[2024-01-24 13:57:42,092] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:42,094] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:42,094] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ad468cc-4887-4440-bfdc-b9b40c57107f/dqc_reference
[2024-01-24 13:57:43,539] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:43,540] [INFO] Task started: Prodigal
[2024-01-24 13:57:43,540] [INFO] Running command: gunzip -c /var/lib/cwl/stg00ed43c6-e753-4458-bdb3-04e9ecdfdf2d/GCF_016863215.1_ASM1686321v1_genomic.fna.gz | prodigal -d GCF_016863215.1_ASM1686321v1_genomic.fna/cds.fna -a GCF_016863215.1_ASM1686321v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:03,068] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:03,069] [INFO] Task started: HMMsearch
[2024-01-24 13:58:03,069] [INFO] Running command: hmmsearch --tblout GCF_016863215.1_ASM1686321v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ad468cc-4887-4440-bfdc-b9b40c57107f/dqc_reference/reference_markers.hmm GCF_016863215.1_ASM1686321v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:03,445] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:03,446] [INFO] Found 6/6 markers.
[2024-01-24 13:58:03,515] [INFO] Query marker FASTA was written to GCF_016863215.1_ASM1686321v1_genomic.fna/markers.fasta
[2024-01-24 13:58:03,515] [INFO] Task started: Blastn
[2024-01-24 13:58:03,516] [INFO] Running command: blastn -query GCF_016863215.1_ASM1686321v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ad468cc-4887-4440-bfdc-b9b40c57107f/dqc_reference/reference_markers.fasta -out GCF_016863215.1_ASM1686321v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:04,878] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:04,881] [INFO] Selected 15 target genomes.
[2024-01-24 13:58:04,882] [INFO] Target genome list was writen to GCF_016863215.1_ASM1686321v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:04,889] [INFO] Task started: fastANI
[2024-01-24 13:58:04,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg00ed43c6-e753-4458-bdb3-04e9ecdfdf2d/GCF_016863215.1_ASM1686321v1_genomic.fna.gz --refList GCF_016863215.1_ASM1686321v1_genomic.fna/target_genomes.txt --output GCF_016863215.1_ASM1686321v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:38,188] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:38,189] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ad468cc-4887-4440-bfdc-b9b40c57107f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:38,190] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ad468cc-4887-4440-bfdc-b9b40c57107f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:38,205] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:58:38,205] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:58:38,205] [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 sphaerica	strain=JCM 9374	GCA_001653075.1	161355	161355	type	True	97.6347	2236	2513	95	inconclusive
Planomonospora parontospora subsp. antibiotica	strain=NBRC 15869	GCA_016863235.1	97193	58119	type	True	95.9179	2073	2513	95	inconclusive
Planomonospora parontospora subsp. antibiotica	strain=JCM 3094	GCA_014647955.1	97193	58119	type	True	95.8784	2125	2513	95	inconclusive
Planobispora rosea	strain=JCM 3166	GCA_014648175.1	35762	35762	type	True	86.0902	1775	2513	95	below_threshold
Planobispora longispora	strain=NBRC 13918	GCA_016863135.1	28887	28887	type	True	86.0607	1783	2513	95	below_threshold
Planobispora rosea	strain=NBRC 15558	GCA_016863155.1	35762	35762	type	True	86.0341	1770	2513	95	below_threshold
Planobispora siamensis	strain=NBRC 107568	GCA_016863175.1	936338	936338	type	True	85.9539	1789	2513	95	below_threshold
Planobispora takensis	strain=NBRC 109077	GCA_016863195.1	1367882	1367882	type	True	85.9241	1793	2513	95	below_threshold
Streptosporangium canum	strain=CGMCC 4.2126	GCA_900113865.1	324952	324952	type	True	84.6471	1627	2513	95	below_threshold
Streptosporangium album	strain=DSM 43023	GCA_014203795.1	47479	47479	type	True	83.8801	1449	2513	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	80.5809	944	2513	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	80.5079	1381	2513	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	80.2946	1349	2513	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	80.2233	1349	2513	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	79.8505	1358	2513	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:38,207] [INFO] DFAST Taxonomy check result was written to GCF_016863215.1_ASM1686321v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:38,208] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:38,208] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:38,209] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ad468cc-4887-4440-bfdc-b9b40c57107f/dqc_reference/checkm_data
[2024-01-24 13:58:38,210] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:38,319] [INFO] Task started: CheckM
[2024-01-24 13:58:38,320] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016863215.1_ASM1686321v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016863215.1_ASM1686321v1_genomic.fna/checkm_input GCF_016863215.1_ASM1686321v1_genomic.fna/checkm_result
[2024-01-24 13:59:42,089] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:42,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:42,118] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:42,118] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:42,118] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016863215.1_ASM1686321v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:42,119] [INFO] Task started: Blastn
[2024-01-24 13:59:42,119] [INFO] Running command: blastn -query GCF_016863215.1_ASM1686321v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ad468cc-4887-4440-bfdc-b9b40c57107f/dqc_reference/reference_markers_gtdb.fasta -out GCF_016863215.1_ASM1686321v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:44,401] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:44,405] [INFO] Selected 11 target genomes.
[2024-01-24 13:59:44,405] [INFO] Target genome list was writen to GCF_016863215.1_ASM1686321v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:44,415] [INFO] Task started: fastANI
[2024-01-24 13:59:44,415] [INFO] Running command: fastANI --query /var/lib/cwl/stg00ed43c6-e753-4458-bdb3-04e9ecdfdf2d/GCF_016863215.1_ASM1686321v1_genomic.fna.gz --refList GCF_016863215.1_ASM1686321v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016863215.1_ASM1686321v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:09,729] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:09,742] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:09,743] [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	99.9946	2509	2513	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	93.1086	1891	2513	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	86.7922	1810	2513	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	86.367	1803	2513	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_014648175.1	s__Planobispora rosea	86.0999	1774	2513	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	99.82	99.64	0.97	0.95	3	-
GCF_016863135.1	s__Planobispora longispora	86.0164	1790	2513	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863175.1	s__Planobispora siamensis	85.9596	1789	2513	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCF_016863195.1	s__Planobispora takensis	85.9134	1794	2513	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	84.6413	1627	2513	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	84.5363	1714	2513	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203795.1	s__Streptosporangium album	83.8713	1449	2513	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 14:00:09,744] [INFO] GTDB search result was written to GCF_016863215.1_ASM1686321v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:09,745] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:09,748] [INFO] DFAST_QC result json was written to GCF_016863215.1_ASM1686321v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:09,748] [INFO] DFAST_QC completed!
[2024-01-24 14:00:09,748] [INFO] Total running time: 0h2m28s