[2024-01-24 12:37:37,922] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:37,927] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:37,927] [INFO] DQC Reference Directory: /var/lib/cwl/stgacd17326-fd01-4148-aa3d-ee37320fae84/dqc_reference
[2024-01-24 12:37:41,014] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:41,015] [INFO] Task started: Prodigal
[2024-01-24 12:37:41,015] [INFO] Running command: gunzip -c /var/lib/cwl/stgac4ad183-ecb6-4a16-9137-b44890c89fec/GCF_014647955.1_ASM1464795v1_genomic.fna.gz | prodigal -d GCF_014647955.1_ASM1464795v1_genomic.fna/cds.fna -a GCF_014647955.1_ASM1464795v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:38:01,592] [INFO] Task succeeded: Prodigal
[2024-01-24 12:38:01,593] [INFO] Task started: HMMsearch
[2024-01-24 12:38:01,593] [INFO] Running command: hmmsearch --tblout GCF_014647955.1_ASM1464795v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgacd17326-fd01-4148-aa3d-ee37320fae84/dqc_reference/reference_markers.hmm GCF_014647955.1_ASM1464795v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:38:01,966] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:38:01,968] [INFO] Found 6/6 markers.
[2024-01-24 12:38:02,042] [INFO] Query marker FASTA was written to GCF_014647955.1_ASM1464795v1_genomic.fna/markers.fasta
[2024-01-24 12:38:02,042] [INFO] Task started: Blastn
[2024-01-24 12:38:02,042] [INFO] Running command: blastn -query GCF_014647955.1_ASM1464795v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacd17326-fd01-4148-aa3d-ee37320fae84/dqc_reference/reference_markers.fasta -out GCF_014647955.1_ASM1464795v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:03,411] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:03,414] [INFO] Selected 22 target genomes.
[2024-01-24 12:38:03,414] [INFO] Target genome list was writen to GCF_014647955.1_ASM1464795v1_genomic.fna/target_genomes.txt
[2024-01-24 12:38:03,442] [INFO] Task started: fastANI
[2024-01-24 12:38:03,443] [INFO] Running command: fastANI --query /var/lib/cwl/stgac4ad183-ecb6-4a16-9137-b44890c89fec/GCF_014647955.1_ASM1464795v1_genomic.fna.gz --refList GCF_014647955.1_ASM1464795v1_genomic.fna/target_genomes.txt --output GCF_014647955.1_ASM1464795v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:38:48,184] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:48,185] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgacd17326-fd01-4148-aa3d-ee37320fae84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:38:48,186] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgacd17326-fd01-4148-aa3d-ee37320fae84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:38:48,203] [INFO] Found 21 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:38:48,204] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:38:48,204] [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
Planomonospora parontospora subsp. antibiotica	strain=JCM 3094	GCA_014647955.1	97193	58119	type	True	100.0	2562	2567	95	inconclusive
Planomonospora parontospora subsp. antibiotica	strain=NBRC 15869	GCA_016863235.1	97193	58119	type	True	99.9723	2446	2567	95	inconclusive
Planomonospora sphaerica	strain=JCM 9374	GCA_001653075.1	161355	161355	type	True	95.9597	2197	2567	95	inconclusive
Planobispora rosea	strain=NBRC 15558	GCA_016863155.1	35762	35762	type	True	86.1845	1746	2567	95	below_threshold
Planobispora longispora	strain=NBRC 13918	GCA_016863135.1	28887	28887	type	True	86.1789	1754	2567	95	below_threshold
Planobispora rosea	strain=JCM 3166	GCA_014648175.1	35762	35762	type	True	86.1343	1781	2567	95	below_threshold
Planobispora siamensis	strain=NBRC 107568	GCA_016863175.1	936338	936338	type	True	86.0888	1787	2567	95	below_threshold
Streptosporangium canum	strain=CGMCC 4.2126	GCA_900113865.1	324952	324952	type	True	84.7135	1608	2567	95	below_threshold
Streptosporangium minutum	strain=M26	GCA_002149035.1	569862	569862	type	True	84.5439	1567	2567	95	below_threshold
Streptosporangium sandarakinum	strain=DSM 45763	GCA_013409935.1	1260955	1260955	type	True	83.7519	1459	2567	95	below_threshold
Streptosporangium pseudovulgare	strain=JCM 3115	GCA_014648055.1	35765	35765	type	True	83.5862	1541	2567	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	80.7116	922	2567	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	80.5696	1373	2567	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	80.2156	1358	2567	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	80.2115	1359	2567	95	below_threshold
Nonomuraea mesophila	strain=6K102	GCA_004352805.1	2530382	2530382	type	True	80.0989	1233	2567	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	79.874	1364	2567	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	76.7272	770	2567	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	76.675	802	2567	95	below_threshold
Actinacidiphila oryziradicis	strain=NEAU-C40	GCA_005047355.1	2571141	2571141	type	True	76.4886	648	2567	95	below_threshold
Amycolatopsis endophytica	strain=DSM 104006	GCA_013410405.1	860233	860233	type	True	76.2531	564	2567	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:38:48,205] [INFO] DFAST Taxonomy check result was written to GCF_014647955.1_ASM1464795v1_genomic.fna/tc_result.tsv
[2024-01-24 12:38:48,206] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:38:48,206] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:38:48,206] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgacd17326-fd01-4148-aa3d-ee37320fae84/dqc_reference/checkm_data
[2024-01-24 12:38:48,207] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:38:48,288] [INFO] Task started: CheckM
[2024-01-24 12:38:48,289] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014647955.1_ASM1464795v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014647955.1_ASM1464795v1_genomic.fna/checkm_input GCF_014647955.1_ASM1464795v1_genomic.fna/checkm_result
[2024-01-24 12:39:55,566] [INFO] Task succeeded: CheckM
[2024-01-24 12:39:55,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:39:55,593] [INFO] ===== Completeness check finished =====
[2024-01-24 12:39:55,593] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:39:55,594] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014647955.1_ASM1464795v1_genomic.fna/markers.fasta)
[2024-01-24 12:39:55,594] [INFO] Task started: Blastn
[2024-01-24 12:39:55,595] [INFO] Running command: blastn -query GCF_014647955.1_ASM1464795v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacd17326-fd01-4148-aa3d-ee37320fae84/dqc_reference/reference_markers_gtdb.fasta -out GCF_014647955.1_ASM1464795v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:57,746] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:57,750] [INFO] Selected 15 target genomes.
[2024-01-24 12:39:57,750] [INFO] Target genome list was writen to GCF_014647955.1_ASM1464795v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:39:57,765] [INFO] Task started: fastANI
[2024-01-24 12:39:57,766] [INFO] Running command: fastANI --query /var/lib/cwl/stgac4ad183-ecb6-4a16-9137-b44890c89fec/GCF_014647955.1_ASM1464795v1_genomic.fna.gz --refList GCF_014647955.1_ASM1464795v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014647955.1_ASM1464795v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:27,768] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:27,788] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:27,788] [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
GCA_014647935.1	s__Planomonospora parontospora	95.8775	2149	2567	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora	95.0	97.40	95.90	0.89	0.84	6	conclusive
GCF_015711645.1	s__Planomonospora sp015711645	93.013	1908	2567	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203605.1	s__Planomonospora_A venezuelensis	87.0462	1791	2567	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015711605.1	s__Planomonospora_A sp015711605	86.5844	1802	2567	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863135.1	s__Planobispora longispora	86.1233	1763	2567	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648175.1	s__Planobispora rosea	86.1146	1783	2567	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	99.82	99.64	0.97	0.95	3	-
GCF_016863175.1	s__Planobispora siamensis	86.0805	1790	2567	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCF_900113865.1	s__Streptosporangium canum	84.72	1606	2567	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	96.48	96.48	0.86	0.86	2	-
GCF_000024865.1	s__Streptosporangium roseum	84.5105	1720	2567	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409935.1	s__Streptosporangium sandarakinum	83.7457	1460	2567	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	96.6013	N/A	N/A	N/A	N/A	1	-
GCF_014648055.1	s__Streptosporangium pseudovulgare	83.6007	1539	2567	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	96.6013	N/A	N/A	N/A	N/A	1	-
GCF_003236385.1	s__Desertactinospora gelatinilytica	80.097	1002	2567	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Desertactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017592665.1	s__NEAU-GS5 sp017592665	79.2146	1102	2567	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__NEAU-GS5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410405.1	s__Amycolatopsis endophytica	76.2815	555	2567	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577565.1	s__ZC4RG19 sp017577565	75.3836	400	2567	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:27,790] [INFO] GTDB search result was written to GCF_014647955.1_ASM1464795v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:27,790] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:27,796] [INFO] DFAST_QC result json was written to GCF_014647955.1_ASM1464795v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:27,797] [INFO] DFAST_QC completed!
[2024-01-24 12:40:27,797] [INFO] Total running time: 0h2m50s