[2024-01-24 10:58:06,469] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:06,472] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:06,472] [INFO] DQC Reference Directory: /var/lib/cwl/stgb69d769d-5849-4045-b8d3-ef58c7e993af/dqc_reference
[2024-01-24 10:58:09,632] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:09,633] [INFO] Task started: Prodigal
[2024-01-24 10:58:09,633] [INFO] Running command: gunzip -c /var/lib/cwl/stgcac46b07-b296-4c15-87ce-fc7dc67345de/GCF_004345665.1_ASM434566v1_genomic.fna.gz | prodigal -d GCF_004345665.1_ASM434566v1_genomic.fna/cds.fna -a GCF_004345665.1_ASM434566v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:32,809] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:32,810] [INFO] Task started: HMMsearch
[2024-01-24 10:58:32,810] [INFO] Running command: hmmsearch --tblout GCF_004345665.1_ASM434566v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb69d769d-5849-4045-b8d3-ef58c7e993af/dqc_reference/reference_markers.hmm GCF_004345665.1_ASM434566v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:33,279] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:33,281] [INFO] Found 6/6 markers.
[2024-01-24 10:58:33,347] [INFO] Query marker FASTA was written to GCF_004345665.1_ASM434566v1_genomic.fna/markers.fasta
[2024-01-24 10:58:33,348] [INFO] Task started: Blastn
[2024-01-24 10:58:33,348] [INFO] Running command: blastn -query GCF_004345665.1_ASM434566v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb69d769d-5849-4045-b8d3-ef58c7e993af/dqc_reference/reference_markers.fasta -out GCF_004345665.1_ASM434566v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:34,604] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:34,608] [INFO] Selected 16 target genomes.
[2024-01-24 10:58:34,608] [INFO] Target genome list was writen to GCF_004345665.1_ASM434566v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:34,625] [INFO] Task started: fastANI
[2024-01-24 10:58:34,625] [INFO] Running command: fastANI --query /var/lib/cwl/stgcac46b07-b296-4c15-87ce-fc7dc67345de/GCF_004345665.1_ASM434566v1_genomic.fna.gz --refList GCF_004345665.1_ASM434566v1_genomic.fna/target_genomes.txt --output GCF_004345665.1_ASM434566v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:59:03,683] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:03,683] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb69d769d-5849-4045-b8d3-ef58c7e993af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:59:03,684] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb69d769d-5849-4045-b8d3-ef58c7e993af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:59:03,699] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:59:03,700] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:59:03,700] [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
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	85.6736	1637	2689	95	below_threshold
Kribbella capetownensis	strain=YM53	GCA_004331485.1	1572659	1572659	type	True	85.1114	1847	2689	95	below_threshold
Kribbella pittospori	strain=NRRL B-24813	GCA_004331465.1	722689	722689	type	True	85.1064	1853	2689	95	below_threshold
Kribbella jiaozuonensis	strain=NEAU-THZ27	GCA_005233875.1	2575441	2575441	type	True	84.0582	1754	2689	95	below_threshold
Kribbella sindirgiensis	strain=DSM 27082	GCA_004331435.1	1124744	1124744	type	True	84.0179	1822	2689	95	below_threshold
Kribbella speibonae	strain=YM55	GCA_004331375.1	1572660	1572660	type	True	83.9737	1864	2689	95	below_threshold
Kribbella shirazensis	strain=DSM 45490	GCA_011761605.1	1105143	1105143	type	True	83.9172	1780	2689	95	below_threshold
Kribbella aluminosa	strain=DSM 18824	GCA_017876295.1	416017	416017	type	True	83.7529	1689	2689	95	below_threshold
Kribbella jejuensis	strain=DSM 17305	GCA_006715085.1	236068	236068	type	True	83.7251	1673	2689	95	below_threshold
Kribbella solani	strain=DSM 17294	GCA_014205295.1	236067	236067	type	True	83.234	1567	2689	95	below_threshold
Kribbella flavida	strain=DSM 17836	GCA_000024345.1	182640	182640	type	True	83.0811	1505	2689	95	below_threshold
Kribbella sandramycini	strain=DSM 15626	GCA_014207795.1	60450	60450	type	True	83.0802	1530	2689	95	below_threshold
Kribbella sandramycini	strain=ATCC 39419	GCA_013131805.1	60450	60450	type	True	83.0656	1535	2689	95	below_threshold
Kribbella amoyensis	strain=DSM 24683	GCA_007828865.1	996641	996641	type	True	82.983	1551	2689	95	below_threshold
Kribbella antibiotica	strain=JCM 13523	GCA_004349055.1	190195	190195	type	True	82.4454	1515	2689	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	77.8781	497	2689	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:59:03,701] [INFO] DFAST Taxonomy check result was written to GCF_004345665.1_ASM434566v1_genomic.fna/tc_result.tsv
[2024-01-24 10:59:03,702] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:59:03,702] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:59:03,702] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb69d769d-5849-4045-b8d3-ef58c7e993af/dqc_reference/checkm_data
[2024-01-24 10:59:03,703] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:59:03,782] [INFO] Task started: CheckM
[2024-01-24 10:59:03,783] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004345665.1_ASM434566v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004345665.1_ASM434566v1_genomic.fna/checkm_input GCF_004345665.1_ASM434566v1_genomic.fna/checkm_result
[2024-01-24 11:00:13,208] [INFO] Task succeeded: CheckM
[2024-01-24 11:00:13,210] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:00:13,235] [INFO] ===== Completeness check finished =====
[2024-01-24 11:00:13,235] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:00:13,236] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004345665.1_ASM434566v1_genomic.fna/markers.fasta)
[2024-01-24 11:00:13,236] [INFO] Task started: Blastn
[2024-01-24 11:00:13,237] [INFO] Running command: blastn -query GCF_004345665.1_ASM434566v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb69d769d-5849-4045-b8d3-ef58c7e993af/dqc_reference/reference_markers_gtdb.fasta -out GCF_004345665.1_ASM434566v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:00:15,171] [INFO] Task succeeded: Blastn
[2024-01-24 11:00:15,176] [INFO] Selected 15 target genomes.
[2024-01-24 11:00:15,176] [INFO] Target genome list was writen to GCF_004345665.1_ASM434566v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:00:15,187] [INFO] Task started: fastANI
[2024-01-24 11:00:15,187] [INFO] Running command: fastANI --query /var/lib/cwl/stgcac46b07-b296-4c15-87ce-fc7dc67345de/GCF_004345665.1_ASM434566v1_genomic.fna.gz --refList GCF_004345665.1_ASM434566v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004345665.1_ASM434566v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:00:44,779] [INFO] Task succeeded: fastANI
[2024-01-24 11:00:44,798] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:00:44,809] [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_004345665.1	s__Kribbella sp004345665	100.0	2686	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004342025.1	s__Kribbella sp004342025	86.5461	2023	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348725.1	s__Kribbella sp004348725	85.6944	1633	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331485.1	s__Kribbella sp004331485	85.1248	1845	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331465.1	s__Kribbella pittospori	85.0901	1857	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216905.1	s__Kribbella sp004216905	84.1395	1829	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331345.1	s__Kribbella soli	84.1255	1854	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366075.1	s__Kribbella sp004366075	84.1131	1838	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	97.22	95.50	0.92	0.87	3	-
GCF_005233875.1	s__Kribbella sp005233875	84.113	1744	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365875.1	s__Kribbella sp004365875	84.0356	1787	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761605.1	s__Kribbella shirazensis	83.9382	1776	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217145.1	s__Kribbella soli_A	83.7597	1800	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876295.1	s__Kribbella aluminosa	83.7465	1690	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715085.1	s__Kribbella jejuensis	83.7164	1675	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007828865.1	s__Kribbella amoyensis	82.9859	1551	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:00:44,811] [INFO] GTDB search result was written to GCF_004345665.1_ASM434566v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:00:44,812] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:00:44,818] [INFO] DFAST_QC result json was written to GCF_004345665.1_ASM434566v1_genomic.fna/dqc_result.json
[2024-01-24 11:00:44,818] [INFO] DFAST_QC completed!
[2024-01-24 11:00:44,818] [INFO] Total running time: 0h2m38s