[2024-01-24 12:21:54,619] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:54,621] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:54,622] [INFO] DQC Reference Directory: /var/lib/cwl/stge906d6db-6198-4ef8-9a71-12dd51326676/dqc_reference
[2024-01-24 12:21:55,840] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:55,840] [INFO] Task started: Prodigal
[2024-01-24 12:21:55,841] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd77b3f6-6ce8-47ca-8b75-e2892085fa54/GCF_000342005.1_Whole_genome_assembly_genomic.fna.gz | prodigal -d GCF_000342005.1_Whole_genome_assembly_genomic.fna/cds.fna -a GCF_000342005.1_Whole_genome_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:27,509] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:27,509] [INFO] Task started: HMMsearch
[2024-01-24 12:22:27,509] [INFO] Running command: hmmsearch --tblout GCF_000342005.1_Whole_genome_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge906d6db-6198-4ef8-9a71-12dd51326676/dqc_reference/reference_markers.hmm GCF_000342005.1_Whole_genome_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:27,923] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:27,925] [INFO] Found 6/6 markers.
[2024-01-24 12:22:28,002] [INFO] Query marker FASTA was written to GCF_000342005.1_Whole_genome_assembly_genomic.fna/markers.fasta
[2024-01-24 12:22:28,003] [INFO] Task started: Blastn
[2024-01-24 12:22:28,003] [INFO] Running command: blastn -query GCF_000342005.1_Whole_genome_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge906d6db-6198-4ef8-9a71-12dd51326676/dqc_reference/reference_markers.fasta -out GCF_000342005.1_Whole_genome_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:29,332] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:29,337] [INFO] Selected 16 target genomes.
[2024-01-24 12:22:29,337] [INFO] Target genome list was writen to GCF_000342005.1_Whole_genome_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:22:29,343] [INFO] Task started: fastANI
[2024-01-24 12:22:29,343] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd77b3f6-6ce8-47ca-8b75-e2892085fa54/GCF_000342005.1_Whole_genome_assembly_genomic.fna.gz --refList GCF_000342005.1_Whole_genome_assembly_genomic.fna/target_genomes.txt --output GCF_000342005.1_Whole_genome_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:04,951] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:04,952] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge906d6db-6198-4ef8-9a71-12dd51326676/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:04,952] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge906d6db-6198-4ef8-9a71-12dd51326676/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:04,967] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:23:04,967] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:23:04,967] [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
Amycolatopsis japonica	strain=MG417-CF17	GCA_000732925.1	208439	208439	type	True	92.7046	2268	2808	95	below_threshold
Amycolatopsis keratiniphila subsp. keratiniphila	strain=DSM 44409	GCA_001620365.2	227715	129921	type	True	92.5137	2288	2808	95	below_threshold
Amycolatopsis keratiniphila subsp. nogabecina	strain=FH 1893	GCA_001953855.1	208442	129921	type	True	92.4782	2296	2808	95	below_threshold
Amycolatopsis lurida	strain=NRRL 2430	GCA_000749465.3	31959	31959	type	True	92.4052	2241	2808	95	below_threshold
Amycolatopsis lurida	strain=DSM 43134	GCA_900105055.1	31959	31959	type	True	92.3846	2278	2808	95	below_threshold
Amycolatopsis roodepoortensis	strain=DSM 46661	GCA_014873915.1	700274	700274	type	True	92.3693	2259	2808	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_000340415.1	36819	36819	type	True	91.8641	2250	2808	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_001995215.1	36819	36819	type	True	91.8194	2300	2808	95	below_threshold
Amycolatopsis thailandensis	strain=JCM 16380	GCA_002234405.1	589330	589330	type	True	91.6908	2097	2808	95	below_threshold
Amycolatopsis orientalis	strain=KCTC 9412	GCA_000478275.1	31958	31958	type	True	90.5073	2227	2808	95	below_threshold
Amycolatopsis regifaucium	strain=GY080	GCA_001613935.1	546365	546365	type	True	90.0505	2170	2808	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	81.6615	1578	2808	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	79.9581	1049	2808	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.0238	987	2808	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	78.7357	988	2808	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.1531	765	2808	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:04,969] [INFO] DFAST Taxonomy check result was written to GCF_000342005.1_Whole_genome_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:23:04,969] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:04,970] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:04,970] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge906d6db-6198-4ef8-9a71-12dd51326676/dqc_reference/checkm_data
[2024-01-24 12:23:04,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:05,059] [INFO] Task started: CheckM
[2024-01-24 12:23:05,060] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000342005.1_Whole_genome_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000342005.1_Whole_genome_assembly_genomic.fna/checkm_input GCF_000342005.1_Whole_genome_assembly_genomic.fna/checkm_result
[2024-01-24 12:24:37,640] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:37,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:37,670] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:37,671] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:37,671] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000342005.1_Whole_genome_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:24:37,672] [INFO] Task started: Blastn
[2024-01-24 12:24:37,672] [INFO] Running command: blastn -query GCF_000342005.1_Whole_genome_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge906d6db-6198-4ef8-9a71-12dd51326676/dqc_reference/reference_markers_gtdb.fasta -out GCF_000342005.1_Whole_genome_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:39,613] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:39,617] [INFO] Selected 10 target genomes.
[2024-01-24 12:24:39,617] [INFO] Target genome list was writen to GCF_000342005.1_Whole_genome_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:39,633] [INFO] Task started: fastANI
[2024-01-24 12:24:39,634] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd77b3f6-6ce8-47ca-8b75-e2892085fa54/GCF_000342005.1_Whole_genome_assembly_genomic.fna.gz --refList GCF_000342005.1_Whole_genome_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_000342005.1_Whole_genome_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:04,216] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:04,228] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:04,228] [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_000342005.1	s__Amycolatopsis decaplanina	100.0	2805	2808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000732925.1	s__Amycolatopsis japonica	92.709	2268	2808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	97.30	96.67	0.90	0.88	4	-
GCF_001620365.2	s__Amycolatopsis keratiniphila	92.5125	2288	2808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	97.78	96.67	0.89	0.86	5	-
GCF_900105055.1	s__Amycolatopsis lurida	92.3876	2278	2808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	97.56	95.13	0.93	0.86	3	-
GCF_014873915.1	s__Amycolatopsis roodepoortensis	92.3851	2257	2808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	96.45	96.45	0.88	0.88	2	-
GCF_003947415.1	s__Amycolatopsis sp003947415	92.1182	2301	2808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	96.38	96.38	0.89	0.88	3	-
GCF_014654365.1	s__Amycolatopsis oliviviridis	91.9416	2305	2808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001995215.1	s__Amycolatopsis azurea	91.8279	2299	2808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002234405.1	s__Amycolatopsis thailandensis	91.6506	2103	2808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000478275.1	s__Amycolatopsis orientalis	90.5041	2227	2808	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	96.64	96.64	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:04,230] [INFO] GTDB search result was written to GCF_000342005.1_Whole_genome_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:04,231] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:04,235] [INFO] DFAST_QC result json was written to GCF_000342005.1_Whole_genome_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:25:04,235] [INFO] DFAST_QC completed!
[2024-01-24 12:25:04,235] [INFO] Total running time: 0h3m10s