[2024-01-24 12:14:34,127] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:34,128] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:34,128] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b52b960-91d3-45d9-823b-fd2dc9363a50/dqc_reference
[2024-01-24 12:14:35,347] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,348] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,348] [INFO] Running command: gunzip -c /var/lib/cwl/stg64ed8c8f-f2e3-4052-946e-c6d7a108fd6c/GCF_001997295.1_ASM199729v1_genomic.fna.gz | prodigal -d GCF_001997295.1_ASM199729v1_genomic.fna/cds.fna -a GCF_001997295.1_ASM199729v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:43,951] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:43,951] [INFO] Task started: HMMsearch
[2024-01-24 12:14:43,951] [INFO] Running command: hmmsearch --tblout GCF_001997295.1_ASM199729v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b52b960-91d3-45d9-823b-fd2dc9363a50/dqc_reference/reference_markers.hmm GCF_001997295.1_ASM199729v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:44,216] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:44,217] [INFO] Found 6/6 markers.
[2024-01-24 12:14:44,243] [INFO] Query marker FASTA was written to GCF_001997295.1_ASM199729v1_genomic.fna/markers.fasta
[2024-01-24 12:14:44,243] [INFO] Task started: Blastn
[2024-01-24 12:14:44,243] [INFO] Running command: blastn -query GCF_001997295.1_ASM199729v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b52b960-91d3-45d9-823b-fd2dc9363a50/dqc_reference/reference_markers.fasta -out GCF_001997295.1_ASM199729v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:45,227] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:45,229] [INFO] Selected 10 target genomes.
[2024-01-24 12:14:45,229] [INFO] Target genome list was writen to GCF_001997295.1_ASM199729v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:45,272] [INFO] Task started: fastANI
[2024-01-24 12:14:45,272] [INFO] Running command: fastANI --query /var/lib/cwl/stg64ed8c8f-f2e3-4052-946e-c6d7a108fd6c/GCF_001997295.1_ASM199729v1_genomic.fna.gz --refList GCF_001997295.1_ASM199729v1_genomic.fna/target_genomes.txt --output GCF_001997295.1_ASM199729v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:53,355] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:53,355] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b52b960-91d3-45d9-823b-fd2dc9363a50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:53,356] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b52b960-91d3-45d9-823b-fd2dc9363a50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:53,365] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:14:53,365] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:53,365] [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
Tessaracoccus flavus	strain=RP1	GCA_001997295.1	1610493	1610493	type	True	100.0	1074	1074	95	conclusive
Tessaracoccus flavus	strain=RP1	GCA_900107385.1	1610493	1610493	type	True	99.9721	1043	1074	95	conclusive
Tessaracoccus lapidicaptus	strain=IPBSL-7	GCA_001693815.1	1427523	1427523	type	True	80.9762	510	1074	95	below_threshold
Tessaracoccus defluvii	strain=JCM 17540	GCA_014489575.1	1285901	1285901	type	True	80.4168	492	1074	95	below_threshold
Tessaracoccus coleopterorum	strain=HDW20	GCA_011174705.1	2714950	2714950	type	True	80.2399	471	1074	95	below_threshold
Tessaracoccus flavescens	strain=SST-39T	GCA_001998865.1	399497	399497	type	True	80.0851	474	1074	95	below_threshold
Tessaracoccus aquimaris	strain=NSG39	GCA_001997345.1	1332264	1332264	type	True	79.8543	486	1074	95	below_threshold
Propioniciclava sinopodophylli	strain=KCTC 33808	GCA_004324755.1	1837344	1837344	type	True	78.4027	282	1074	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	76.8197	238	1074	95	below_threshold
Nocardioides astragali	strain=CGMCC 4.7327	GCA_024436375.1	1776736	1776736	type	True	76.7536	204	1074	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:53,366] [INFO] DFAST Taxonomy check result was written to GCF_001997295.1_ASM199729v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:53,366] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:53,367] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:53,367] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b52b960-91d3-45d9-823b-fd2dc9363a50/dqc_reference/checkm_data
[2024-01-24 12:14:53,367] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:53,407] [INFO] Task started: CheckM
[2024-01-24 12:14:53,407] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001997295.1_ASM199729v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001997295.1_ASM199729v1_genomic.fna/checkm_input GCF_001997295.1_ASM199729v1_genomic.fna/checkm_result
[2024-01-24 12:15:23,065] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:23,067] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:23,084] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:23,085] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:23,085] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001997295.1_ASM199729v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:23,085] [INFO] Task started: Blastn
[2024-01-24 12:15:23,085] [INFO] Running command: blastn -query GCF_001997295.1_ASM199729v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b52b960-91d3-45d9-823b-fd2dc9363a50/dqc_reference/reference_markers_gtdb.fasta -out GCF_001997295.1_ASM199729v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:24,611] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:24,613] [INFO] Selected 11 target genomes.
[2024-01-24 12:15:24,614] [INFO] Target genome list was writen to GCF_001997295.1_ASM199729v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:24,619] [INFO] Task started: fastANI
[2024-01-24 12:15:24,619] [INFO] Running command: fastANI --query /var/lib/cwl/stg64ed8c8f-f2e3-4052-946e-c6d7a108fd6c/GCF_001997295.1_ASM199729v1_genomic.fna.gz --refList GCF_001997295.1_ASM199729v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001997295.1_ASM199729v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:33,304] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:33,312] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:33,312] [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_001997295.1	s__Arachnia flava	100.0	1074	1074	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_001693815.1	s__Arachnia lapidicapta	80.9335	513	1074	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	98.86	97.76	0.95	0.93	4	-
GCF_014164775.1	s__Arachnia sp014164775	80.5322	528	1074	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	97.46	97.46	0.87	0.87	2	-
GCF_014489575.1	s__Arachnia defluvii	80.4165	493	1074	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012837465.1	s__Arachnia sp012837465	80.278	414	1074	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011174705.1	s__Arachnia coleopterorum	80.2538	469	1074	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826065.2	s__Arachnia massiliensis	80.2338	501	1074	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001998865.1	s__Arachnia flavescens	80.0942	473	1074	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017815535.1	s__Arachnia sp001956895	80.0393	509	1074	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	97.64	95.92	0.92	0.88	4	-
GCF_001997345.1	s__Arachnia aquimaris	79.8577	486	1074	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714275.1	s__Arachnia sp016714275	79.5564	446	1074	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:33,313] [INFO] GTDB search result was written to GCF_001997295.1_ASM199729v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:33,314] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:33,316] [INFO] DFAST_QC result json was written to GCF_001997295.1_ASM199729v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:33,316] [INFO] DFAST_QC completed!
[2024-01-24 12:15:33,316] [INFO] Total running time: 0h0m59s