[2024-01-24 12:23:03,402] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,404] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,404] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc8b8cb9-5641-4344-a4d6-39e1e870e743/dqc_reference
[2024-01-24 12:23:04,697] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:04,698] [INFO] Task started: Prodigal
[2024-01-24 12:23:04,698] [INFO] Running command: gunzip -c /var/lib/cwl/stgff5337f7-5282-4a21-b83a-83ba091a0412/GCF_024701535.1_ASM2470153v1_genomic.fna.gz | prodigal -d GCF_024701535.1_ASM2470153v1_genomic.fna/cds.fna -a GCF_024701535.1_ASM2470153v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:22,778] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:22,778] [INFO] Task started: HMMsearch
[2024-01-24 12:23:22,778] [INFO] Running command: hmmsearch --tblout GCF_024701535.1_ASM2470153v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc8b8cb9-5641-4344-a4d6-39e1e870e743/dqc_reference/reference_markers.hmm GCF_024701535.1_ASM2470153v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:23,058] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:23,060] [INFO] Found 6/6 markers.
[2024-01-24 12:23:23,105] [INFO] Query marker FASTA was written to GCF_024701535.1_ASM2470153v1_genomic.fna/markers.fasta
[2024-01-24 12:23:23,105] [INFO] Task started: Blastn
[2024-01-24 12:23:23,105] [INFO] Running command: blastn -query GCF_024701535.1_ASM2470153v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc8b8cb9-5641-4344-a4d6-39e1e870e743/dqc_reference/reference_markers.fasta -out GCF_024701535.1_ASM2470153v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:24,335] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:24,338] [INFO] Selected 11 target genomes.
[2024-01-24 12:23:24,338] [INFO] Target genome list was writen to GCF_024701535.1_ASM2470153v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:24,344] [INFO] Task started: fastANI
[2024-01-24 12:23:24,345] [INFO] Running command: fastANI --query /var/lib/cwl/stgff5337f7-5282-4a21-b83a-83ba091a0412/GCF_024701535.1_ASM2470153v1_genomic.fna.gz --refList GCF_024701535.1_ASM2470153v1_genomic.fna/target_genomes.txt --output GCF_024701535.1_ASM2470153v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:38,099] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:38,099] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc8b8cb9-5641-4344-a4d6-39e1e870e743/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:38,100] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc8b8cb9-5641-4344-a4d6-39e1e870e743/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:38,115] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:23:38,115] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:38,115] [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 jinghuaiqii	strain=zg-686	GCA_024701535.1	2758710	2758710	type	True	100.0	1727	1735	95	conclusive
Gordonia jinghuaiqii	strain=zg-686	GCA_014041935.1	2758710	2758710	type	True	99.9998	1712	1735	95	conclusive
Gordonia westfalica	strain=DSM 44215	GCA_900105725.1	158898	158898	type	True	83.9963	1248	1735	95	below_threshold
Gordonia alkanivorans	strain=NBRC 16433	GCA_000225505.1	84096	84096	type	True	83.659	1184	1735	95	below_threshold
Gordonia namibiensis	strain=NBRC 108229	GCA_000298235.1	168480	168480	type	True	83.6444	1212	1735	95	below_threshold
Gordonia amicalis	strain=NBRC 100051	GCA_000332995.1	89053	89053	type	True	83.5488	1167	1735	95	below_threshold
Gordonia amicalis	strain=DSM 44461	GCA_012395955.1	89053	89053	type	True	83.5399	1169	1735	95	below_threshold
Gordonia lacunae	strain=BS2	GCA_002149015.1	417102	417102	type	True	83.4221	1198	1735	95	below_threshold
Gordonia terrae	strain=3612	GCA_001698225.1	2055	2055	suspected-type	True	83.4014	1192	1735	95	below_threshold
Gordonia terrae	strain=NRRL B-16283	GCA_003183825.1	2055	2055	suspected-type	True	83.324	1214	1735	95	below_threshold
Gordonia terrae	strain=NBRC 100016	GCA_000248035.2	2055	2055	suspected-type	True	83.2978	1185	1735	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:38,117] [INFO] DFAST Taxonomy check result was written to GCF_024701535.1_ASM2470153v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:38,118] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:38,118] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:38,118] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc8b8cb9-5641-4344-a4d6-39e1e870e743/dqc_reference/checkm_data
[2024-01-24 12:23:38,119] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:38,171] [INFO] Task started: CheckM
[2024-01-24 12:23:38,171] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024701535.1_ASM2470153v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024701535.1_ASM2470153v1_genomic.fna/checkm_input GCF_024701535.1_ASM2470153v1_genomic.fna/checkm_result
[2024-01-24 12:24:38,990] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:38,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 12.50%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:39,026] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:39,026] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:39,027] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024701535.1_ASM2470153v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:39,027] [INFO] Task started: Blastn
[2024-01-24 12:24:39,027] [INFO] Running command: blastn -query GCF_024701535.1_ASM2470153v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc8b8cb9-5641-4344-a4d6-39e1e870e743/dqc_reference/reference_markers_gtdb.fasta -out GCF_024701535.1_ASM2470153v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:40,818] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:40,822] [INFO] Selected 10 target genomes.
[2024-01-24 12:24:40,822] [INFO] Target genome list was writen to GCF_024701535.1_ASM2470153v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:40,834] [INFO] Task started: fastANI
[2024-01-24 12:24:40,834] [INFO] Running command: fastANI --query /var/lib/cwl/stgff5337f7-5282-4a21-b83a-83ba091a0412/GCF_024701535.1_ASM2470153v1_genomic.fna.gz --refList GCF_024701535.1_ASM2470153v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024701535.1_ASM2470153v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:53,558] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:53,568] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:53,568] [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
GCA_014041935.1	s__Gordonia sp014041935	99.9998	1712	1735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.20	99.20	0.95	0.95	2	conclusive
GCF_900105725.1	s__Gordonia westfalica	84.0276	1245	1735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000225505.1	s__Gordonia alkanivorans	83.6726	1182	1735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.26	97.87	0.90	0.88	6	-
GCF_000298235.1	s__Gordonia namibiensis	83.6498	1211	1735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.13	97.13	0.90	0.90	2	-
GCF_000327325.1	s__Gordonia rubripertincta	83.5463	1173	1735	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	83.5283	1169	1735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.45	97.39	0.94	0.91	7	-
GCF_011290605.1	s__Gordonia sp002009645	83.5109	1189	1735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.70	97.37	0.91	0.88	14	-
GCF_000143885.2	s__Gordonia sp000143885	83.5104	1193	1735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.85	97.53	0.90	0.88	3	-
GCF_002149015.1	s__Gordonia lacunae	83.4255	1198	1735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001698225.1	s__Gordonia terrae	83.3906	1194	1735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.37	97.67	0.96	0.87	7	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:53,570] [INFO] GTDB search result was written to GCF_024701535.1_ASM2470153v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:53,571] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:53,576] [INFO] DFAST_QC result json was written to GCF_024701535.1_ASM2470153v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:53,577] [INFO] DFAST_QC completed!
[2024-01-24 12:24:53,577] [INFO] Total running time: 0h1m50s