[2024-01-24 14:22:33,064] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:33,066] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:33,066] [INFO] DQC Reference Directory: /var/lib/cwl/stgf817d437-3138-4f2d-ad73-a02e81d7d397/dqc_reference
[2024-01-24 14:22:34,313] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:34,314] [INFO] Task started: Prodigal
[2024-01-24 14:22:34,314] [INFO] Running command: gunzip -c /var/lib/cwl/stgab0d7cd1-b9bd-404e-8e18-ecf1126cf5bf/GCF_012933505.1_ASM1293350v1_genomic.fna.gz | prodigal -d GCF_012933505.1_ASM1293350v1_genomic.fna/cds.fna -a GCF_012933505.1_ASM1293350v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:54,775] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:54,775] [INFO] Task started: HMMsearch
[2024-01-24 14:22:54,776] [INFO] Running command: hmmsearch --tblout GCF_012933505.1_ASM1293350v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf817d437-3138-4f2d-ad73-a02e81d7d397/dqc_reference/reference_markers.hmm GCF_012933505.1_ASM1293350v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:55,124] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:55,126] [INFO] Found 6/6 markers.
[2024-01-24 14:22:55,188] [INFO] Query marker FASTA was written to GCF_012933505.1_ASM1293350v1_genomic.fna/markers.fasta
[2024-01-24 14:22:55,189] [INFO] Task started: Blastn
[2024-01-24 14:22:55,189] [INFO] Running command: blastn -query GCF_012933505.1_ASM1293350v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf817d437-3138-4f2d-ad73-a02e81d7d397/dqc_reference/reference_markers.fasta -out GCF_012933505.1_ASM1293350v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:56,412] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:56,416] [INFO] Selected 15 target genomes.
[2024-01-24 14:22:56,416] [INFO] Target genome list was writen to GCF_012933505.1_ASM1293350v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:56,424] [INFO] Task started: fastANI
[2024-01-24 14:22:56,425] [INFO] Running command: fastANI --query /var/lib/cwl/stgab0d7cd1-b9bd-404e-8e18-ecf1126cf5bf/GCF_012933505.1_ASM1293350v1_genomic.fna.gz --refList GCF_012933505.1_ASM1293350v1_genomic.fna/target_genomes.txt --output GCF_012933505.1_ASM1293350v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:15,426] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:15,427] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf817d437-3138-4f2d-ad73-a02e81d7d397/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:15,428] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf817d437-3138-4f2d-ad73-a02e81d7d397/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:15,449] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:15,449] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:15,450] [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 asplenii	strain=TBRC 11910	GCA_012933505.1	2725283	2725283	type	True	100.0	2165	2166	95	conclusive
Gordonia effusa	strain=NBRC 100432	GCA_000241305.2	263908	263908	type	True	79.7936	843	2166	95	below_threshold
Gordonia namibiensis	strain=NBRC 108229	GCA_000298235.1	168480	168480	type	True	79.0446	659	2166	95	below_threshold
Gordonia paraffinivorans	strain=NBRC 108238	GCA_000344155.1	175628	175628	type	True	79.0397	686	2166	95	below_threshold
Gordonia alkanivorans	strain=NBRC 16433	GCA_000225505.1	84096	84096	type	True	78.9717	677	2166	95	below_threshold
Gordonia desulfuricans	strain=NBRC 100010	GCA_001485495.1	89051	89051	type	True	78.9266	712	2166	95	below_threshold
Gordonia desulfuricans	strain=213E	GCA_010119475.1	89051	89051	type	True	78.9241	714	2166	95	below_threshold
Gordonia crocea	strain=NBRC 107697	GCA_009932435.1	589162	589162	type	True	78.8936	538	2166	95	below_threshold
Gordonia bronchialis	strain=FDAARGOS_1594	GCA_020731255.1	2054	2054	type	True	78.8802	670	2166	95	below_threshold
Gordonia bronchialis	strain=DSM 43247	GCA_000024785.1	2054	2054	type	True	78.8663	665	2166	95	below_threshold
Gordonia bronchialis	strain=NCTC10667	GCA_900450805.1	2054	2054	type	True	78.8445	675	2166	95	below_threshold
Gordonia rhizosphera	strain=NBRC 16068	GCA_000298195.1	83341	83341	type	True	78.6359	669	2166	95	below_threshold
Gordonia polyisoprenivorans	strain=ATCC BAA-14	GCA_012396285.1	84595	84595	type	True	78.5573	703	2166	95	below_threshold
Gordonia polyisoprenivorans	strain=NBRC 16320	GCA_000241325.2	84595	84595	type	True	78.5491	708	2166	95	below_threshold
Gordonia pseudamarae	strain=CON9	GCA_025273675.1	2831662	2831662	type	True	78.3737	620	2166	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:15,451] [INFO] DFAST Taxonomy check result was written to GCF_012933505.1_ASM1293350v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:15,452] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:15,452] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:15,452] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf817d437-3138-4f2d-ad73-a02e81d7d397/dqc_reference/checkm_data
[2024-01-24 14:23:15,453] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:15,528] [INFO] Task started: CheckM
[2024-01-24 14:23:15,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012933505.1_ASM1293350v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012933505.1_ASM1293350v1_genomic.fna/checkm_input GCF_012933505.1_ASM1293350v1_genomic.fna/checkm_result
[2024-01-24 14:24:17,045] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:17,047] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:17,070] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:17,070] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:17,071] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012933505.1_ASM1293350v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:17,071] [INFO] Task started: Blastn
[2024-01-24 14:24:17,072] [INFO] Running command: blastn -query GCF_012933505.1_ASM1293350v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf817d437-3138-4f2d-ad73-a02e81d7d397/dqc_reference/reference_markers_gtdb.fasta -out GCF_012933505.1_ASM1293350v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:19,102] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:19,106] [INFO] Selected 15 target genomes.
[2024-01-24 14:24:19,106] [INFO] Target genome list was writen to GCF_012933505.1_ASM1293350v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:19,121] [INFO] Task started: fastANI
[2024-01-24 14:24:19,122] [INFO] Running command: fastANI --query /var/lib/cwl/stgab0d7cd1-b9bd-404e-8e18-ecf1126cf5bf/GCF_012933505.1_ASM1293350v1_genomic.fna.gz --refList GCF_012933505.1_ASM1293350v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012933505.1_ASM1293350v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:40,076] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:40,094] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:40,094] [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_012933505.1	s__Gordonia asplenii	100.0	2165	2166	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_000241305.1	s__Gordonia effusa	79.8156	839	2166	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	79.0317	661	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.13	97.13	0.90	0.90	2	-
GCF_000344155.1	s__Gordonia paraffinivorans	79.0293	687	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.97	98.74	0.93	0.90	12	-
GCF_001485495.1	s__Gordonia desulfuricans	78.9601	706	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.37	98.77	0.95	0.92	3	-
GCF_009932435.1	s__Gordonia crocea	78.8975	538	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024785.1	s__Gordonia bronchialis	78.8652	666	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	3	-
GCF_002149015.1	s__Gordonia lacunae	78.6512	649	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000298195.1	s__Gordonia rhizosphera	78.6364	669	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011290605.1	s__Gordonia sp002009645	78.6255	659	2166	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	78.6134	658	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.85	97.53	0.90	0.88	3	-
GCA_004193205.1	s__Gordonia sediminis	78.5578	726	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017654315.1	s__Gordonia polyisoprenivorans_A	78.5361	689	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797825.1	s__Gordonia sp003797825	78.4127	675	2166	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009862785.1	s__Gordonia sp009862785	78.3651	592	2166	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 14:24:40,096] [INFO] GTDB search result was written to GCF_012933505.1_ASM1293350v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:40,096] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:40,100] [INFO] DFAST_QC result json was written to GCF_012933505.1_ASM1293350v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:40,100] [INFO] DFAST_QC completed!
[2024-01-24 14:24:40,100] [INFO] Total running time: 0h2m7s