[2024-01-24 15:14:51,842] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:14:51,848] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:14:51,848] [INFO] DQC Reference Directory: /var/lib/cwl/stg62adb888-c4e1-4550-8dd0-b9e1ffc0e4c4/dqc_reference
[2024-01-24 15:14:53,199] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:14:53,200] [INFO] Task started: Prodigal
[2024-01-24 15:14:53,200] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a125487-6932-4f53-804b-1013d4c165ba/GCF_014646695.1_ASM1464669v1_genomic.fna.gz | prodigal -d GCF_014646695.1_ASM1464669v1_genomic.fna/cds.fna -a GCF_014646695.1_ASM1464669v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:15:18,976] [INFO] Task succeeded: Prodigal
[2024-01-24 15:15:18,976] [INFO] Task started: HMMsearch
[2024-01-24 15:15:18,977] [INFO] Running command: hmmsearch --tblout GCF_014646695.1_ASM1464669v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62adb888-c4e1-4550-8dd0-b9e1ffc0e4c4/dqc_reference/reference_markers.hmm GCF_014646695.1_ASM1464669v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:15:19,333] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:15:19,334] [INFO] Found 6/6 markers.
[2024-01-24 15:15:19,400] [INFO] Query marker FASTA was written to GCF_014646695.1_ASM1464669v1_genomic.fna/markers.fasta
[2024-01-24 15:15:19,401] [INFO] Task started: Blastn
[2024-01-24 15:15:19,401] [INFO] Running command: blastn -query GCF_014646695.1_ASM1464669v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62adb888-c4e1-4550-8dd0-b9e1ffc0e4c4/dqc_reference/reference_markers.fasta -out GCF_014646695.1_ASM1464669v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:15:20,777] [INFO] Task succeeded: Blastn
[2024-01-24 15:15:20,780] [INFO] Selected 16 target genomes.
[2024-01-24 15:15:20,781] [INFO] Target genome list was writen to GCF_014646695.1_ASM1464669v1_genomic.fna/target_genomes.txt
[2024-01-24 15:15:20,786] [INFO] Task started: fastANI
[2024-01-24 15:15:20,786] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a125487-6932-4f53-804b-1013d4c165ba/GCF_014646695.1_ASM1464669v1_genomic.fna.gz --refList GCF_014646695.1_ASM1464669v1_genomic.fna/target_genomes.txt --output GCF_014646695.1_ASM1464669v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:15:52,410] [INFO] Task succeeded: fastANI
[2024-01-24 15:15:52,411] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62adb888-c4e1-4550-8dd0-b9e1ffc0e4c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:15:52,411] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62adb888-c4e1-4550-8dd0-b9e1ffc0e4c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:15:52,427] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:15:52,427] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:15:52,428] [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 melleum	strain=JCM 13064	GCA_014646695.1	321316	321316	type	True	100.0	2814	2821	95	conclusive
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	83.1939	1662	2821	95	below_threshold
Sphaerisporangium album	strain=CCTCC AA 208026	GCA_003323745.1	509200	509200	type	True	83.0677	1611	2821	95	below_threshold
Sphaerisporangium siamense	strain=DSM 45784	GCA_014205275.1	795645	795645	type	True	82.8894	1500	2821	95	below_threshold
Sphaerisporangium siamense	strain=NBRC 107570	GCA_016863415.1	795645	795645	type	True	82.8667	1498	2821	95	below_threshold
Sphaerisporangium krabiense	strain=DSM 45790	GCA_014200435.1	763782	763782	type	True	82.808	1519	2821	95	below_threshold
Sphaerisporangium krabiense	strain=NBRC 107571	GCA_016863355.1	763782	763782	type	True	82.7859	1524	2821	95	below_threshold
Sphaerisporangium rufum	strain=NBRC 109079	GCA_016863395.1	1381558	1381558	type	True	82.5702	1541	2821	95	below_threshold
Sphaerisporangium rubeum	strain=DSM 44936	GCA_014207705.1	321317	321317	type	True	82.1746	1457	2821	95	below_threshold
Planobispora takensis	strain=NBRC 109077	GCA_016863195.1	1367882	1367882	type	True	80.1998	1272	2821	95	below_threshold
Planobispora siamensis	strain=NBRC 107568	GCA_016863175.1	936338	936338	type	True	80.1776	1293	2821	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	80.1115	1207	2821	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.9129	854	2821	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	79.7715	1329	2821	95	below_threshold
Streptosporangium album	strain=DSM 43023	GCA_014203795.1	47479	47479	type	True	79.6925	1167	2821	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	79.0578	1245	2821	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:15:52,429] [INFO] DFAST Taxonomy check result was written to GCF_014646695.1_ASM1464669v1_genomic.fna/tc_result.tsv
[2024-01-24 15:15:52,430] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:15:52,430] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:15:52,430] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62adb888-c4e1-4550-8dd0-b9e1ffc0e4c4/dqc_reference/checkm_data
[2024-01-24 15:15:52,431] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:15:52,510] [INFO] Task started: CheckM
[2024-01-24 15:15:52,511] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646695.1_ASM1464669v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646695.1_ASM1464669v1_genomic.fna/checkm_input GCF_014646695.1_ASM1464669v1_genomic.fna/checkm_result
[2024-01-24 15:17:14,082] [INFO] Task succeeded: CheckM
[2024-01-24 15:17:14,084] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 1.97%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2024-01-24 15:17:14,114] [INFO] ===== Completeness check finished =====
[2024-01-24 15:17:14,115] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:17:14,115] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646695.1_ASM1464669v1_genomic.fna/markers.fasta)
[2024-01-24 15:17:14,116] [INFO] Task started: Blastn
[2024-01-24 15:17:14,116] [INFO] Running command: blastn -query GCF_014646695.1_ASM1464669v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62adb888-c4e1-4550-8dd0-b9e1ffc0e4c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646695.1_ASM1464669v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:17:16,254] [INFO] Task succeeded: Blastn
[2024-01-24 15:17:16,257] [INFO] Selected 12 target genomes.
[2024-01-24 15:17:16,257] [INFO] Target genome list was writen to GCF_014646695.1_ASM1464669v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:17:16,268] [INFO] Task started: fastANI
[2024-01-24 15:17:16,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a125487-6932-4f53-804b-1013d4c165ba/GCF_014646695.1_ASM1464669v1_genomic.fna.gz --refList GCF_014646695.1_ASM1464669v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646695.1_ASM1464669v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:17:42,986] [INFO] Task succeeded: fastANI
[2024-01-24 15:17:43,007] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:17:43,008] [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_014646695.1	s__Sphaerisporangium melleum	100.0	2814	2821	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_003323745.1	s__Sphaerisporangium album	83.07	1611	2821	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	83.0476	1674	2821	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205275.1	s__Sphaerisporangium siamense	82.8794	1502	2821	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014200435.1	s__Sphaerisporangium krabiense	82.7704	1526	2821	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	82.5973	1536	2821	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207705.1	s__Sphaerisporangium rubeum	82.1651	1459	2821	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863175.1	s__Planobispora siamensis	80.2097	1284	2821	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCF_015711645.1	s__Planomonospora sp015711645	80.1414	1204	2821	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113865.1	s__Streptosporangium canum	80.0994	1275	2821	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	96.48	96.48	0.86	0.86	2	-
GCF_017896165.1	s__Microbispora sp017896165	80.0982	1211	2821	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203795.1	s__Streptosporangium album	79.7113	1163	2821	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:17:43,010] [INFO] GTDB search result was written to GCF_014646695.1_ASM1464669v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:17:43,010] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:17:43,014] [INFO] DFAST_QC result json was written to GCF_014646695.1_ASM1464669v1_genomic.fna/dqc_result.json
[2024-01-24 15:17:43,015] [INFO] DFAST_QC completed!
[2024-01-24 15:17:43,015] [INFO] Total running time: 0h2m51s