[2024-01-25 17:53:50,649] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:53:50,650] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:53:50,650] [INFO] DQC Reference Directory: /var/lib/cwl/stga018502b-bf24-4f26-ab2b-622cb8250312/dqc_reference
[2024-01-25 17:53:51,861] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:53:51,862] [INFO] Task started: Prodigal
[2024-01-25 17:53:51,862] [INFO] Running command: gunzip -c /var/lib/cwl/stg59ef700b-a440-4f37-ace2-40109757b3ae/GCF_011045165.1_ASM1104516v1_genomic.fna.gz | prodigal -d GCF_011045165.1_ASM1104516v1_genomic.fna/cds.fna -a GCF_011045165.1_ASM1104516v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:54:04,492] [INFO] Task succeeded: Prodigal
[2024-01-25 17:54:04,493] [INFO] Task started: HMMsearch
[2024-01-25 17:54:04,493] [INFO] Running command: hmmsearch --tblout GCF_011045165.1_ASM1104516v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga018502b-bf24-4f26-ab2b-622cb8250312/dqc_reference/reference_markers.hmm GCF_011045165.1_ASM1104516v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:54:04,737] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:54:04,738] [INFO] Found 6/6 markers.
[2024-01-25 17:54:04,774] [INFO] Query marker FASTA was written to GCF_011045165.1_ASM1104516v1_genomic.fna/markers.fasta
[2024-01-25 17:54:04,774] [INFO] Task started: Blastn
[2024-01-25 17:54:04,774] [INFO] Running command: blastn -query GCF_011045165.1_ASM1104516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga018502b-bf24-4f26-ab2b-622cb8250312/dqc_reference/reference_markers.fasta -out GCF_011045165.1_ASM1104516v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:05,672] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:05,676] [INFO] Selected 12 target genomes.
[2024-01-25 17:54:05,676] [INFO] Target genome list was writen to GCF_011045165.1_ASM1104516v1_genomic.fna/target_genomes.txt
[2024-01-25 17:54:05,680] [INFO] Task started: fastANI
[2024-01-25 17:54:05,680] [INFO] Running command: fastANI --query /var/lib/cwl/stg59ef700b-a440-4f37-ace2-40109757b3ae/GCF_011045165.1_ASM1104516v1_genomic.fna.gz --refList GCF_011045165.1_ASM1104516v1_genomic.fna/target_genomes.txt --output GCF_011045165.1_ASM1104516v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:54:17,651] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:17,651] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga018502b-bf24-4f26-ab2b-622cb8250312/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:54:17,651] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga018502b-bf24-4f26-ab2b-622cb8250312/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:54:17,659] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:54:17,659] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:54:17,660] [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 silviterrae	strain=DSM 27180	GCA_011045165.1	2026658	2026658	type	True	100.0	1376	1382	95	conclusive
Arthrobacter wenxiniae	strain=AETb3-4	GCA_013376105.1	2713570	2713570	type	True	83.4503	902	1382	95	below_threshold
Arthrobacter dokdonellae		GCA_003268655.1	2211210	2211210	type	True	83.067	890	1382	95	below_threshold
Arthrobacter livingstonensis	strain=LI2	GCA_003219815.1	670078	670078	type	True	82.4164	917	1382	95	below_threshold
Arthrobacter stackebrandtii	strain=DSM 16005	GCA_017876675.1	272161	272161	type	True	81.655	763	1382	95	below_threshold
Arthrobacter glacialis	strain=HLT2-12-2	GCA_002909445.1	1664	1664	type	True	80.2633	613	1382	95	below_threshold
Arthrobacter alpinus	strain=DSM 22274	GCA_900105965.1	656366	656366	suspected-type	True	80.0218	560	1382	95	below_threshold
Arthrobacter cryoconiti	strain=Cr6-08	GCA_020905375.1	748907	748907	type	True	78.9481	408	1382	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	78.3251	314	1382	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.3235	355	1382	95	below_threshold
Arthrobacter ulcerisalmonis		GCA_900609065.1	2483813	2483813	type	True	78.2583	332	1382	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:54:17,661] [INFO] DFAST Taxonomy check result was written to GCF_011045165.1_ASM1104516v1_genomic.fna/tc_result.tsv
[2024-01-25 17:54:17,662] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:54:17,662] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:54:17,662] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga018502b-bf24-4f26-ab2b-622cb8250312/dqc_reference/checkm_data
[2024-01-25 17:54:17,663] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:54:17,704] [INFO] Task started: CheckM
[2024-01-25 17:54:17,704] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011045165.1_ASM1104516v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011045165.1_ASM1104516v1_genomic.fna/checkm_input GCF_011045165.1_ASM1104516v1_genomic.fna/checkm_result
[2024-01-25 17:54:57,179] [INFO] Task succeeded: CheckM
[2024-01-25 17:54:57,179] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:54:57,199] [INFO] ===== Completeness check finished =====
[2024-01-25 17:54:57,199] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:54:57,199] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011045165.1_ASM1104516v1_genomic.fna/markers.fasta)
[2024-01-25 17:54:57,199] [INFO] Task started: Blastn
[2024-01-25 17:54:57,199] [INFO] Running command: blastn -query GCF_011045165.1_ASM1104516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga018502b-bf24-4f26-ab2b-622cb8250312/dqc_reference/reference_markers_gtdb.fasta -out GCF_011045165.1_ASM1104516v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:58,601] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:58,604] [INFO] Selected 17 target genomes.
[2024-01-25 17:54:58,604] [INFO] Target genome list was writen to GCF_011045165.1_ASM1104516v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:54:58,613] [INFO] Task started: fastANI
[2024-01-25 17:54:58,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg59ef700b-a440-4f37-ace2-40109757b3ae/GCF_011045165.1_ASM1104516v1_genomic.fna.gz --refList GCF_011045165.1_ASM1104516v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011045165.1_ASM1104516v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:55:14,591] [INFO] Task succeeded: fastANI
[2024-01-25 17:55:14,600] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:55:14,600] [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_011045165.1	s__Specibacter silviterrae	100.0	1376	1382	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	83.45	902	1382	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	83.1738	891	1382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003268655.1	s__Specibacter dokdonellae	83.0255	895	1382	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	82.4583	823	1382	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	82.4246	916	1382	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	81.6571	764	1382	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	81.5176	728	1382	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	80.8211	629	1382	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	80.7935	701	1382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001294625.1	s__Specibacter alpinus_A	80.5956	666	1382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	99.52	99.48	0.93	0.92	3	-
GCF_900105965.1	s__Specibacter alpinus	80.044	558	1382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	96.92	96.92	0.91	0.91	2	-
GCF_017368795.1	s__PO-11 sp017368795	79.1695	437	1382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__PO-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000619965.1	s__Arachnia sp000619965	76.1337	85	1382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:55:14,601] [INFO] GTDB search result was written to GCF_011045165.1_ASM1104516v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:55:14,601] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:55:14,604] [INFO] DFAST_QC result json was written to GCF_011045165.1_ASM1104516v1_genomic.fna/dqc_result.json
[2024-01-25 17:55:14,604] [INFO] DFAST_QC completed!
[2024-01-25 17:55:14,604] [INFO] Total running time: 0h1m24s