[2024-01-25 17:36:05,766] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:36:05,768] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:36:05,768] [INFO] DQC Reference Directory: /var/lib/cwl/stg80f398da-e9e6-4400-821e-c8e9b4ed7168/dqc_reference
[2024-01-25 17:36:06,925] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:36:06,926] [INFO] Task started: Prodigal
[2024-01-25 17:36:06,926] [INFO] Running command: gunzip -c /var/lib/cwl/stgf50f1ff3-4cd6-46cb-8066-acd7ff65bd51/GCF_003751945.1_ASM375194v1_genomic.fna.gz | prodigal -d GCF_003751945.1_ASM375194v1_genomic.fna/cds.fna -a GCF_003751945.1_ASM375194v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:36:32,016] [INFO] Task succeeded: Prodigal
[2024-01-25 17:36:32,016] [INFO] Task started: HMMsearch
[2024-01-25 17:36:32,016] [INFO] Running command: hmmsearch --tblout GCF_003751945.1_ASM375194v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80f398da-e9e6-4400-821e-c8e9b4ed7168/dqc_reference/reference_markers.hmm GCF_003751945.1_ASM375194v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:36:32,318] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:36:32,319] [INFO] Found 6/6 markers.
[2024-01-25 17:36:32,383] [INFO] Query marker FASTA was written to GCF_003751945.1_ASM375194v1_genomic.fna/markers.fasta
[2024-01-25 17:36:32,383] [INFO] Task started: Blastn
[2024-01-25 17:36:32,383] [INFO] Running command: blastn -query GCF_003751945.1_ASM375194v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80f398da-e9e6-4400-821e-c8e9b4ed7168/dqc_reference/reference_markers.fasta -out GCF_003751945.1_ASM375194v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:33,528] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:33,531] [INFO] Selected 20 target genomes.
[2024-01-25 17:36:33,531] [INFO] Target genome list was writen to GCF_003751945.1_ASM375194v1_genomic.fna/target_genomes.txt
[2024-01-25 17:36:33,541] [INFO] Task started: fastANI
[2024-01-25 17:36:33,541] [INFO] Running command: fastANI --query /var/lib/cwl/stgf50f1ff3-4cd6-46cb-8066-acd7ff65bd51/GCF_003751945.1_ASM375194v1_genomic.fna.gz --refList GCF_003751945.1_ASM375194v1_genomic.fna/target_genomes.txt --output GCF_003751945.1_ASM375194v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:37:16,879] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:16,879] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80f398da-e9e6-4400-821e-c8e9b4ed7168/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:37:16,879] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80f398da-e9e6-4400-821e-c8e9b4ed7168/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:37:16,891] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:37:16,891] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:37:16,891] [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
Couchioplanes caeruleus	strain=DSM 43634	GCA_003751945.1	56438	56438	type	True	100.0	2807	2809	95	conclusive
Couchioplanes caeruleus subsp. caeruleus	strain=DSM 43634	GCA_001884705.1	56427	56438	type	True	99.8667	2436	2809	95	conclusive
Actinoplanes nipponensis	strain=NBRC 14063	GCA_016862275.1	135950	135950	type	True	82.843	1554	2809	95	below_threshold
Actinoplanes auranticolor	strain=NBRC 12245	GCA_018332655.1	47988	47988	type	True	82.7528	1519	2809	95	below_threshold
Actinoplanes digitatis	strain=NBRC 12512	GCA_016862155.1	1868	1868	type	True	82.5929	1534	2809	95	below_threshold
Actinoplanes digitatis	strain=DSM 43149	GCA_014205335.1	1868	1868	type	True	82.5478	1596	2809	95	below_threshold
Actinoplanes friuliensis	strain=DSM 7358	GCA_000494755.1	196914	196914	type	True	82.1875	1482	2809	95	below_threshold
Actinoplanes consettensis	strain=NBRC 14913	GCA_018332715.1	113560	113560	type	True	81.7037	1412	2809	95	below_threshold
Actinoplanes humidus	strain=NBRC 14915	GCA_016862215.1	113566	113566	type	True	81.5839	1431	2809	95	below_threshold
Actinoplanes abujensis	strain=DSM 45518	GCA_014204895.1	882441	882441	type	True	80.5133	1265	2809	95	below_threshold
Actinoplanes lichenicola	strain=LDG1-01	GCA_016785085.1	2802976	2802976	type	True	80.4058	1366	2809	95	below_threshold
Actinoplanes regularis	strain=DSM 43151	GCA_900188005.1	52697	52697	type	True	80.3244	1263	2809	95	below_threshold
Actinoplanes missouriensis	strain=431	GCA_000284295.1	1866	1866	type	True	80.3024	1208	2809	95	below_threshold
Actinoplanes bogorensis	strain=NBRC 110975	GCA_018829635.1	1610840	1610840	type	True	80.2919	1301	2809	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	79.9601	1281	2809	95	below_threshold
Actinoplanes xinjiangensis	strain=DSM 45184	GCA_003148685.1	512350	512350	type	True	79.7342	1325	2809	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	79.3678	807	2809	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.8163	910	2809	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	77.7207	1000	2809	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	77.5824	1193	2809	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:37:16,893] [INFO] DFAST Taxonomy check result was written to GCF_003751945.1_ASM375194v1_genomic.fna/tc_result.tsv
[2024-01-25 17:37:16,893] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:37:16,893] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:37:16,894] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80f398da-e9e6-4400-821e-c8e9b4ed7168/dqc_reference/checkm_data
[2024-01-25 17:37:16,894] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:37:16,971] [INFO] Task started: CheckM
[2024-01-25 17:37:16,971] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003751945.1_ASM375194v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003751945.1_ASM375194v1_genomic.fna/checkm_input GCF_003751945.1_ASM375194v1_genomic.fna/checkm_result
[2024-01-25 17:39:05,977] [INFO] Task succeeded: CheckM
[2024-01-25 17:39:05,978] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:39:06,009] [INFO] ===== Completeness check finished =====
[2024-01-25 17:39:06,009] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:39:06,010] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003751945.1_ASM375194v1_genomic.fna/markers.fasta)
[2024-01-25 17:39:06,010] [INFO] Task started: Blastn
[2024-01-25 17:39:06,010] [INFO] Running command: blastn -query GCF_003751945.1_ASM375194v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80f398da-e9e6-4400-821e-c8e9b4ed7168/dqc_reference/reference_markers_gtdb.fasta -out GCF_003751945.1_ASM375194v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:07,986] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:07,989] [INFO] Selected 10 target genomes.
[2024-01-25 17:39:07,989] [INFO] Target genome list was writen to GCF_003751945.1_ASM375194v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:39:07,994] [INFO] Task started: fastANI
[2024-01-25 17:39:07,994] [INFO] Running command: fastANI --query /var/lib/cwl/stgf50f1ff3-4cd6-46cb-8066-acd7ff65bd51/GCF_003751945.1_ASM375194v1_genomic.fna.gz --refList GCF_003751945.1_ASM375194v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003751945.1_ASM375194v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:39:31,559] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:31,566] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:39:31,567] [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_003751945.1	s__Actinoplanes caeruleus	100.0	2808	2809	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.98	0.98	2	conclusive
GCF_014648355.1	s__Actinoplanes azureus	91.2943	2036	2809	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002065.1	s__Actinoplanes ferrugineus_A	84.9289	1604	2809	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.31	99.31	0.94	0.94	2	-
GCF_016464385.1	s__Actinoplanes sp016464385	84.0396	1585	2809	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862275.1	s__Actinoplanes nipponensis	82.8449	1552	2809	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018332655.1	s__Actinoplanes auranticolor	82.759	1517	2809	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205335.1	s__Actinoplanes digitatis	82.5668	1593	2809	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000389965.1	s__Actinoplanes sp000389965	82.2018	1439	2809	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003999975.1	s__Actinoplanes sp003999975	80.3879	1266	2809	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148685.1	s__Actinoplanes xinjiangensis	79.7259	1327	2809	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:39:31,568] [INFO] GTDB search result was written to GCF_003751945.1_ASM375194v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:39:31,568] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:39:31,572] [INFO] DFAST_QC result json was written to GCF_003751945.1_ASM375194v1_genomic.fna/dqc_result.json
[2024-01-25 17:39:31,572] [INFO] DFAST_QC completed!
[2024-01-25 17:39:31,572] [INFO] Total running time: 0h3m26s