[2024-01-24 13:22:11,378] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:11,388] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:11,388] [INFO] DQC Reference Directory: /var/lib/cwl/stg81594fbf-a623-4bcc-8e10-f24a82db1faf/dqc_reference
[2024-01-24 13:22:13,354] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:13,355] [INFO] Task started: Prodigal
[2024-01-24 13:22:13,355] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5e2e69b-cdea-4613-9589-4de0241a91e7/GCF_001552575.1_ASM155257v1_genomic.fna.gz | prodigal -d GCF_001552575.1_ASM155257v1_genomic.fna/cds.fna -a GCF_001552575.1_ASM155257v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:30,242] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:30,242] [INFO] Task started: HMMsearch
[2024-01-24 13:22:30,243] [INFO] Running command: hmmsearch --tblout GCF_001552575.1_ASM155257v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81594fbf-a623-4bcc-8e10-f24a82db1faf/dqc_reference/reference_markers.hmm GCF_001552575.1_ASM155257v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:30,597] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:30,599] [INFO] Found 6/6 markers.
[2024-01-24 13:22:30,680] [INFO] Query marker FASTA was written to GCF_001552575.1_ASM155257v1_genomic.fna/markers.fasta
[2024-01-24 13:22:30,680] [INFO] Task started: Blastn
[2024-01-24 13:22:30,680] [INFO] Running command: blastn -query GCF_001552575.1_ASM155257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81594fbf-a623-4bcc-8e10-f24a82db1faf/dqc_reference/reference_markers.fasta -out GCF_001552575.1_ASM155257v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:31,938] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:31,941] [INFO] Selected 7 target genomes.
[2024-01-24 13:22:31,941] [INFO] Target genome list was writen to GCF_001552575.1_ASM155257v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:31,944] [INFO] Task started: fastANI
[2024-01-24 13:22:31,944] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5e2e69b-cdea-4613-9589-4de0241a91e7/GCF_001552575.1_ASM155257v1_genomic.fna.gz --refList GCF_001552575.1_ASM155257v1_genomic.fna/target_genomes.txt --output GCF_001552575.1_ASM155257v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:41,216] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:41,216] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81594fbf-a623-4bcc-8e10-f24a82db1faf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:41,217] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81594fbf-a623-4bcc-8e10-f24a82db1faf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:41,223] [INFO] Found 7 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:22:41,223] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:41,223] [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
Prescottella equi	strain=NBRC 101255	GCA_001552575.1	43767	43767	type	True	100.0	1702	1707	95	conclusive
Prescottella equi	strain=NCTC1621	GCA_900455845.1	43767	43767	type	True	99.9988	1706	1707	95	conclusive
Prescottella equi	strain=C 7	GCA_000473915.1	43767	43767	type	True	99.9812	1686	1707	95	conclusive
Prescottella equi	strain=DSM 20307	GCA_002094305.1	43767	43767	type	True	99.9796	1695	1707	95	conclusive
Prescottella agglutinans	strain=CCTCC AB2014297	GCA_004011865.1	1644129	1644129	type	True	85.9379	1317	1707	95	below_threshold
Prescottella defluvii	strain=Ca11	GCA_000738775.1	1323361	1323361	type	True	85.2901	1225	1707	95	below_threshold
Rhodococcus xishaensis	strain=LHW51113	GCA_004011825.1	2487364	2487364	type	True	82.077	869	1707	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:41,225] [INFO] DFAST Taxonomy check result was written to GCF_001552575.1_ASM155257v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:41,225] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:41,225] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:41,226] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81594fbf-a623-4bcc-8e10-f24a82db1faf/dqc_reference/checkm_data
[2024-01-24 13:22:41,226] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:41,277] [INFO] Task started: CheckM
[2024-01-24 13:22:41,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001552575.1_ASM155257v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001552575.1_ASM155257v1_genomic.fna/checkm_input GCF_001552575.1_ASM155257v1_genomic.fna/checkm_result
[2024-01-24 13:23:37,163] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:37,164] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:37,177] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:37,177] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:37,177] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001552575.1_ASM155257v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:37,178] [INFO] Task started: Blastn
[2024-01-24 13:23:37,178] [INFO] Running command: blastn -query GCF_001552575.1_ASM155257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81594fbf-a623-4bcc-8e10-f24a82db1faf/dqc_reference/reference_markers_gtdb.fasta -out GCF_001552575.1_ASM155257v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:39,096] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:39,099] [INFO] Selected 9 target genomes.
[2024-01-24 13:23:39,099] [INFO] Target genome list was writen to GCF_001552575.1_ASM155257v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:39,103] [INFO] Task started: fastANI
[2024-01-24 13:23:39,104] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5e2e69b-cdea-4613-9589-4de0241a91e7/GCF_001552575.1_ASM155257v1_genomic.fna.gz --refList GCF_001552575.1_ASM155257v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001552575.1_ASM155257v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:50,122] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:50,128] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:50,128] [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_001646645.1	s__Rhodococcus hoagii	98.7077	1451	1707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.01	98.63	0.96	0.88	61	conclusive
GCF_003051005.1	s__Rhodococcus sp003051005	86.7079	1396	1707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011865.1	s__Rhodococcus agglutinans	85.9244	1319	1707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000738775.1	s__Rhodococcus defluvii	85.2857	1225	1707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005484805.1	s__Rhodococcus sp005484805	84.9731	1274	1707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013348805.1	s__Rhodococcus sp003350365	84.8918	1252	1707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.85	98.85	0.92	0.92	2	-
GCF_005434945.1	s__Rhodococcus subtropicus	83.5295	991	1707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011835.1	s__Rhodococcus sp004011835	82.1899	860	1707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011825.1	s__Rhodococcus sp004011825	82.0611	872	1707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:50,130] [INFO] GTDB search result was written to GCF_001552575.1_ASM155257v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:50,130] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:50,132] [INFO] DFAST_QC result json was written to GCF_001552575.1_ASM155257v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:50,133] [INFO] DFAST_QC completed!
[2024-01-24 13:23:50,133] [INFO] Total running time: 0h1m39s