[2024-01-25 18:57:50,931] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:57:50,932] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:57:50,932] [INFO] DQC Reference Directory: /var/lib/cwl/stge14142a9-0e77-47e7-b62f-71f56518d60d/dqc_reference
[2024-01-25 18:57:52,136] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:57:52,137] [INFO] Task started: Prodigal
[2024-01-25 18:57:52,137] [INFO] Running command: gunzip -c /var/lib/cwl/stg623d6521-fd90-4d0f-ad16-e19a1a0e4dcc/GCF_014197435.1_ASM1419743v1_genomic.fna.gz | prodigal -d GCF_014197435.1_ASM1419743v1_genomic.fna/cds.fna -a GCF_014197435.1_ASM1419743v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:58:05,684] [INFO] Task succeeded: Prodigal
[2024-01-25 18:58:05,684] [INFO] Task started: HMMsearch
[2024-01-25 18:58:05,684] [INFO] Running command: hmmsearch --tblout GCF_014197435.1_ASM1419743v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge14142a9-0e77-47e7-b62f-71f56518d60d/dqc_reference/reference_markers.hmm GCF_014197435.1_ASM1419743v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:58:06,051] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:58:06,053] [INFO] Found 6/6 markers.
[2024-01-25 18:58:06,120] [INFO] Query marker FASTA was written to GCF_014197435.1_ASM1419743v1_genomic.fna/markers.fasta
[2024-01-25 18:58:06,121] [INFO] Task started: Blastn
[2024-01-25 18:58:06,121] [INFO] Running command: blastn -query GCF_014197435.1_ASM1419743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge14142a9-0e77-47e7-b62f-71f56518d60d/dqc_reference/reference_markers.fasta -out GCF_014197435.1_ASM1419743v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:07,283] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:07,286] [INFO] Selected 11 target genomes.
[2024-01-25 18:58:07,286] [INFO] Target genome list was writen to GCF_014197435.1_ASM1419743v1_genomic.fna/target_genomes.txt
[2024-01-25 18:58:07,298] [INFO] Task started: fastANI
[2024-01-25 18:58:07,298] [INFO] Running command: fastANI --query /var/lib/cwl/stg623d6521-fd90-4d0f-ad16-e19a1a0e4dcc/GCF_014197435.1_ASM1419743v1_genomic.fna.gz --refList GCF_014197435.1_ASM1419743v1_genomic.fna/target_genomes.txt --output GCF_014197435.1_ASM1419743v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:58:19,262] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:19,262] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge14142a9-0e77-47e7-b62f-71f56518d60d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:58:19,263] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge14142a9-0e77-47e7-b62f-71f56518d60d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:58:19,271] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:58:19,271] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:58:19,272] [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 humi	strain=DSM 45298	GCA_014197435.1	686429	686429	type	True	100.0	1692	1694	95	conclusive
Gordonia spumicola	strain=NBRC 107696	GCA_009932475.1	589161	589161	type	True	81.6508	880	1694	95	below_threshold
Gordonia malaquae	strain=DSM 45064	GCA_900105435.1	410332	410332	type	True	80.9012	835	1694	95	below_threshold
Gordonia malaquae	strain=NBRC 108250	GCA_000344135.1	410332	410332	type	True	80.8824	808	1694	95	below_threshold
Gordonia phthalatica	strain=QH-11	GCA_001305675.1	1136941	1136941	type	True	80.8026	785	1694	95	below_threshold
Gordonia zhaorongruii	strain=HY186	GCA_007559005.1	2597659	2597659	type	True	80.5973	701	1694	95	below_threshold
Gordonia neofelifaecis	strain=NRRL B-59395	GCA_000192435.2	945692	945692	type	True	80.3976	735	1694	95	below_threshold
Gordonia shandongensis	strain=DSM 45094	GCA_000423025.1	376351	376351	type	True	80.0543	629	1694	95	below_threshold
Gordonia hydrophobica	strain=NBRC 16057	GCA_001592365.1	40516	40516	type	True	80.0293	805	1694	95	below_threshold
Gordonia westfalica	strain=DSM 44215	GCA_900105725.1	158898	158898	type	True	79.1497	628	1694	95	below_threshold
Gordonia alkanivorans	strain=NBRC 16433	GCA_000225505.1	84096	84096	type	True	79.0098	579	1694	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:58:19,273] [INFO] DFAST Taxonomy check result was written to GCF_014197435.1_ASM1419743v1_genomic.fna/tc_result.tsv
[2024-01-25 18:58:19,274] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:58:19,274] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:58:19,274] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge14142a9-0e77-47e7-b62f-71f56518d60d/dqc_reference/checkm_data
[2024-01-25 18:58:19,275] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:58:19,338] [INFO] Task started: CheckM
[2024-01-25 18:58:19,338] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014197435.1_ASM1419743v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014197435.1_ASM1419743v1_genomic.fna/checkm_input GCF_014197435.1_ASM1419743v1_genomic.fna/checkm_result
[2024-01-25 18:59:25,536] [INFO] Task succeeded: CheckM
[2024-01-25 18:59:25,538] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:59:25,557] [INFO] ===== Completeness check finished =====
[2024-01-25 18:59:25,557] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:59:25,558] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014197435.1_ASM1419743v1_genomic.fna/markers.fasta)
[2024-01-25 18:59:25,558] [INFO] Task started: Blastn
[2024-01-25 18:59:25,558] [INFO] Running command: blastn -query GCF_014197435.1_ASM1419743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge14142a9-0e77-47e7-b62f-71f56518d60d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014197435.1_ASM1419743v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:27,264] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:27,267] [INFO] Selected 12 target genomes.
[2024-01-25 18:59:27,268] [INFO] Target genome list was writen to GCF_014197435.1_ASM1419743v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:59:27,285] [INFO] Task started: fastANI
[2024-01-25 18:59:27,285] [INFO] Running command: fastANI --query /var/lib/cwl/stg623d6521-fd90-4d0f-ad16-e19a1a0e4dcc/GCF_014197435.1_ASM1419743v1_genomic.fna.gz --refList GCF_014197435.1_ASM1419743v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014197435.1_ASM1419743v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:59:39,331] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:39,339] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:59:39,340] [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_014197435.1	s__Gordonia humi	100.0	1692	1694	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_009932475.1	s__Gordonia spumicola	81.6441	883	1694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919385.1	s__Gordonia sp016919385	81.006	788	1694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000344135.1	s__Gordonia malaquae	80.8822	808	1694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001305675.1	s__Gordonia phthalatica	80.827	791	1694	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	80.5669	698	1694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.65	99.65	0.97	0.97	2	-
GCF_000192435.1	s__Gordonia neofelifaecis	80.3897	736	1694	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	80.2866	633	1694	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	80.0633	800	1694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000423025.1	s__Gordonia shandongensis	80.055	629	1694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105725.1	s__Gordonia westfalica	79.21	627	1694	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	79.0245	577	1694	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.26	97.87	0.90	0.88	6	-
--------------------------------------------------------------------------------
[2024-01-25 18:59:39,341] [INFO] GTDB search result was written to GCF_014197435.1_ASM1419743v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:59:39,342] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:59:39,344] [INFO] DFAST_QC result json was written to GCF_014197435.1_ASM1419743v1_genomic.fna/dqc_result.json
[2024-01-25 18:59:39,344] [INFO] DFAST_QC completed!
[2024-01-25 18:59:39,344] [INFO] Total running time: 0h1m48s