[2024-01-24 15:10:40,934] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:40,935] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:40,936] [INFO] DQC Reference Directory: /var/lib/cwl/stgeff77538-d8c2-4a24-b15e-662ce2219838/dqc_reference
[2024-01-24 15:10:42,394] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:42,406] [INFO] Task started: Prodigal
[2024-01-24 15:10:42,407] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3c54f10-618f-404d-b1c8-893aff401191/GCF_003855095.1_ASM385509v1_genomic.fna.gz | prodigal -d GCF_003855095.1_ASM385509v1_genomic.fna/cds.fna -a GCF_003855095.1_ASM385509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:04,354] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:04,354] [INFO] Task started: HMMsearch
[2024-01-24 15:11:04,354] [INFO] Running command: hmmsearch --tblout GCF_003855095.1_ASM385509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeff77538-d8c2-4a24-b15e-662ce2219838/dqc_reference/reference_markers.hmm GCF_003855095.1_ASM385509v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:04,749] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:04,750] [INFO] Found 6/6 markers.
[2024-01-24 15:11:04,798] [INFO] Query marker FASTA was written to GCF_003855095.1_ASM385509v1_genomic.fna/markers.fasta
[2024-01-24 15:11:04,799] [INFO] Task started: Blastn
[2024-01-24 15:11:04,799] [INFO] Running command: blastn -query GCF_003855095.1_ASM385509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeff77538-d8c2-4a24-b15e-662ce2219838/dqc_reference/reference_markers.fasta -out GCF_003855095.1_ASM385509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:05,972] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:05,975] [INFO] Selected 15 target genomes.
[2024-01-24 15:11:05,976] [INFO] Target genome list was writen to GCF_003855095.1_ASM385509v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:05,982] [INFO] Task started: fastANI
[2024-01-24 15:11:05,982] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3c54f10-618f-404d-b1c8-893aff401191/GCF_003855095.1_ASM385509v1_genomic.fna.gz --refList GCF_003855095.1_ASM385509v1_genomic.fna/target_genomes.txt --output GCF_003855095.1_ASM385509v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:25,559] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:25,560] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeff77538-d8c2-4a24-b15e-662ce2219838/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:25,560] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeff77538-d8c2-4a24-b15e-662ce2219838/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:25,579] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:25,580] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:25,580] [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 insulae	strain=MMS17-SY073	GCA_003855095.1	2420509	2420509	type	True	100.0	1986	1987	95	conclusive
Gordonia hankookensis	strain=ON-33	GCA_014673215.1	589403	589403	type	True	82.2863	1290	1987	95	below_threshold
Gordonia mangrovi	strain=HNM0687	GCA_024734075.1	2665643	2665643	type	True	81.2789	1035	1987	95	below_threshold
Gordonia mangrovi	strain=HNM0687	GCA_009828195.1	2665643	2665643	type	True	81.2076	1018	1987	95	below_threshold
Gordonia rhizosphera	strain=NBRC 16068	GCA_000298195.1	83341	83341	type	True	80.8775	1040	1987	95	below_threshold
Gordonia bronchialis	strain=DSM 43247	GCA_000024785.1	2054	2054	type	True	80.1838	896	1987	95	below_threshold
Gordonia bronchialis	strain=NCTC10667	GCA_900450805.1	2054	2054	type	True	80.1417	908	1987	95	below_threshold
Gordonia bronchialis	strain=FDAARGOS_1594	GCA_020731255.1	2054	2054	type	True	80.1151	911	1987	95	below_threshold
Gordonia amicalis	strain=DSM 44461	GCA_012395955.1	89053	89053	type	True	79.9409	862	1987	95	below_threshold
Gordonia terrae	strain=NRRL B-16283	GCA_003183825.1	2055	2055	suspected-type	True	79.8924	891	1987	95	below_threshold
Gordonia terrae	strain=3612	GCA_001698225.1	2055	2055	suspected-type	True	79.8676	892	1987	95	below_threshold
Gordonia lacunae	strain=BS2	GCA_002149015.1	417102	417102	type	True	79.836	901	1987	95	below_threshold
Gordonia amarae	strain=NBRC 15530	GCA_000241345.2	36821	36821	type	True	79.4114	727	1987	95	below_threshold
Gordonia sputi	strain=ATCC 29627	GCA_012396255.1	36823	36823	type	True	79.0746	736	1987	95	below_threshold
Gordonia sputi	strain=NBRC 100414	GCA_000248055.2	36823	36823	type	True	79.0033	727	1987	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:25,621] [INFO] DFAST Taxonomy check result was written to GCF_003855095.1_ASM385509v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:25,622] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:25,622] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:25,623] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeff77538-d8c2-4a24-b15e-662ce2219838/dqc_reference/checkm_data
[2024-01-24 15:11:25,624] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:25,681] [INFO] Task started: CheckM
[2024-01-24 15:11:25,682] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003855095.1_ASM385509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003855095.1_ASM385509v1_genomic.fna/checkm_input GCF_003855095.1_ASM385509v1_genomic.fna/checkm_result
[2024-01-24 15:13:00,206] [INFO] Task succeeded: CheckM
[2024-01-24 15:13:00,207] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:13:00,230] [INFO] ===== Completeness check finished =====
[2024-01-24 15:13:00,230] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:13:00,230] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003855095.1_ASM385509v1_genomic.fna/markers.fasta)
[2024-01-24 15:13:00,231] [INFO] Task started: Blastn
[2024-01-24 15:13:00,231] [INFO] Running command: blastn -query GCF_003855095.1_ASM385509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeff77538-d8c2-4a24-b15e-662ce2219838/dqc_reference/reference_markers_gtdb.fasta -out GCF_003855095.1_ASM385509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:13:01,952] [INFO] Task succeeded: Blastn
[2024-01-24 15:13:01,956] [INFO] Selected 13 target genomes.
[2024-01-24 15:13:01,956] [INFO] Target genome list was writen to GCF_003855095.1_ASM385509v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:13:01,969] [INFO] Task started: fastANI
[2024-01-24 15:13:01,969] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3c54f10-618f-404d-b1c8-893aff401191/GCF_003855095.1_ASM385509v1_genomic.fna.gz --refList GCF_003855095.1_ASM385509v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003855095.1_ASM385509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:13:18,375] [INFO] Task succeeded: fastANI
[2024-01-24 15:13:18,390] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:13:18,390] [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_003855095.1	s__Gordonia insulae	100.0	1986	1987	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_003797825.1	s__Gordonia sp003797825	82.5087	1310	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014673215.1	s__Gordonia hankookensis	82.2884	1289	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.33	98.32	0.95	0.94	3	-
GCF_009862785.1	s__Gordonia sp009862785	81.7848	1168	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828195.1	s__Gordonia sp009828195	81.2142	1018	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700145.1	s__Gordonia sp002700145	81.0537	975	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004193205.1	s__Gordonia sediminis	81.0133	1088	1987	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	80.9165	1032	1987	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	80.1852	896	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000298235.1	s__Gordonia namibiensis	80.02	868	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.13	97.13	0.90	0.90	2	-
GCF_000332995.1	s__Gordonia amicalis	79.9531	845	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.45	97.39	0.94	0.91	7	-
GCF_002149015.1	s__Gordonia lacunae	79.8281	902	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000241345.1	s__Gordonia amarae	79.3816	731	1987	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.98	99.98	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:13:18,392] [INFO] GTDB search result was written to GCF_003855095.1_ASM385509v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:13:18,393] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:13:18,396] [INFO] DFAST_QC result json was written to GCF_003855095.1_ASM385509v1_genomic.fna/dqc_result.json
[2024-01-24 15:13:18,396] [INFO] DFAST_QC completed!
[2024-01-24 15:13:18,396] [INFO] Total running time: 0h2m37s