[2024-01-24 14:12:45,754] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:45,756] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:45,756] [INFO] DQC Reference Directory: /var/lib/cwl/stg20d591a0-4139-4ae2-97f1-9bd10831192f/dqc_reference
[2024-01-24 14:12:47,042] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:47,043] [INFO] Task started: Prodigal
[2024-01-24 14:12:47,044] [INFO] Running command: gunzip -c /var/lib/cwl/stg11443028-07e4-4266-95f1-972e1a9b59c6/GCF_003268655.1_ASM326865v1_genomic.fna.gz | prodigal -d GCF_003268655.1_ASM326865v1_genomic.fna/cds.fna -a GCF_003268655.1_ASM326865v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:02,182] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:02,182] [INFO] Task started: HMMsearch
[2024-01-24 14:13:02,182] [INFO] Running command: hmmsearch --tblout GCF_003268655.1_ASM326865v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20d591a0-4139-4ae2-97f1-9bd10831192f/dqc_reference/reference_markers.hmm GCF_003268655.1_ASM326865v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:02,500] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:02,501] [INFO] Found 6/6 markers.
[2024-01-24 14:13:02,547] [INFO] Query marker FASTA was written to GCF_003268655.1_ASM326865v1_genomic.fna/markers.fasta
[2024-01-24 14:13:02,547] [INFO] Task started: Blastn
[2024-01-24 14:13:02,547] [INFO] Running command: blastn -query GCF_003268655.1_ASM326865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20d591a0-4139-4ae2-97f1-9bd10831192f/dqc_reference/reference_markers.fasta -out GCF_003268655.1_ASM326865v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:03,654] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:03,658] [INFO] Selected 12 target genomes.
[2024-01-24 14:13:03,658] [INFO] Target genome list was writen to GCF_003268655.1_ASM326865v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:03,664] [INFO] Task started: fastANI
[2024-01-24 14:13:03,664] [INFO] Running command: fastANI --query /var/lib/cwl/stg11443028-07e4-4266-95f1-972e1a9b59c6/GCF_003268655.1_ASM326865v1_genomic.fna.gz --refList GCF_003268655.1_ASM326865v1_genomic.fna/target_genomes.txt --output GCF_003268655.1_ASM326865v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:14,579] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:14,580] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20d591a0-4139-4ae2-97f1-9bd10831192f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:14,580] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20d591a0-4139-4ae2-97f1-9bd10831192f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:14,594] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:14,594] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:14,594] [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 dokdonellae		GCA_003268655.1	2211210	2211210	type	True	100.0	1506	1510	95	conclusive
Arthrobacter wenxiniae	strain=AETb3-4	GCA_013376105.1	2713570	2713570	type	True	86.9821	1030	1510	95	below_threshold
Arthrobacter livingstonensis	strain=LI2	GCA_003219815.1	670078	670078	type	True	84.5275	1024	1510	95	below_threshold
Arthrobacter silviterrae	strain=DSM 27180	GCA_011045165.1	2026658	2026658	type	True	83.0655	896	1510	95	below_threshold
Arthrobacter stackebrandtii	strain=DSM 16005	GCA_017876675.1	272161	272161	type	True	81.7908	750	1510	95	below_threshold
Arthrobacter alpinus	strain=DSM 22274	GCA_900105965.1	656366	656366	suspected-type	True	80.0209	569	1510	95	below_threshold
Arthrobacter cupressi	strain=DSM 24664	GCA_013409905.1	1045773	1045773	type	True	79.3893	470	1510	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.9003	342	1510	95	below_threshold
Arthrobacter pascens	strain=DSM 20545	GCA_017052465.1	1677	1677	type	True	78.8279	452	1510	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	78.6242	340	1510	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	78.5787	347	1510	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.5062	399	1510	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:14,596] [INFO] DFAST Taxonomy check result was written to GCF_003268655.1_ASM326865v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:14,597] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:14,597] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:14,597] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20d591a0-4139-4ae2-97f1-9bd10831192f/dqc_reference/checkm_data
[2024-01-24 14:13:14,598] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:14,645] [INFO] Task started: CheckM
[2024-01-24 14:13:14,645] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003268655.1_ASM326865v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003268655.1_ASM326865v1_genomic.fna/checkm_input GCF_003268655.1_ASM326865v1_genomic.fna/checkm_result
[2024-01-24 14:14:02,548] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:02,550] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:02,575] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:02,576] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:02,576] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003268655.1_ASM326865v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:02,577] [INFO] Task started: Blastn
[2024-01-24 14:14:02,577] [INFO] Running command: blastn -query GCF_003268655.1_ASM326865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20d591a0-4139-4ae2-97f1-9bd10831192f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003268655.1_ASM326865v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:04,370] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:04,376] [INFO] Selected 9 target genomes.
[2024-01-24 14:14:04,376] [INFO] Target genome list was writen to GCF_003268655.1_ASM326865v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:04,396] [INFO] Task started: fastANI
[2024-01-24 14:14:04,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg11443028-07e4-4266-95f1-972e1a9b59c6/GCF_003268655.1_ASM326865v1_genomic.fna.gz --refList GCF_003268655.1_ASM326865v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003268655.1_ASM326865v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:16,093] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:16,106] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:16,116] [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_003268655.1	s__Specibacter dokdonellae	100.0	1502	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013376105.1	s__Specibacter sp013376105	86.9704	1031	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013376095.1	s__Specibacter sp013376095	85.2219	946	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003219815.1	s__Specibacter livingstonensis	84.5298	1024	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045165.1	s__Specibacter silviterrae	83.0266	900	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001281315.1	s__Specibacter sp001281315	82.6194	863	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876675.1	s__Specibacter stackebrandtii	81.7911	750	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946885.1	s__Specibacter cremeus	80.7086	687	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929305.1	s__Specibacter sp002929305	80.4187	637	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:16,132] [INFO] GTDB search result was written to GCF_003268655.1_ASM326865v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:16,133] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:16,136] [INFO] DFAST_QC result json was written to GCF_003268655.1_ASM326865v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:16,137] [INFO] DFAST_QC completed!
[2024-01-24 14:14:16,137] [INFO] Total running time: 0h1m30s