[2024-01-24 14:22:33,318] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:33,321] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:33,322] [INFO] DQC Reference Directory: /var/lib/cwl/stg26313e32-9bd7-4b4a-8c4f-93e0904095c0/dqc_reference
[2024-01-24 14:22:34,637] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:34,638] [INFO] Task started: Prodigal
[2024-01-24 14:22:34,639] [INFO] Running command: gunzip -c /var/lib/cwl/stga807a3fe-920f-44c7-9a4d-320403655299/GCF_003219795.1_ASM321979v1_genomic.fna.gz | prodigal -d GCF_003219795.1_ASM321979v1_genomic.fna/cds.fna -a GCF_003219795.1_ASM321979v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:47,130] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:47,131] [INFO] Task started: HMMsearch
[2024-01-24 14:22:47,131] [INFO] Running command: hmmsearch --tblout GCF_003219795.1_ASM321979v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26313e32-9bd7-4b4a-8c4f-93e0904095c0/dqc_reference/reference_markers.hmm GCF_003219795.1_ASM321979v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:47,588] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:47,589] [INFO] Found 6/6 markers.
[2024-01-24 14:22:47,669] [INFO] Query marker FASTA was written to GCF_003219795.1_ASM321979v1_genomic.fna/markers.fasta
[2024-01-24 14:22:47,669] [INFO] Task started: Blastn
[2024-01-24 14:22:47,669] [INFO] Running command: blastn -query GCF_003219795.1_ASM321979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26313e32-9bd7-4b4a-8c4f-93e0904095c0/dqc_reference/reference_markers.fasta -out GCF_003219795.1_ASM321979v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:48,809] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:48,813] [INFO] Selected 14 target genomes.
[2024-01-24 14:22:48,814] [INFO] Target genome list was writen to GCF_003219795.1_ASM321979v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:48,826] [INFO] Task started: fastANI
[2024-01-24 14:22:48,826] [INFO] Running command: fastANI --query /var/lib/cwl/stga807a3fe-920f-44c7-9a4d-320403655299/GCF_003219795.1_ASM321979v1_genomic.fna.gz --refList GCF_003219795.1_ASM321979v1_genomic.fna/target_genomes.txt --output GCF_003219795.1_ASM321979v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:59,694] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:59,695] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26313e32-9bd7-4b4a-8c4f-93e0904095c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:59,695] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26313e32-9bd7-4b4a-8c4f-93e0904095c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:59,710] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:59,710] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:59,711] [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 psychrolactophilus	strain=B7	GCA_003219795.1	92442	92442	type	True	100.0	1261	1263	95	conclusive
Arthrobacter alpinus	strain=DSM 22274	GCA_900105965.1	656366	656366	suspected-type	True	82.6724	786	1263	95	below_threshold
Arthrobacter glacialis	strain=HLT2-12-2	GCA_002909445.1	1664	1664	type	True	80.9776	652	1263	95	below_threshold
Arthrobacter stackebrandtii	strain=DSM 16005	GCA_017876675.1	272161	272161	type	True	80.7403	672	1263	95	below_threshold
Arthrobacter psychrochitiniphilus	strain=DSM 23143	GCA_013408645.1	291045	291045	type	True	80.1366	517	1263	95	below_threshold
Arthrobacter psychrochitiniphilus	strain=GP3	GCA_003185915.1	291045	291045	type	True	80.0257	529	1263	95	below_threshold
Arthrobacter wenxiniae	strain=AETb3-4	GCA_013376105.1	2713570	2713570	type	True	79.7266	507	1263	95	below_threshold
Arthrobacter silviterrae	strain=DSM 27180	GCA_011045165.1	2026658	2026658	type	True	79.6392	500	1263	95	below_threshold
Arthrobacter dokdonellae		GCA_003268655.1	2211210	2211210	type	True	79.3997	519	1263	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	78.3637	221	1263	95	below_threshold
Paenarthrobacter nicotinovorans	strain=ATCC 49919	GCA_021919345.1	29320	29320	suspected-type	True	78.2483	249	1263	95	below_threshold
Arthrobacter cupressi	strain=DSM 24664	GCA_013409905.1	1045773	1045773	type	True	78.2467	265	1263	95	below_threshold
Arthrobacter ulcerisalmonis		GCA_900609065.1	2483813	2483813	type	True	78.0786	217	1263	95	below_threshold
Arthrobacter pullicola	strain=Sa2BUA2	GCA_014836875.1	2762224	2762224	type	True	77.7508	188	1263	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:59,712] [INFO] DFAST Taxonomy check result was written to GCF_003219795.1_ASM321979v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:59,713] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:59,713] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:59,713] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26313e32-9bd7-4b4a-8c4f-93e0904095c0/dqc_reference/checkm_data
[2024-01-24 14:22:59,715] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:59,756] [INFO] Task started: CheckM
[2024-01-24 14:22:59,756] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003219795.1_ASM321979v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003219795.1_ASM321979v1_genomic.fna/checkm_input GCF_003219795.1_ASM321979v1_genomic.fna/checkm_result
[2024-01-24 14:23:38,495] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:38,497] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:38,522] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:38,522] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:38,523] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003219795.1_ASM321979v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:38,524] [INFO] Task started: Blastn
[2024-01-24 14:23:38,524] [INFO] Running command: blastn -query GCF_003219795.1_ASM321979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26313e32-9bd7-4b4a-8c4f-93e0904095c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_003219795.1_ASM321979v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:39,866] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:39,869] [INFO] Selected 10 target genomes.
[2024-01-24 14:23:39,870] [INFO] Target genome list was writen to GCF_003219795.1_ASM321979v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:39,880] [INFO] Task started: fastANI
[2024-01-24 14:23:39,880] [INFO] Running command: fastANI --query /var/lib/cwl/stga807a3fe-920f-44c7-9a4d-320403655299/GCF_003219795.1_ASM321979v1_genomic.fna.gz --refList GCF_003219795.1_ASM321979v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003219795.1_ASM321979v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:49,095] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:49,115] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:49,116] [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_003219795.1	s__Specibacter psychrolactophilus	100.0	1261	1263	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_900105965.1	s__Specibacter alpinus	82.6796	786	1263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	96.92	96.92	0.91	0.91	2	-
GCF_001445575.1	s__Specibacter alpinus_C	81.4983	645	1263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929705.1	s__Specibacter sp002929705	81.4976	677	1263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820535.1	s__Specibacter sp016820535	81.195	658	1263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000785535.1	s__Specibacter sp000785535	81.0677	665	1263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002909445.1	s__Specibacter glacialis	80.9776	652	1263	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	99.29	99.29	0.92	0.92	2	-
GCF_017876675.1	s__Specibacter stackebrandtii	80.7408	672	1263	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	80.105	508	1263	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	79.664	507	1263	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 14:23:49,119] [INFO] GTDB search result was written to GCF_003219795.1_ASM321979v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:49,120] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:49,123] [INFO] DFAST_QC result json was written to GCF_003219795.1_ASM321979v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:49,123] [INFO] DFAST_QC completed!
[2024-01-24 14:23:49,123] [INFO] Total running time: 0h1m16s