[2024-01-24 13:41:40,569] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:40,570] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:40,571] [INFO] DQC Reference Directory: /var/lib/cwl/stg7787e9a7-deac-4eff-9e2c-eb4189f131a8/dqc_reference
[2024-01-24 13:41:41,858] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:41,859] [INFO] Task started: Prodigal
[2024-01-24 13:41:41,859] [INFO] Running command: gunzip -c /var/lib/cwl/stg86f11a2e-67cd-448a-a2c2-df591259d663/GCF_014207705.1_ASM1420770v1_genomic.fna.gz | prodigal -d GCF_014207705.1_ASM1420770v1_genomic.fna/cds.fna -a GCF_014207705.1_ASM1420770v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:42:18,187] [INFO] Task succeeded: Prodigal
[2024-01-24 13:42:18,187] [INFO] Task started: HMMsearch
[2024-01-24 13:42:18,187] [INFO] Running command: hmmsearch --tblout GCF_014207705.1_ASM1420770v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7787e9a7-deac-4eff-9e2c-eb4189f131a8/dqc_reference/reference_markers.hmm GCF_014207705.1_ASM1420770v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:42:18,517] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:42:18,518] [INFO] Found 6/6 markers.
[2024-01-24 13:42:18,578] [INFO] Query marker FASTA was written to GCF_014207705.1_ASM1420770v1_genomic.fna/markers.fasta
[2024-01-24 13:42:18,578] [INFO] Task started: Blastn
[2024-01-24 13:42:18,578] [INFO] Running command: blastn -query GCF_014207705.1_ASM1420770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7787e9a7-deac-4eff-9e2c-eb4189f131a8/dqc_reference/reference_markers.fasta -out GCF_014207705.1_ASM1420770v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:19,862] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:19,866] [INFO] Selected 16 target genomes.
[2024-01-24 13:42:19,867] [INFO] Target genome list was writen to GCF_014207705.1_ASM1420770v1_genomic.fna/target_genomes.txt
[2024-01-24 13:42:19,908] [INFO] Task started: fastANI
[2024-01-24 13:42:19,908] [INFO] Running command: fastANI --query /var/lib/cwl/stg86f11a2e-67cd-448a-a2c2-df591259d663/GCF_014207705.1_ASM1420770v1_genomic.fna.gz --refList GCF_014207705.1_ASM1420770v1_genomic.fna/target_genomes.txt --output GCF_014207705.1_ASM1420770v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:50,725] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:50,726] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7787e9a7-deac-4eff-9e2c-eb4189f131a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:50,726] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7787e9a7-deac-4eff-9e2c-eb4189f131a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:50,741] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:42:50,742] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:50,742] [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 rubeum	strain=DSM 44936	GCA_014207705.1	321317	321317	type	True	100.0	2501	2501	95	conclusive
Sphaerisporangium melleum	strain=JCM 13064	GCA_014646695.1	321316	321316	type	True	82.1549	1436	2501	95	below_threshold
Sphaerisporangium siamense	strain=DSM 45784	GCA_014205275.1	795645	795645	type	True	81.9376	1354	2501	95	below_threshold
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	81.8991	1435	2501	95	below_threshold
Sphaerisporangium album	strain=CCTCC AA 208026	GCA_003323745.1	509200	509200	type	True	81.882	1436	2501	95	below_threshold
Sphaerisporangium siamense	strain=NBRC 107570	GCA_016863415.1	795645	795645	type	True	81.852	1316	2501	95	below_threshold
Sphaerisporangium krabiense	strain=DSM 45790	GCA_014200435.1	763782	763782	type	True	81.842	1380	2501	95	below_threshold
Sphaerisporangium krabiense	strain=NBRC 107571	GCA_016863355.1	763782	763782	type	True	81.6792	1368	2501	95	below_threshold
Sphaerisporangium rufum	strain=NBRC 109079	GCA_016863395.1	1381558	1381558	type	True	81.6598	1338	2501	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	79.5925	1057	2501	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	79.4879	1189	2501	95	below_threshold
Nonomuraea ceibae	strain=KCTC 39826	GCA_019396325.1	1935170	1935170	type	True	79.4157	1128	2501	95	below_threshold
Planotetraspora thailandica	strain=NBRC 104271	GCA_016863335.1	487172	487172	type	True	79.3262	981	2501	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.325	790	2501	95	below_threshold
Nonomuraea maritima	strain=CGMCC 4.5681	GCA_900100395.1	683260	683260	type	True	79.2182	1022	2501	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	78.7026	1069	2501	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:50,744] [INFO] DFAST Taxonomy check result was written to GCF_014207705.1_ASM1420770v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:50,744] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:50,745] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:50,745] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7787e9a7-deac-4eff-9e2c-eb4189f131a8/dqc_reference/checkm_data
[2024-01-24 13:42:50,746] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:50,816] [INFO] Task started: CheckM
[2024-01-24 13:42:50,816] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014207705.1_ASM1420770v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014207705.1_ASM1420770v1_genomic.fna/checkm_input GCF_014207705.1_ASM1420770v1_genomic.fna/checkm_result
[2024-01-24 13:45:13,622] [INFO] Task succeeded: CheckM
[2024-01-24 13:45:13,623] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.36%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-24 13:45:13,647] [INFO] ===== Completeness check finished =====
[2024-01-24 13:45:13,647] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:45:13,647] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014207705.1_ASM1420770v1_genomic.fna/markers.fasta)
[2024-01-24 13:45:13,648] [INFO] Task started: Blastn
[2024-01-24 13:45:13,648] [INFO] Running command: blastn -query GCF_014207705.1_ASM1420770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7787e9a7-deac-4eff-9e2c-eb4189f131a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_014207705.1_ASM1420770v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:45:15,686] [INFO] Task succeeded: Blastn
[2024-01-24 13:45:15,691] [INFO] Selected 11 target genomes.
[2024-01-24 13:45:15,691] [INFO] Target genome list was writen to GCF_014207705.1_ASM1420770v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:45:15,728] [INFO] Task started: fastANI
[2024-01-24 13:45:15,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg86f11a2e-67cd-448a-a2c2-df591259d663/GCF_014207705.1_ASM1420770v1_genomic.fna.gz --refList GCF_014207705.1_ASM1420770v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014207705.1_ASM1420770v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:45:40,145] [INFO] Task succeeded: fastANI
[2024-01-24 13:45:40,158] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:45:40,158] [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_014207705.1	s__Sphaerisporangium rubeum	100.0	2501	2501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014646695.1	s__Sphaerisporangium melleum	82.1346	1440	2501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_014205275.1	s__Sphaerisporangium siamense	81.9184	1357	2501	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	81.8669	1438	2501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200435.1	s__Sphaerisporangium krabiense	81.8408	1388	2501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_016863395.1	s__Sphaerisporangium rufum	81.69	1333	2501	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	81.6244	1385	2501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863335.1	s__Planotetraspora thailandica	79.3259	982	2501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planotetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001083785.1	s__Nonomuraea sp001083785	79.2732	1124	2501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100395.1	s__Nonomuraea maritima	79.1916	1027	2501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001935.1	s__Nonomuraea fuscirosea	79.0305	1170	2501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:45:40,160] [INFO] GTDB search result was written to GCF_014207705.1_ASM1420770v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:45:40,161] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:45:40,164] [INFO] DFAST_QC result json was written to GCF_014207705.1_ASM1420770v1_genomic.fna/dqc_result.json
[2024-01-24 13:45:40,164] [INFO] DFAST_QC completed!
[2024-01-24 13:45:40,164] [INFO] Total running time: 0h3m60s