[2024-01-24 10:47:06,896] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,899] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,899] [INFO] DQC Reference Directory: /var/lib/cwl/stg781b7e7d-7766-48a9-997d-174c6e794a57/dqc_reference
[2024-01-24 10:47:11,830] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:11,922] [INFO] Task started: Prodigal
[2024-01-24 10:47:11,923] [INFO] Running command: gunzip -c /var/lib/cwl/stg33782f9a-7e9d-47ae-ab88-32146f1c529a/GCF_016863355.1_ASM1686335v1_genomic.fna.gz | prodigal -d GCF_016863355.1_ASM1686335v1_genomic.fna/cds.fna -a GCF_016863355.1_ASM1686335v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:34,640] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:34,640] [INFO] Task started: HMMsearch
[2024-01-24 10:47:34,640] [INFO] Running command: hmmsearch --tblout GCF_016863355.1_ASM1686335v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg781b7e7d-7766-48a9-997d-174c6e794a57/dqc_reference/reference_markers.hmm GCF_016863355.1_ASM1686335v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:35,033] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:35,036] [INFO] Found 6/6 markers.
[2024-01-24 10:47:35,106] [INFO] Query marker FASTA was written to GCF_016863355.1_ASM1686335v1_genomic.fna/markers.fasta
[2024-01-24 10:47:35,107] [INFO] Task started: Blastn
[2024-01-24 10:47:35,107] [INFO] Running command: blastn -query GCF_016863355.1_ASM1686335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg781b7e7d-7766-48a9-997d-174c6e794a57/dqc_reference/reference_markers.fasta -out GCF_016863355.1_ASM1686335v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:36,459] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:36,462] [INFO] Selected 10 target genomes.
[2024-01-24 10:47:36,463] [INFO] Target genome list was writen to GCF_016863355.1_ASM1686335v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:36,509] [INFO] Task started: fastANI
[2024-01-24 10:47:36,510] [INFO] Running command: fastANI --query /var/lib/cwl/stg33782f9a-7e9d-47ae-ab88-32146f1c529a/GCF_016863355.1_ASM1686335v1_genomic.fna.gz --refList GCF_016863355.1_ASM1686335v1_genomic.fna/target_genomes.txt --output GCF_016863355.1_ASM1686335v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:01,323] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:01,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg781b7e7d-7766-48a9-997d-174c6e794a57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:01,324] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg781b7e7d-7766-48a9-997d-174c6e794a57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:01,348] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:48:01,348] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:01,348] [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
Sphaerisporangium krabiense	strain=NBRC 107571	GCA_016863355.1	763782	763782	type	True	100.0	2787	2789	95	conclusive
Sphaerisporangium krabiense	strain=DSM 45790	GCA_014200435.1	763782	763782	type	True	99.9989	2770	2789	95	conclusive
Sphaerisporangium siamense	strain=NBRC 107570	GCA_016863415.1	795645	795645	type	True	94.5804	2391	2789	95	below_threshold
Sphaerisporangium siamense	strain=DSM 45784	GCA_014205275.1	795645	795645	type	True	94.5739	2405	2789	95	below_threshold
Sphaerisporangium album	strain=CCTCC AA 208026	GCA_003323745.1	509200	509200	type	True	86.2639	1804	2789	95	below_threshold
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	83.0452	1569	2789	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	79.7608	1353	2789	95	below_threshold
Sphaerimonospora thailandensis	strain=NBRC 107569	GCA_016863115.1	795644	795644	type	True	79.5584	935	2789	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.5504	887	2789	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	79.355	1300	2789	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:01,350] [INFO] DFAST Taxonomy check result was written to GCF_016863355.1_ASM1686335v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:01,351] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:01,351] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:01,351] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg781b7e7d-7766-48a9-997d-174c6e794a57/dqc_reference/checkm_data
[2024-01-24 10:48:01,353] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:01,437] [INFO] Task started: CheckM
[2024-01-24 10:48:01,437] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016863355.1_ASM1686335v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016863355.1_ASM1686335v1_genomic.fna/checkm_input GCF_016863355.1_ASM1686335v1_genomic.fna/checkm_result
[2024-01-24 10:49:13,838] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:13,839] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.61%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:13,863] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:13,863] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:13,864] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016863355.1_ASM1686335v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:13,864] [INFO] Task started: Blastn
[2024-01-24 10:49:13,865] [INFO] Running command: blastn -query GCF_016863355.1_ASM1686335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg781b7e7d-7766-48a9-997d-174c6e794a57/dqc_reference/reference_markers_gtdb.fasta -out GCF_016863355.1_ASM1686335v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:16,013] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:16,018] [INFO] Selected 6 target genomes.
[2024-01-24 10:49:16,018] [INFO] Target genome list was writen to GCF_016863355.1_ASM1686335v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:16,023] [INFO] Task started: fastANI
[2024-01-24 10:49:16,023] [INFO] Running command: fastANI --query /var/lib/cwl/stg33782f9a-7e9d-47ae-ab88-32146f1c529a/GCF_016863355.1_ASM1686335v1_genomic.fna.gz --refList GCF_016863355.1_ASM1686335v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016863355.1_ASM1686335v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:31,172] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:31,180] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:31,181] [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_014200435.1	s__Sphaerisporangium krabiense	99.9989	2770	2789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_014205275.1	s__Sphaerisporangium siamense	94.5739	2405	2789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003323745.1	s__Sphaerisporangium album	86.2551	1805	2789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531465.1	s__Sphaerisporangium sp018531465	82.8175	1639	2789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646695.1	s__Sphaerisporangium melleum	82.7803	1499	2789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_016863395.1	s__Sphaerisporangium rufum	81.9303	1412	2789	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:31,182] [INFO] GTDB search result was written to GCF_016863355.1_ASM1686335v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:31,183] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:31,186] [INFO] DFAST_QC result json was written to GCF_016863355.1_ASM1686335v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:31,186] [INFO] DFAST_QC completed!
[2024-01-24 10:49:31,187] [INFO] Total running time: 0h2m24s