[2024-01-24 14:40:02,435] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:40:02,438] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:40:02,438] [INFO] DQC Reference Directory: /var/lib/cwl/stg1403c7a7-ac30-4c8e-b55b-ec102fcc6086/dqc_reference
[2024-01-24 14:40:03,805] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:40:03,806] [INFO] Task started: Prodigal
[2024-01-24 14:40:03,806] [INFO] Running command: gunzip -c /var/lib/cwl/stg9de88661-dbe8-401f-a267-44f3b1225455/GCF_900129495.1_IMG-taxon_2695420953_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129495.1_IMG-taxon_2695420953_annotated_assembly_genomic.fna/cds.fna -a GCF_900129495.1_IMG-taxon_2695420953_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:40:16,553] [INFO] Task succeeded: Prodigal
[2024-01-24 14:40:16,553] [INFO] Task started: HMMsearch
[2024-01-24 14:40:16,553] [INFO] Running command: hmmsearch --tblout GCF_900129495.1_IMG-taxon_2695420953_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1403c7a7-ac30-4c8e-b55b-ec102fcc6086/dqc_reference/reference_markers.hmm GCF_900129495.1_IMG-taxon_2695420953_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:40:16,886] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:40:16,888] [INFO] Found 6/6 markers.
[2024-01-24 14:40:16,936] [INFO] Query marker FASTA was written to GCF_900129495.1_IMG-taxon_2695420953_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:40:16,937] [INFO] Task started: Blastn
[2024-01-24 14:40:16,937] [INFO] Running command: blastn -query GCF_900129495.1_IMG-taxon_2695420953_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1403c7a7-ac30-4c8e-b55b-ec102fcc6086/dqc_reference/reference_markers.fasta -out GCF_900129495.1_IMG-taxon_2695420953_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:18,288] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:18,293] [INFO] Selected 11 target genomes.
[2024-01-24 14:40:18,293] [INFO] Target genome list was writen to GCF_900129495.1_IMG-taxon_2695420953_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:40:18,298] [INFO] Task started: fastANI
[2024-01-24 14:40:18,299] [INFO] Running command: fastANI --query /var/lib/cwl/stg9de88661-dbe8-401f-a267-44f3b1225455/GCF_900129495.1_IMG-taxon_2695420953_annotated_assembly_genomic.fna.gz --refList GCF_900129495.1_IMG-taxon_2695420953_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129495.1_IMG-taxon_2695420953_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:38,702] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:38,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1403c7a7-ac30-4c8e-b55b-ec102fcc6086/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:38,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1403c7a7-ac30-4c8e-b55b-ec102fcc6086/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:38,716] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:38,716] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:38,716] [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
Geodermatophilus nigrescens	strain=DSM 45408	GCA_900129495.1	1070870	1070870	type	True	100.0	1572	1573	95	conclusive
Geodermatophilus aquaeductus	strain=DSM 46834	GCA_900182545.1	1564161	1564161	type	True	88.3832	1277	1573	95	below_threshold
Geodermatophilus normandii	strain=DSM 45417	GCA_003182485.1	1137989	1137989	type	True	88.1374	1238	1573	95	below_threshold
Geodermatophilus saharensis	strain=DSM 45423	GCA_900188205.1	1137994	1137994	type	True	88.1362	1204	1573	95	below_threshold
Geodermatophilus amargosae	strain=DSM 46136	GCA_900116515.1	1296565	1296565	type	True	87.9335	1248	1573	95	below_threshold
Geodermatophilus tzadiensis	strain=DSM 45416	GCA_003002915.1	1137988	1137988	type	True	87.688	1154	1573	95	below_threshold
Geodermatophilus telluris	strain=DSM 45421	GCA_900102745.1	1190417	1190417	type	True	87.5371	1163	1573	95	below_threshold
Geodermatophilus bullaregiensis	strain=DSM 46841	GCA_016907675.1	1564160	1564160	type	True	87.0211	1179	1573	95	below_threshold
Klenkia taihuensis	strain=CGMCC 1.12303	GCA_014653095.1	1225127	1225127	type	True	82.2183	947	1573	95	below_threshold
Klenkia brasiliensis	strain=DSM 44526	GCA_900100695.1	333142	333142	type	True	82.1427	922	1573	95	below_threshold
Klenkia taihuensis	strain=DSM 45962	GCA_900112525.1	1225127	1225127	type	True	82.1182	944	1573	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:38,718] [INFO] DFAST Taxonomy check result was written to GCF_900129495.1_IMG-taxon_2695420953_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:40:38,719] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:38,719] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:38,719] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1403c7a7-ac30-4c8e-b55b-ec102fcc6086/dqc_reference/checkm_data
[2024-01-24 14:40:38,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:38,768] [INFO] Task started: CheckM
[2024-01-24 14:40:38,768] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129495.1_IMG-taxon_2695420953_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129495.1_IMG-taxon_2695420953_annotated_assembly_genomic.fna/checkm_input GCF_900129495.1_IMG-taxon_2695420953_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:41:38,705] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:38,706] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:38,729] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:38,729] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:38,730] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129495.1_IMG-taxon_2695420953_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:41:38,730] [INFO] Task started: Blastn
[2024-01-24 14:41:38,730] [INFO] Running command: blastn -query GCF_900129495.1_IMG-taxon_2695420953_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1403c7a7-ac30-4c8e-b55b-ec102fcc6086/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129495.1_IMG-taxon_2695420953_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:40,676] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:40,683] [INFO] Selected 13 target genomes.
[2024-01-24 14:41:40,684] [INFO] Target genome list was writen to GCF_900129495.1_IMG-taxon_2695420953_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:40,703] [INFO] Task started: fastANI
[2024-01-24 14:41:40,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg9de88661-dbe8-401f-a267-44f3b1225455/GCF_900129495.1_IMG-taxon_2695420953_annotated_assembly_genomic.fna.gz --refList GCF_900129495.1_IMG-taxon_2695420953_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129495.1_IMG-taxon_2695420953_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:42:04,021] [INFO] Task succeeded: fastANI
[2024-01-24 14:42:04,033] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:42:04,034] [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_900129495.1	s__Geodermatophilus nigrescens	100.0	1572	1573	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900182545.1	s__Geodermatophilus aquaeductus	88.3424	1281	1573	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	96.01	96.01	0.85	0.85	2	-
GCF_900188205.1	s__Geodermatophilus saharensis	88.1638	1202	1573	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182485.1	s__Geodermatophilus normandii	88.0738	1244	1573	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115395.1	s__Geodermatophilus obscurus_B	88.0592	1231	1573	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116515.1	s__Geodermatophilus amargosae	87.923	1249	1573	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	95.87	95.87	0.85	0.85	2	-
GCF_003002915.1	s__Geodermatophilus tzadiensis	87.7003	1153	1573	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102745.1	s__Geodermatophilus telluris	87.5801	1159	1573	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115505.1	s__Geodermatophilus dictyosporus	87.3682	1173	1573	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907675.1	s__Geodermatophilus bullaregiensis	87.0363	1177	1573	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004571075.1	s__Blastococcus sp004571075	83.5619	918	1573	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112525.1	s__Klenkia taihuensis	82.1537	938	1573	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Klenkia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900100695.1	s__Klenkia brasiliensis	82.124	924	1573	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Klenkia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:42:04,036] [INFO] GTDB search result was written to GCF_900129495.1_IMG-taxon_2695420953_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:42:04,036] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:42:04,041] [INFO] DFAST_QC result json was written to GCF_900129495.1_IMG-taxon_2695420953_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:42:04,041] [INFO] DFAST_QC completed!
[2024-01-24 14:42:04,041] [INFO] Total running time: 0h2m2s