[2024-01-24 11:58:57,287] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:57,290] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:57,290] [INFO] DQC Reference Directory: /var/lib/cwl/stg1746a132-03e7-4951-894d-14ef680f8dfc/dqc_reference
[2024-01-24 11:58:58,680] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:58,681] [INFO] Task started: Prodigal
[2024-01-24 11:58:58,681] [INFO] Running command: gunzip -c /var/lib/cwl/stg49caab83-9209-404a-9b9a-8dffb6925ea1/GCF_003149145.1_ASM314914v1_genomic.fna.gz | prodigal -d GCF_003149145.1_ASM314914v1_genomic.fna/cds.fna -a GCF_003149145.1_ASM314914v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:12,349] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:12,350] [INFO] Task started: HMMsearch
[2024-01-24 11:59:12,350] [INFO] Running command: hmmsearch --tblout GCF_003149145.1_ASM314914v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1746a132-03e7-4951-894d-14ef680f8dfc/dqc_reference/reference_markers.hmm GCF_003149145.1_ASM314914v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:12,695] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:12,697] [INFO] Found 6/6 markers.
[2024-01-24 11:59:12,743] [INFO] Query marker FASTA was written to GCF_003149145.1_ASM314914v1_genomic.fna/markers.fasta
[2024-01-24 11:59:12,744] [INFO] Task started: Blastn
[2024-01-24 11:59:12,744] [INFO] Running command: blastn -query GCF_003149145.1_ASM314914v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1746a132-03e7-4951-894d-14ef680f8dfc/dqc_reference/reference_markers.fasta -out GCF_003149145.1_ASM314914v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:13,923] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:13,927] [INFO] Selected 18 target genomes.
[2024-01-24 11:59:13,927] [INFO] Target genome list was writen to GCF_003149145.1_ASM314914v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:13,933] [INFO] Task started: fastANI
[2024-01-24 11:59:13,933] [INFO] Running command: fastANI --query /var/lib/cwl/stg49caab83-9209-404a-9b9a-8dffb6925ea1/GCF_003149145.1_ASM314914v1_genomic.fna.gz --refList GCF_003149145.1_ASM314914v1_genomic.fna/target_genomes.txt --output GCF_003149145.1_ASM314914v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:30,991] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:30,992] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1746a132-03e7-4951-894d-14ef680f8dfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:30,992] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1746a132-03e7-4951-894d-14ef680f8dfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:31,007] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:59:31,007] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:31,007] [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
Quadrisphaera granulorum	strain=DSM 44889	GCA_003149145.1	317664	317664	type	True	100.0	1583	1586	95	conclusive
Quadrisphaera granulorum	strain=DSM 44889	GCA_900218025.1	317664	317664	type	True	100.0	1583	1586	95	conclusive
Quadrisphaera setariae	strain=DD2A	GCA_008041935.1	2593304	2593304	type	True	86.3228	1114	1586	95	below_threshold
Pseudokineococcus marinus	strain=JCM 14547	GCA_013004605.1	351215	351215	type	True	77.6469	416	1586	95	below_threshold
Kineococcus xinjiangensis	strain=DSM 22857	GCA_002934625.1	512762	512762	type	True	77.4684	490	1586	95	below_threshold
Pseudokineococcus lusitanus	strain=CECT 7306	GCA_003751265.1	763993	763993	type	True	77.4409	539	1586	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	77.1941	418	1586	95	below_threshold
Ornithinimicrobium tianjinense	strain=CGMCC 1.12160	GCA_014636495.1	1195761	1195761	type	True	77.0707	307	1586	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	77.0199	377	1586	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	76.9098	318	1586	95	below_threshold
Cellulomonas oligotrophica	strain=DSM 24482	GCA_013409875.1	931536	931536	type	True	76.8515	465	1586	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	76.8137	278	1586	95	below_threshold
Cellulomonas endophytica	strain=SYSUP0004	GCA_004123805.1	2494735	2494735	type	True	76.7528	423	1586	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.7021	421	1586	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	76.582	216	1586	95	below_threshold
Actinokineospora baliensis	strain=DSM 45656	GCA_016907695.1	547056	547056	type	True	76.2699	369	1586	95	below_threshold
Kitasatospora phosalacinea	strain=NRRL B-16230	GCA_000716545.1	2065	2065	type	True	76.2295	470	1586	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	76.0167	362	1586	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:31,009] [INFO] DFAST Taxonomy check result was written to GCF_003149145.1_ASM314914v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:31,010] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:31,010] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:31,010] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1746a132-03e7-4951-894d-14ef680f8dfc/dqc_reference/checkm_data
[2024-01-24 11:59:31,011] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:31,058] [INFO] Task started: CheckM
[2024-01-24 11:59:31,058] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003149145.1_ASM314914v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003149145.1_ASM314914v1_genomic.fna/checkm_input GCF_003149145.1_ASM314914v1_genomic.fna/checkm_result
[2024-01-24 12:00:24,530] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:24,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:24,550] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:24,550] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:24,550] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003149145.1_ASM314914v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:24,551] [INFO] Task started: Blastn
[2024-01-24 12:00:24,551] [INFO] Running command: blastn -query GCF_003149145.1_ASM314914v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1746a132-03e7-4951-894d-14ef680f8dfc/dqc_reference/reference_markers_gtdb.fasta -out GCF_003149145.1_ASM314914v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:26,351] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:26,355] [INFO] Selected 10 target genomes.
[2024-01-24 12:00:26,355] [INFO] Target genome list was writen to GCF_003149145.1_ASM314914v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:26,362] [INFO] Task started: fastANI
[2024-01-24 12:00:26,362] [INFO] Running command: fastANI --query /var/lib/cwl/stg49caab83-9209-404a-9b9a-8dffb6925ea1/GCF_003149145.1_ASM314914v1_genomic.fna.gz --refList GCF_003149145.1_ASM314914v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003149145.1_ASM314914v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:36,976] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:36,986] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:36,986] [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_003149145.1	s__Quadrisphaera granulorum	100.0	1583	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_008041935.1	s__Quadrisphaera sp008041935	86.298	1116	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006335115.1	s__Quadrisphaera sp006335115	85.6481	1054	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014270065.1	s__Quadrisphaera sp014270065	85.5502	1081	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015390235.1	s__Quadrisphaera sp015390235	83.5244	898	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101335.1	s__Quadrisphaera sp900101335	79.0035	570	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013004605.1	s__Pseudokineococcus marinus	77.6845	411	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Pseudokineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751265.1	s__Pseudokineococcus lusitanus	77.5033	528	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Pseudokineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990265.1	s__Cellulomonas terrae	77.0309	392	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013359775.1	s__Cellulomonas humilata	76.8412	395	1586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:36,988] [INFO] GTDB search result was written to GCF_003149145.1_ASM314914v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:36,988] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:36,993] [INFO] DFAST_QC result json was written to GCF_003149145.1_ASM314914v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:36,993] [INFO] DFAST_QC completed!
[2024-01-24 12:00:36,993] [INFO] Total running time: 0h1m40s