[2024-01-25 17:35:05,462] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:35:05,464] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:35:05,464] [INFO] DQC Reference Directory: /var/lib/cwl/stgf42cc226-d6a8-4ac1-974d-fcc73a8587c4/dqc_reference
[2024-01-25 17:35:06,629] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:35:06,630] [INFO] Task started: Prodigal
[2024-01-25 17:35:06,630] [INFO] Running command: gunzip -c /var/lib/cwl/stgea35f881-d81a-4afb-b448-90e2fd44c63e/GCF_014203795.1_ASM1420379v1_genomic.fna.gz | prodigal -d GCF_014203795.1_ASM1420379v1_genomic.fna/cds.fna -a GCF_014203795.1_ASM1420379v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:35:42,556] [INFO] Task succeeded: Prodigal
[2024-01-25 17:35:42,556] [INFO] Task started: HMMsearch
[2024-01-25 17:35:42,556] [INFO] Running command: hmmsearch --tblout GCF_014203795.1_ASM1420379v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf42cc226-d6a8-4ac1-974d-fcc73a8587c4/dqc_reference/reference_markers.hmm GCF_014203795.1_ASM1420379v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:35:42,918] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:35:42,919] [INFO] Found 6/6 markers.
[2024-01-25 17:35:42,984] [INFO] Query marker FASTA was written to GCF_014203795.1_ASM1420379v1_genomic.fna/markers.fasta
[2024-01-25 17:35:42,984] [INFO] Task started: Blastn
[2024-01-25 17:35:42,984] [INFO] Running command: blastn -query GCF_014203795.1_ASM1420379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf42cc226-d6a8-4ac1-974d-fcc73a8587c4/dqc_reference/reference_markers.fasta -out GCF_014203795.1_ASM1420379v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:44,304] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:44,307] [INFO] Selected 21 target genomes.
[2024-01-25 17:35:44,307] [INFO] Target genome list was writen to GCF_014203795.1_ASM1420379v1_genomic.fna/target_genomes.txt
[2024-01-25 17:35:44,333] [INFO] Task started: fastANI
[2024-01-25 17:35:44,334] [INFO] Running command: fastANI --query /var/lib/cwl/stgea35f881-d81a-4afb-b448-90e2fd44c63e/GCF_014203795.1_ASM1420379v1_genomic.fna.gz --refList GCF_014203795.1_ASM1420379v1_genomic.fna/target_genomes.txt --output GCF_014203795.1_ASM1420379v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:36:29,258] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:29,259] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf42cc226-d6a8-4ac1-974d-fcc73a8587c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:36:29,260] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf42cc226-d6a8-4ac1-974d-fcc73a8587c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:36:29,272] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:36:29,272] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:36:29,273] [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
Streptosporangium album	strain=DSM 43023	GCA_014203795.1	47479	47479	type	True	100.0	2997	3000	95	conclusive
Streptosporangium roseum	strain=DSM 43021	GCA_000024865.1	2001	2001	type	True	88.574	1962	3000	95	below_threshold
Streptosporangium canum	strain=CGMCC 4.2126	GCA_900113865.1	324952	324952	type	True	88.5482	1912	3000	95	below_threshold
Streptosporangium minutum	strain=M26	GCA_002149035.1	569862	569862	type	True	88.3563	1798	3000	95	below_threshold
Streptosporangium sandarakinum	strain=DSM 45763	GCA_013409935.1	1260955	1260955	type	True	84.5778	1608	3000	95	below_threshold
Streptosporangium amethystogenes	strain=NRRL B-2639	GCA_000721075.1	2002	2002	type	True	84.4003	1659	3000	95	below_threshold
Streptosporangium violaceochromogenes	strain=JCM 3281	GCA_014654615.1	46188	46188	type	True	84.3111	1252	3000	95	below_threshold
Streptosporangium pseudovulgare	strain=JCM 3115	GCA_014648055.1	35765	35765	type	True	84.2988	1690	3000	95	below_threshold
Planobispora rosea	strain=NBRC 15558	GCA_016863155.1	35762	35762	type	True	83.7648	1437	3000	95	below_threshold
Planobispora siamensis	strain=NBRC 107568	GCA_016863175.1	936338	936338	type	True	83.6318	1528	3000	95	below_threshold
Planobispora takensis	strain=NBRC 109077	GCA_016863195.1	1367882	1367882	type	True	83.6185	1533	3000	95	below_threshold
Planobispora longispora	strain=NBRC 13918	GCA_016863135.1	28887	28887	type	True	83.5633	1518	3000	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	80.2069	903	3000	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	80.1749	1383	3000	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	79.9256	1327	3000	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	79.8609	1320	3000	95	below_threshold
Microbispora bryophytorum	strain=DSM 46710	GCA_006874465.1	1460882	1460882	type	True	79.7561	1116	3000	95	below_threshold
Microbispora bryophytorum	strain=CGMCC 4.7138	GCA_014645855.1	1460882	1460882	type	True	79.7166	1115	3000	95	below_threshold
Microbispora bryophytorum	strain=NEAU-TX2-2	GCA_014712735.1	1460882	1460882	type	True	79.7082	1117	3000	95	below_threshold
Microbispora camponoti	strain=2C-HV3	GCA_014712745.1	1677852	1677852	type	True	79.6556	1129	3000	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	79.6468	1332	3000	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:36:29,275] [INFO] DFAST Taxonomy check result was written to GCF_014203795.1_ASM1420379v1_genomic.fna/tc_result.tsv
[2024-01-25 17:36:29,275] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:36:29,275] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:36:29,275] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf42cc226-d6a8-4ac1-974d-fcc73a8587c4/dqc_reference/checkm_data
[2024-01-25 17:36:29,276] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:36:29,358] [INFO] Task started: CheckM
[2024-01-25 17:36:29,358] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014203795.1_ASM1420379v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014203795.1_ASM1420379v1_genomic.fna/checkm_input GCF_014203795.1_ASM1420379v1_genomic.fna/checkm_result
[2024-01-25 17:38:19,608] [INFO] Task succeeded: CheckM
[2024-01-25 17:38:19,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:38:19,667] [INFO] ===== Completeness check finished =====
[2024-01-25 17:38:19,667] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:38:19,668] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014203795.1_ASM1420379v1_genomic.fna/markers.fasta)
[2024-01-25 17:38:19,668] [INFO] Task started: Blastn
[2024-01-25 17:38:19,668] [INFO] Running command: blastn -query GCF_014203795.1_ASM1420379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf42cc226-d6a8-4ac1-974d-fcc73a8587c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_014203795.1_ASM1420379v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:21,773] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:21,777] [INFO] Selected 17 target genomes.
[2024-01-25 17:38:21,777] [INFO] Target genome list was writen to GCF_014203795.1_ASM1420379v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:38:21,787] [INFO] Task started: fastANI
[2024-01-25 17:38:21,787] [INFO] Running command: fastANI --query /var/lib/cwl/stgea35f881-d81a-4afb-b448-90e2fd44c63e/GCF_014203795.1_ASM1420379v1_genomic.fna.gz --refList GCF_014203795.1_ASM1420379v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014203795.1_ASM1420379v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:38:59,289] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:59,300] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:38:59,301] [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_014203795.1	s__Streptosporangium album	100.0	2995	3000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000024865.1	s__Streptosporangium roseum	88.6201	1956	3000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113865.1	s__Streptosporangium canum	88.5534	1911	3000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	96.48	96.48	0.86	0.86	2	-
GCF_002149035.1	s__Streptosporangium minutum	88.4432	1786	3000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	N/A	N/A	N/A	N/A	1	-
GCF_900188345.1	s__Streptosporangium subroseum	85.3247	1800	3000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	95.81	95.81	0.87	0.87	2	-
GCF_000721075.1	s__Streptosporangium amethystogenes	84.3489	1668	3000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648055.1	s__Streptosporangium pseudovulgare	84.3216	1685	3000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	96.6013	N/A	N/A	N/A	N/A	1	-
GCF_014654615.1	s__Streptosporangium violaceochromogenes	84.3126	1252	3000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203605.1	s__Planomonospora_A venezuelensis	84.2014	1486	3000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014647935.1	s__Planomonospora parontospora	83.8757	1464	3000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora	95.0	97.40	95.90	0.89	0.84	6	-
GCF_014648175.1	s__Planobispora rosea	83.6969	1453	3000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	99.82	99.64	0.97	0.95	3	-
GCF_016863195.1	s__Planobispora takensis	83.6517	1527	3000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCF_016863175.1	s__Planobispora siamensis	83.6108	1531	3000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCF_016863135.1	s__Planobispora longispora	83.5715	1517	3000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001570385.1	s__Microtetraspora glauca	80.5337	1287	3000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006874465.1	s__Microbispora bryophytorum	79.7559	1116	3000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	99.22	97.66	0.97	0.91	4	-
GCF_016862895.1	s__Planotetraspora kaengkrachanensis	79.4161	1104	3000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planotetraspora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:38:59,303] [INFO] GTDB search result was written to GCF_014203795.1_ASM1420379v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:38:59,303] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:38:59,307] [INFO] DFAST_QC result json was written to GCF_014203795.1_ASM1420379v1_genomic.fna/dqc_result.json
[2024-01-25 17:38:59,307] [INFO] DFAST_QC completed!
[2024-01-25 17:38:59,307] [INFO] Total running time: 0h3m54s