[2024-01-24 11:50:49,795] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:50:49,797] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:50:49,798] [INFO] DQC Reference Directory: /var/lib/cwl/stg8594ed28-cc08-48f5-9be4-2e37f2d929f9/dqc_reference
[2024-01-24 11:50:51,031] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:50:51,031] [INFO] Task started: Prodigal
[2024-01-24 11:50:51,032] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9ec07d7-dc87-487a-b362-039e9d6d6373/GCF_008041935.1_ASM804193v1_genomic.fna.gz | prodigal -d GCF_008041935.1_ASM804193v1_genomic.fna/cds.fna -a GCF_008041935.1_ASM804193v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:04,572] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:04,572] [INFO] Task started: HMMsearch
[2024-01-24 11:51:04,573] [INFO] Running command: hmmsearch --tblout GCF_008041935.1_ASM804193v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8594ed28-cc08-48f5-9be4-2e37f2d929f9/dqc_reference/reference_markers.hmm GCF_008041935.1_ASM804193v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:04,860] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:04,861] [INFO] Found 6/6 markers.
[2024-01-24 11:51:04,901] [INFO] Query marker FASTA was written to GCF_008041935.1_ASM804193v1_genomic.fna/markers.fasta
[2024-01-24 11:51:04,902] [INFO] Task started: Blastn
[2024-01-24 11:51:04,902] [INFO] Running command: blastn -query GCF_008041935.1_ASM804193v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8594ed28-cc08-48f5-9be4-2e37f2d929f9/dqc_reference/reference_markers.fasta -out GCF_008041935.1_ASM804193v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:06,226] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:06,230] [INFO] Selected 17 target genomes.
[2024-01-24 11:51:06,230] [INFO] Target genome list was writen to GCF_008041935.1_ASM804193v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:07,465] [INFO] Task started: fastANI
[2024-01-24 11:51:07,466] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9ec07d7-dc87-487a-b362-039e9d6d6373/GCF_008041935.1_ASM804193v1_genomic.fna.gz --refList GCF_008041935.1_ASM804193v1_genomic.fna/target_genomes.txt --output GCF_008041935.1_ASM804193v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:25,430] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:25,431] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8594ed28-cc08-48f5-9be4-2e37f2d929f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:25,431] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8594ed28-cc08-48f5-9be4-2e37f2d929f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:25,450] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:25,450] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:25,450] [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 setariae	strain=DD2A	GCA_008041935.1	2593304	2593304	type	True	100.0	1619	1622	95	conclusive
Quadrisphaera granulorum	strain=DSM 44889	GCA_900218025.1	317664	317664	type	True	86.2785	1123	1622	95	below_threshold
Quadrisphaera granulorum	strain=DSM 44889	GCA_003149145.1	317664	317664	type	True	86.2784	1123	1622	95	below_threshold
Kineococcus indalonis	strain=T90	GCA_009906395.1	2696566	2696566	type	True	78.2866	518	1622	95	below_threshold
Pseudokineococcus marinus	strain=JCM 14547	GCA_013004605.1	351215	351215	type	True	77.9578	486	1622	95	below_threshold
Pseudokineococcus lusitanus	strain=CECT 7306	GCA_003751265.1	763993	763993	type	True	77.5899	616	1622	95	below_threshold
Kineococcus xinjiangensis	strain=DSM 22857	GCA_002934625.1	512762	512762	type	True	77.5599	583	1622	95	below_threshold
Ornithinicoccus halotolerans	strain=EGI 80423	GCA_009602535.1	1748220	1748220	type	True	77.0471	344	1622	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	77.0415	409	1622	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	77.041	480	1622	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	76.9384	363	1622	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.8358	465	1622	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	76.8093	522	1622	95	below_threshold
Cellulomonas marina	strain=CGMCC 4.6945	GCA_900111925.1	988821	988821	type	True	76.7697	540	1622	95	below_threshold
Actinokineospora baliensis	strain=DSM 45656	GCA_016907695.1	547056	547056	type	True	76.2161	407	1622	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	75.9766	437	1622	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	75.8927	519	1622	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:25,452] [INFO] DFAST Taxonomy check result was written to GCF_008041935.1_ASM804193v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:25,452] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:25,452] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:25,453] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8594ed28-cc08-48f5-9be4-2e37f2d929f9/dqc_reference/checkm_data
[2024-01-24 11:51:25,454] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:25,504] [INFO] Task started: CheckM
[2024-01-24 11:51:25,504] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008041935.1_ASM804193v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008041935.1_ASM804193v1_genomic.fna/checkm_input GCF_008041935.1_ASM804193v1_genomic.fna/checkm_result
[2024-01-24 11:52:46,114] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:46,116] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:46,138] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:46,138] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:46,139] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008041935.1_ASM804193v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:46,139] [INFO] Task started: Blastn
[2024-01-24 11:52:46,140] [INFO] Running command: blastn -query GCF_008041935.1_ASM804193v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8594ed28-cc08-48f5-9be4-2e37f2d929f9/dqc_reference/reference_markers_gtdb.fasta -out GCF_008041935.1_ASM804193v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:48,181] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:48,185] [INFO] Selected 7 target genomes.
[2024-01-24 11:52:48,185] [INFO] Target genome list was writen to GCF_008041935.1_ASM804193v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:48,192] [INFO] Task started: fastANI
[2024-01-24 11:52:48,192] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9ec07d7-dc87-487a-b362-039e9d6d6373/GCF_008041935.1_ASM804193v1_genomic.fna.gz --refList GCF_008041935.1_ASM804193v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008041935.1_ASM804193v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:57,766] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:57,774] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:57,774] [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_008041935.1	s__Quadrisphaera sp008041935	100.0	1619	1622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006335115.1	s__Quadrisphaera sp006335115	88.8307	1237	1622	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	88.7385	1224	1622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149145.1	s__Quadrisphaera granulorum	86.2887	1122	1622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015390235.1	s__Quadrisphaera sp015390235	84.7578	1051	1622	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	79.4439	635	1622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751265.1	s__Pseudokineococcus lusitanus	77.6075	613	1622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Pseudokineococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:57,777] [INFO] GTDB search result was written to GCF_008041935.1_ASM804193v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:57,777] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:57,781] [INFO] DFAST_QC result json was written to GCF_008041935.1_ASM804193v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:57,781] [INFO] DFAST_QC completed!
[2024-01-24 11:52:57,781] [INFO] Total running time: 0h2m8s