[2024-01-24 13:40:34,584] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,588] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,588] [INFO] DQC Reference Directory: /var/lib/cwl/stg06ced1a3-935f-4185-95a6-a6c64166d5fd/dqc_reference
[2024-01-24 13:40:35,994] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:35,994] [INFO] Task started: Prodigal
[2024-01-24 13:40:35,995] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ab16677-8078-497c-8c04-f2a017811d75/GCF_014041935.1_ASM1404193v1_genomic.fna.gz | prodigal -d GCF_014041935.1_ASM1404193v1_genomic.fna/cds.fna -a GCF_014041935.1_ASM1404193v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:01,438] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:01,438] [INFO] Task started: HMMsearch
[2024-01-24 13:41:01,438] [INFO] Running command: hmmsearch --tblout GCF_014041935.1_ASM1404193v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06ced1a3-935f-4185-95a6-a6c64166d5fd/dqc_reference/reference_markers.hmm GCF_014041935.1_ASM1404193v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:01,778] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:01,780] [INFO] Found 6/6 markers.
[2024-01-24 13:41:01,823] [INFO] Query marker FASTA was written to GCF_014041935.1_ASM1404193v1_genomic.fna/markers.fasta
[2024-01-24 13:41:01,823] [INFO] Task started: Blastn
[2024-01-24 13:41:01,823] [INFO] Running command: blastn -query GCF_014041935.1_ASM1404193v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06ced1a3-935f-4185-95a6-a6c64166d5fd/dqc_reference/reference_markers.fasta -out GCF_014041935.1_ASM1404193v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:03,051] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:03,054] [INFO] Selected 11 target genomes.
[2024-01-24 13:41:03,054] [INFO] Target genome list was writen to GCF_014041935.1_ASM1404193v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:03,057] [INFO] Task started: fastANI
[2024-01-24 13:41:03,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ab16677-8078-497c-8c04-f2a017811d75/GCF_014041935.1_ASM1404193v1_genomic.fna.gz --refList GCF_014041935.1_ASM1404193v1_genomic.fna/target_genomes.txt --output GCF_014041935.1_ASM1404193v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:17,351] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:17,352] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06ced1a3-935f-4185-95a6-a6c64166d5fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:17,352] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06ced1a3-935f-4185-95a6-a6c64166d5fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:17,362] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:17,362] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:17,362] [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_014041935.1	2758710	2758710	type	True	100.0	1728	1728	95	conclusive
Gordonia jinghuaiqii	strain=zg-686	GCA_024701535.1	2758710	2758710	type	True	99.9934	1712	1728	95	conclusive
Gordonia westfalica	strain=DSM 44215	GCA_900105725.1	158898	158898	type	True	83.9924	1269	1728	95	below_threshold
Gordonia alkanivorans	strain=NBRC 16433	GCA_000225505.1	84096	84096	type	True	83.6289	1196	1728	95	below_threshold
Gordonia amicalis	strain=DSM 44461	GCA_012395955.1	89053	89053	type	True	83.6227	1163	1728	95	below_threshold
Gordonia namibiensis	strain=NBRC 108229	GCA_000298235.1	168480	168480	type	True	83.6145	1212	1728	95	below_threshold
Gordonia amicalis	strain=NBRC 100051	GCA_000332995.1	89053	89053	type	True	83.5555	1164	1728	95	below_threshold
Gordonia terrae	strain=3612	GCA_001698225.1	2055	2055	suspected-type	True	83.4795	1188	1728	95	below_threshold
Gordonia terrae	strain=NRRL B-16283	GCA_003183825.1	2055	2055	suspected-type	True	83.4673	1195	1728	95	below_threshold
Gordonia lacunae	strain=BS2	GCA_002149015.1	417102	417102	type	True	83.4463	1194	1728	95	below_threshold
Gordonia terrae	strain=NBRC 100016	GCA_000248035.2	2055	2055	suspected-type	True	83.3639	1182	1728	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:17,364] [INFO] DFAST Taxonomy check result was written to GCF_014041935.1_ASM1404193v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:17,365] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:17,365] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:17,365] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06ced1a3-935f-4185-95a6-a6c64166d5fd/dqc_reference/checkm_data
[2024-01-24 13:41:17,366] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:17,420] [INFO] Task started: CheckM
[2024-01-24 13:41:17,421] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014041935.1_ASM1404193v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014041935.1_ASM1404193v1_genomic.fna/checkm_input GCF_014041935.1_ASM1404193v1_genomic.fna/checkm_result
[2024-01-24 13:42:49,554] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:49,555] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:49,578] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:49,578] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:49,579] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014041935.1_ASM1404193v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:49,579] [INFO] Task started: Blastn
[2024-01-24 13:42:49,579] [INFO] Running command: blastn -query GCF_014041935.1_ASM1404193v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06ced1a3-935f-4185-95a6-a6c64166d5fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_014041935.1_ASM1404193v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:51,379] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:51,382] [INFO] Selected 10 target genomes.
[2024-01-24 13:42:51,382] [INFO] Target genome list was writen to GCF_014041935.1_ASM1404193v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:51,392] [INFO] Task started: fastANI
[2024-01-24 13:42:51,393] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ab16677-8078-497c-8c04-f2a017811d75/GCF_014041935.1_ASM1404193v1_genomic.fna.gz --refList GCF_014041935.1_ASM1404193v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014041935.1_ASM1404193v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:04,214] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:04,223] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:04,224] [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	100.0	1728	1728	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	84.0342	1263	1728	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	83.6349	1195	1728	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	83.5931	1215	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.13	97.13	0.90	0.90	2	-
GCF_000143885.2	s__Gordonia sp000143885	83.547	1199	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.85	97.53	0.90	0.88	3	-
GCF_000332995.1	s__Gordonia amicalis	83.531	1166	1728	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	83.5255	1208	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.70	97.37	0.91	0.88	14	-
GCF_000327325.1	s__Gordonia rubripertincta	83.5059	1184	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.55	98.07	0.91	0.87	6	-
GCF_001698225.1	s__Gordonia terrae	83.4737	1189	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.37	97.67	0.96	0.87	7	-
GCF_002149015.1	s__Gordonia lacunae	83.4532	1192	1728	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 13:43:04,225] [INFO] GTDB search result was written to GCF_014041935.1_ASM1404193v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:04,226] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:04,229] [INFO] DFAST_QC result json was written to GCF_014041935.1_ASM1404193v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:04,229] [INFO] DFAST_QC completed!
[2024-01-24 13:43:04,229] [INFO] Total running time: 0h2m30s