HMMsearch
[2024-01-25 18:53:34,089] [INFO] Running command: hmmsearch --tblout GCF_012396285.1_ASM1239628v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga783c774-c176-4bfd-9e2b-9aa3ff34d012/dqc_reference/reference_markers.hmm GCF_012396285.1_ASM1239628v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:53:34,447] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:53:34,448] [INFO] Found 6/6 markers.
[2024-01-25 18:53:34,521] [INFO] Query marker FASTA was written to GCF_012396285.1_ASM1239628v1_genomic.fna/markers.fasta
[2024-01-25 18:53:34,522] [INFO] Task started: Blastn
[2024-01-25 18:53:34,522] [INFO] Running command: blastn -query GCF_012396285.1_ASM1239628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga783c774-c176-4bfd-9e2b-9aa3ff34d012/dqc_reference/reference_markers.fasta -out GCF_012396285.1_ASM1239628v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:35,712] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:35,715] [INFO] Selected 7 target genomes.
[2024-01-25 18:53:35,715] [INFO] Target genome list was writen to GCF_012396285.1_ASM1239628v1_genomic.fna/target_genomes.txt
[2024-01-25 18:53:35,719] [INFO] Task started: fastANI
[2024-01-25 18:53:35,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg53aba966-dcaa-4bd1-8537-9c36f8035a98/GCF_012396285.1_ASM1239628v1_genomic.fna.gz --refList GCF_012396285.1_ASM1239628v1_genomic.fna/target_genomes.txt --output GCF_012396285.1_ASM1239628v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:53:45,620] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:45,621] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga783c774-c176-4bfd-9e2b-9aa3ff34d012/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:53:45,621] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga783c774-c176-4bfd-9e2b-9aa3ff34d012/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:53:45,628] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:53:45,628] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:53:45,628] [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 polyisoprenivorans	strain=ATCC BAA-14	GCA_012396285.1	84595	84595	type	True	100.0	2065	2068	95	conclusive
Gordonia polyisoprenivorans	strain=NBRC 16320	GCA_000241325.2	84595	84595	type	True	99.991	2029	2068	95	conclusive
Gordonia oryzae	strain=RS15-1S	GCA_003797185.1	2487349	2487349	type	True	92.5675	1326	2068	95	below_threshold
Gordonia desulfuricans	strain=NBRC 100010	GCA_001485495.1	89051	89051	type	True	81.0499	1011	2068	95	below_threshold
Gordonia desulfuricans	strain=213E	GCA_010119475.1	89051	89051	type	True	80.9324	1045	2068	95	below_threshold
Gordonia rubripertincta	strain=NBRC 101908	GCA_000327325.1	36822	36822	type	True	80.2093	819	2068	95	below_threshold
Gordonia rubripertincta	strain=ATCC 14352	GCA_012396225.1	36822	36822	type	True	79.799	825	2068	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:53:45,629] [INFO] DFAST Taxonomy check result was written to GCF_012396285.1_ASM1239628v1_genomic.fna/tc_result.tsv
[2024-01-25 18:53:45,631] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:53:45,631] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:53:45,631] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga783c774-c176-4bfd-9e2b-9aa3ff34d012/dqc_reference/checkm_data
[2024-01-25 18:53:45,632] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:53:45,692] [INFO] Task started: CheckM
[2024-01-25 18:53:45,692] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012396285.1_ASM1239628v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012396285.1_ASM1239628v1_genomic.fna/checkm_input GCF_012396285.1_ASM1239628v1_genomic.fna/checkm_result
[2024-01-25 18:55:48,856] [INFO] Task succeeded: CheckM
[2024-01-25 18:55:48,857] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:55:48,884] [INFO] ===== Completeness check finished =====
[2024-01-25 18:55:48,885] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:55:48,886] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012396285.1_ASM1239628v1_genomic.fna/markers.fasta)
[2024-01-25 18:55:48,886] [INFO] Task started: Blastn
[2024-01-25 18:55:48,886] [INFO] Running command: blastn -query GCF_012396285.1_ASM1239628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga783c774-c176-4bfd-9e2b-9aa3ff34d012/dqc_reference/reference_markers_gtdb.fasta -out GCF_012396285.1_ASM1239628v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:50,593] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:50,595] [INFO] Selected 9 target genomes.
[2024-01-25 18:55:50,595] [INFO] Target genome list was writen to GCF_012396285.1_ASM1239628v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:55:50,601] [INFO] Task started: fastANI
[2024-01-25 18:55:50,601] [INFO] Running command: fastANI --query /var/lib/cwl/stg53aba966-dcaa-4bd1-8537-9c36f8035a98/GCF_012396285.1_ASM1239628v1_genomic.fna.gz --refList GCF_012396285.1_ASM1239628v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012396285.1_ASM1239628v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:56:03,069] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:03,075] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:56:03,076] [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_000241325.1	s__Gordonia polyisoprenivorans	99.991	2029	2068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.60	97.62	0.90	0.79	11	conclusive
GCF_017654315.1	s__Gordonia polyisoprenivorans_A	94.3883	1698	2068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797185.1	s__Gordonia oryzae	92.5541	1327	2068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001485495.1	s__Gordonia desulfuricans	81.034	1013	2068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.37	98.77	0.95	0.92	3	-
GCF_000327325.1	s__Gordonia rubripertincta	80.2371	815	2068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.55	98.07	0.91	0.87	6	-
GCF_000332995.1	s__Gordonia amicalis	80.0489	800	2068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.45	97.39	0.94	0.91	7	-
GCF_003797825.1	s__Gordonia sp003797825	79.9627	873	2068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000298235.1	s__Gordonia namibiensis	79.7667	816	2068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.13	97.13	0.90	0.90	2	-
GCA_004193205.1	s__Gordonia sediminis	79.7267	878	2068	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 18:56:03,078] [INFO] GTDB search result was written to GCF_012396285.1_ASM1239628v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:56:03,078] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:56:03,082] [INFO] DFAST_QC result json was written to GCF_012396285.1_ASM1239628v1_genomic.fna/dqc_result.json
[2024-01-25 18:56:03,082] [INFO] DFAST_QC completed!
[2024-01-25 18:56:03,082] [INFO] Total running time: 0h2m57s