[2024-01-24 13:55:20,002] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:20,006] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:20,006] [INFO] DQC Reference Directory: /var/lib/cwl/stg377cb59c-8417-4745-8d49-cc0fccca28fb/dqc_reference
[2024-01-24 13:55:21,333] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:21,334] [INFO] Task started: Prodigal
[2024-01-24 13:55:21,334] [INFO] Running command: gunzip -c /var/lib/cwl/stg875c584c-c115-49a3-82d4-717645246909/GCF_009193255.1_ASM919325v1_genomic.fna.gz | prodigal -d GCF_009193255.1_ASM919325v1_genomic.fna/cds.fna -a GCF_009193255.1_ASM919325v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:32,714] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:32,715] [INFO] Task started: HMMsearch
[2024-01-24 13:55:32,715] [INFO] Running command: hmmsearch --tblout GCF_009193255.1_ASM919325v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg377cb59c-8417-4745-8d49-cc0fccca28fb/dqc_reference/reference_markers.hmm GCF_009193255.1_ASM919325v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:32,979] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:32,980] [INFO] Found 6/6 markers.
[2024-01-24 13:55:33,011] [INFO] Query marker FASTA was written to GCF_009193255.1_ASM919325v1_genomic.fna/markers.fasta
[2024-01-24 13:55:33,012] [INFO] Task started: Blastn
[2024-01-24 13:55:33,012] [INFO] Running command: blastn -query GCF_009193255.1_ASM919325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg377cb59c-8417-4745-8d49-cc0fccca28fb/dqc_reference/reference_markers.fasta -out GCF_009193255.1_ASM919325v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:34,167] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:34,170] [INFO] Selected 10 target genomes.
[2024-01-24 13:55:34,170] [INFO] Target genome list was writen to GCF_009193255.1_ASM919325v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:34,176] [INFO] Task started: fastANI
[2024-01-24 13:55:34,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg875c584c-c115-49a3-82d4-717645246909/GCF_009193255.1_ASM919325v1_genomic.fna.gz --refList GCF_009193255.1_ASM919325v1_genomic.fna/target_genomes.txt --output GCF_009193255.1_ASM919325v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:42,561] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:42,562] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg377cb59c-8417-4745-8d49-cc0fccca28fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:42,562] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg377cb59c-8417-4745-8d49-cc0fccca28fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:42,573] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:42,573] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:42,573] [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
Arthrobacter koreensis	strain=DSM 16760	GCA_009193255.1	199136	199136	type	True	100.0	1174	1175	95	conclusive
Arthrobacter citreus	strain=DSM 20133	GCA_009192745.1	1670	1670	type	True	88.3383	989	1175	95	below_threshold
Arthrobacter luteolus	strain=NBRC 107841	GCA_001552075.1	98672	98672	type	True	82.2819	815	1175	95	below_threshold
Arthrobacter pullicola	strain=Sa2BUA2	GCA_014836875.1	2762224	2762224	type	True	82.1176	792	1175	95	below_threshold
Arthrobacter luteolus	strain=DSM 13067	GCA_008973725.1	98672	98672	type	True	82.105	820	1175	95	below_threshold
Arthrobacter gallicola	strain=Sa2CUA1	GCA_014836775.1	2762225	2762225	type	True	82.0645	758	1175	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	80.5592	572	1175	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	80.4841	571	1175	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	80.2967	554	1175	95	below_threshold
Arthrobacter yangruifuii	strain=785	GCA_009192775.1	2606616	2606616	type	True	80.196	557	1175	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:42,575] [INFO] DFAST Taxonomy check result was written to GCF_009193255.1_ASM919325v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:42,576] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:42,576] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:42,576] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg377cb59c-8417-4745-8d49-cc0fccca28fb/dqc_reference/checkm_data
[2024-01-24 13:55:42,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:42,619] [INFO] Task started: CheckM
[2024-01-24 13:55:42,619] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009193255.1_ASM919325v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009193255.1_ASM919325v1_genomic.fna/checkm_input GCF_009193255.1_ASM919325v1_genomic.fna/checkm_result
[2024-01-24 13:56:16,549] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:16,550] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:16,571] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:16,571] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:16,572] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009193255.1_ASM919325v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:16,572] [INFO] Task started: Blastn
[2024-01-24 13:56:16,572] [INFO] Running command: blastn -query GCF_009193255.1_ASM919325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg377cb59c-8417-4745-8d49-cc0fccca28fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_009193255.1_ASM919325v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:18,361] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:18,366] [INFO] Selected 8 target genomes.
[2024-01-24 13:56:18,366] [INFO] Target genome list was writen to GCF_009193255.1_ASM919325v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:18,378] [INFO] Task started: fastANI
[2024-01-24 13:56:18,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg875c584c-c115-49a3-82d4-717645246909/GCF_009193255.1_ASM919325v1_genomic.fna.gz --refList GCF_009193255.1_ASM919325v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009193255.1_ASM919325v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:25,073] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:25,081] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:25,081] [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_009193255.1	s__Arthrobacter_B koreensis	100.0	1174	1175	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	99.08	99.08	0.97	0.97	2	conclusive
GCF_015355785.1	s__Arthrobacter_B gandavensis_A	89.4935	1010	1175	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009192745.1	s__Arthrobacter_B citreus	88.3383	989	1175	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001307035.1	s__Arthrobacter_B sp001307035	84.7537	908	1175	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	98.39	98.39	0.92	0.92	2	-
GCF_001552075.1	s__Arthrobacter_B luteolus	82.2795	814	1175	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014836875.1	s__Arthrobacter_B sp014836875	82.1268	791	1175	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836775.1	s__Arthrobacter_B sp014836775	82.0645	758	1175	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900016675.1	s__Arthrobacter_B saudimassiliensis	80.6919	609	1175	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:25,083] [INFO] GTDB search result was written to GCF_009193255.1_ASM919325v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:25,083] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:25,086] [INFO] DFAST_QC result json was written to GCF_009193255.1_ASM919325v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:25,086] [INFO] DFAST_QC completed!
[2024-01-24 13:56:25,086] [INFO] Total running time: 0h1m5s