[2024-01-24 11:20:04,001] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:04,002] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:04,003] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bc19819-a73a-4990-91a6-0e1857bf9668/dqc_reference
[2024-01-24 11:20:05,144] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:05,145] [INFO] Task started: Prodigal
[2024-01-24 11:20:05,146] [INFO] Running command: gunzip -c /var/lib/cwl/stg67e2f90c-da39-4eb5-81ff-1bf0ffbcd088/GCF_010119475.1_ASM1011947v1_genomic.fna.gz | prodigal -d GCF_010119475.1_ASM1011947v1_genomic.fna/cds.fna -a GCF_010119475.1_ASM1011947v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:22,398] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:22,398] [INFO] Task started: HMMsearch
[2024-01-24 11:20:22,398] [INFO] Running command: hmmsearch --tblout GCF_010119475.1_ASM1011947v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bc19819-a73a-4990-91a6-0e1857bf9668/dqc_reference/reference_markers.hmm GCF_010119475.1_ASM1011947v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:22,621] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:22,622] [INFO] Found 6/6 markers.
[2024-01-24 11:20:22,664] [INFO] Query marker FASTA was written to GCF_010119475.1_ASM1011947v1_genomic.fna/markers.fasta
[2024-01-24 11:20:22,664] [INFO] Task started: Blastn
[2024-01-24 11:20:22,664] [INFO] Running command: blastn -query GCF_010119475.1_ASM1011947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bc19819-a73a-4990-91a6-0e1857bf9668/dqc_reference/reference_markers.fasta -out GCF_010119475.1_ASM1011947v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:23,851] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:23,854] [INFO] Selected 12 target genomes.
[2024-01-24 11:20:23,854] [INFO] Target genome list was writen to GCF_010119475.1_ASM1011947v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:23,859] [INFO] Task started: fastANI
[2024-01-24 11:20:23,859] [INFO] Running command: fastANI --query /var/lib/cwl/stg67e2f90c-da39-4eb5-81ff-1bf0ffbcd088/GCF_010119475.1_ASM1011947v1_genomic.fna.gz --refList GCF_010119475.1_ASM1011947v1_genomic.fna/target_genomes.txt --output GCF_010119475.1_ASM1011947v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:37,955] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:37,956] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bc19819-a73a-4990-91a6-0e1857bf9668/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:37,956] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bc19819-a73a-4990-91a6-0e1857bf9668/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:37,966] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:20:37,966] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:37,966] [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 desulfuricans	strain=213E	GCA_010119475.1	89051	89051	type	True	100.0	1747	1752	95	conclusive
Gordonia desulfuricans	strain=NBRC 100010	GCA_001485495.1	89051	89051	type	True	99.8991	1623	1752	95	conclusive
Gordonia polyisoprenivorans	strain=NBRC 16320	GCA_000241325.2	84595	84595	type	True	81.0094	1047	1752	95	below_threshold
Gordonia polyisoprenivorans	strain=ATCC BAA-14	GCA_012396285.1	84595	84595	type	True	80.969	1054	1752	95	below_threshold
Gordonia paraffinivorans	strain=NBRC 108238	GCA_000344155.1	175628	175628	type	True	80.644	856	1752	95	below_threshold
Gordonia westfalica	strain=DSM 44215	GCA_900105725.1	158898	158898	type	True	80.6404	878	1752	95	below_threshold
Gordonia amicalis	strain=DSM 44461	GCA_012395955.1	89053	89053	type	True	80.5252	816	1752	95	below_threshold
Gordonia rubripertincta	strain=NBRC 101908	GCA_000327325.1	36822	36822	type	True	80.5206	856	1752	95	below_threshold
Gordonia rubripertincta	strain=ATCC 14352	GCA_012396225.1	36822	36822	type	True	80.4415	871	1752	95	below_threshold
Gordonia oryzae	strain=RS15-1S	GCA_003797185.1	2487349	2487349	type	True	80.4364	886	1752	95	below_threshold
Gordonia soli	strain=NBRC 108243	GCA_000334455.1	320799	320799	type	True	79.6481	770	1752	95	below_threshold
Gordonia otitidis	strain=NBRC 100426	GCA_000248075.2	249058	249058	type	True	79.5504	711	1752	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:37,968] [INFO] DFAST Taxonomy check result was written to GCF_010119475.1_ASM1011947v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:37,969] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:37,969] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:37,969] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bc19819-a73a-4990-91a6-0e1857bf9668/dqc_reference/checkm_data
[2024-01-24 11:20:37,970] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:38,018] [INFO] Task started: CheckM
[2024-01-24 11:20:38,018] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010119475.1_ASM1011947v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010119475.1_ASM1011947v1_genomic.fna/checkm_input GCF_010119475.1_ASM1011947v1_genomic.fna/checkm_result
[2024-01-24 11:22:10,588] [INFO] Task succeeded: CheckM
[2024-01-24 11:22:10,589] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:22:10,607] [INFO] ===== Completeness check finished =====
[2024-01-24 11:22:10,607] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:22:10,607] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010119475.1_ASM1011947v1_genomic.fna/markers.fasta)
[2024-01-24 11:22:10,608] [INFO] Task started: Blastn
[2024-01-24 11:22:10,608] [INFO] Running command: blastn -query GCF_010119475.1_ASM1011947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bc19819-a73a-4990-91a6-0e1857bf9668/dqc_reference/reference_markers_gtdb.fasta -out GCF_010119475.1_ASM1011947v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:22:12,434] [INFO] Task succeeded: Blastn
[2024-01-24 11:22:12,437] [INFO] Selected 14 target genomes.
[2024-01-24 11:22:12,437] [INFO] Target genome list was writen to GCF_010119475.1_ASM1011947v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:22:12,447] [INFO] Task started: fastANI
[2024-01-24 11:22:12,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg67e2f90c-da39-4eb5-81ff-1bf0ffbcd088/GCF_010119475.1_ASM1011947v1_genomic.fna.gz --refList GCF_010119475.1_ASM1011947v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010119475.1_ASM1011947v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:22:27,516] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:27,528] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:22:27,528] [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_001485495.1	s__Gordonia desulfuricans	99.8991	1623	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.37	98.77	0.95	0.92	3	conclusive
GCF_017654315.1	s__Gordonia polyisoprenivorans_A	81.0389	1051	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000241325.1	s__Gordonia polyisoprenivorans	81.0314	1043	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.60	97.62	0.90	0.79	11	-
GCF_000298235.1	s__Gordonia namibiensis	80.7194	838	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.13	97.13	0.90	0.90	2	-
GCF_000225505.1	s__Gordonia alkanivorans	80.7072	811	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.26	97.87	0.90	0.88	6	-
GCF_000344155.1	s__Gordonia paraffinivorans	80.6463	855	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.97	98.74	0.93	0.90	12	-
GCF_900105725.1	s__Gordonia westfalica	80.6306	879	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332995.1	s__Gordonia amicalis	80.5949	797	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.45	97.39	0.94	0.91	7	-
GCF_000327325.1	s__Gordonia rubripertincta	80.523	856	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.55	98.07	0.91	0.87	6	-
GCF_003797185.1	s__Gordonia oryzae	80.4266	887	1752	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	79.9928	834	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.70	97.37	0.91	0.88	14	-
GCA_002700145.1	s__Gordonia sp002700145	79.9156	761	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000334455.1	s__Gordonia soli	79.6578	769	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000248075.1	s__Gordonia otitidis	79.5653	709	1752	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 11:22:27,530] [INFO] GTDB search result was written to GCF_010119475.1_ASM1011947v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:22:27,530] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:22:27,533] [INFO] DFAST_QC result json was written to GCF_010119475.1_ASM1011947v1_genomic.fna/dqc_result.json
[2024-01-24 11:22:27,534] [INFO] DFAST_QC completed!
[2024-01-24 11:22:27,534] [INFO] Total running time: 0h2m24s