[2024-01-24 11:05:34,593] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:34,594] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:34,595] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd2849e4-25dc-48bc-98ed-18e3d0468caf/dqc_reference
[2024-01-24 11:05:35,791] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:35,792] [INFO] Task started: Prodigal
[2024-01-24 11:05:35,792] [INFO] Running command: gunzip -c /var/lib/cwl/stg403fafda-c50d-474b-93f1-32a8f396a695/GCF_016863155.1_ASM1686315v1_genomic.fna.gz | prodigal -d GCF_016863155.1_ASM1686315v1_genomic.fna/cds.fna -a GCF_016863155.1_ASM1686315v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:57,686] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:57,687] [INFO] Task started: HMMsearch
[2024-01-24 11:05:57,687] [INFO] Running command: hmmsearch --tblout GCF_016863155.1_ASM1686315v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd2849e4-25dc-48bc-98ed-18e3d0468caf/dqc_reference/reference_markers.hmm GCF_016863155.1_ASM1686315v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:58,122] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:58,123] [INFO] Found 6/6 markers.
[2024-01-24 11:05:58,196] [INFO] Query marker FASTA was written to GCF_016863155.1_ASM1686315v1_genomic.fna/markers.fasta
[2024-01-24 11:05:58,197] [INFO] Task started: Blastn
[2024-01-24 11:05:58,197] [INFO] Running command: blastn -query GCF_016863155.1_ASM1686315v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd2849e4-25dc-48bc-98ed-18e3d0468caf/dqc_reference/reference_markers.fasta -out GCF_016863155.1_ASM1686315v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:59,511] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:59,519] [INFO] Selected 13 target genomes.
[2024-01-24 11:05:59,519] [INFO] Target genome list was writen to GCF_016863155.1_ASM1686315v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:59,525] [INFO] Task started: fastANI
[2024-01-24 11:05:59,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg403fafda-c50d-474b-93f1-32a8f396a695/GCF_016863155.1_ASM1686315v1_genomic.fna.gz --refList GCF_016863155.1_ASM1686315v1_genomic.fna/target_genomes.txt --output GCF_016863155.1_ASM1686315v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:29,253] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:29,254] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd2849e4-25dc-48bc-98ed-18e3d0468caf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:29,255] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd2849e4-25dc-48bc-98ed-18e3d0468caf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:29,267] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:06:29,268] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:29,268] [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
Planobispora rosea	strain=NBRC 15558	GCA_016863155.1	35762	35762	type	True	100.0	2739	2745	95	conclusive
Planobispora rosea	strain=JCM 3166	GCA_014648175.1	35762	35762	type	True	99.9982	2734	2745	95	conclusive
Planobispora longispora	strain=NBRC 13918	GCA_016863135.1	28887	28887	type	True	92.2492	2227	2745	95	below_threshold
Planobispora siamensis	strain=NBRC 107568	GCA_016863175.1	936338	936338	type	True	87.8136	2054	2745	95	below_threshold
Planobispora takensis	strain=NBRC 109077	GCA_016863195.1	1367882	1367882	type	True	87.7568	2049	2745	95	below_threshold
Planomonospora parontospora subsp. antibiotica	strain=NBRC 15869	GCA_016863235.1	97193	58119	type	True	86.1445	1744	2745	95	below_threshold
Planomonospora sphaerica	strain=JCM 9374	GCA_001653075.1	161355	161355	type	True	85.9084	1836	2745	95	below_threshold
Streptosporangium minutum	strain=M26	GCA_002149035.1	569862	569862	type	True	84.3248	1567	2745	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	80.5318	964	2745	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	80.3896	1407	2745	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	80.0152	1409	2745	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	79.9979	1398	2745	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	79.9839	1389	2745	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:29,269] [INFO] DFAST Taxonomy check result was written to GCF_016863155.1_ASM1686315v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:29,270] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:29,270] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:29,270] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd2849e4-25dc-48bc-98ed-18e3d0468caf/dqc_reference/checkm_data
[2024-01-24 11:06:29,271] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:29,345] [INFO] Task started: CheckM
[2024-01-24 11:06:29,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016863155.1_ASM1686315v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016863155.1_ASM1686315v1_genomic.fna/checkm_input GCF_016863155.1_ASM1686315v1_genomic.fna/checkm_result
[2024-01-24 11:08:07,198] [INFO] Task succeeded: CheckM
[2024-01-24 11:08:07,200] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:08:07,225] [INFO] ===== Completeness check finished =====
[2024-01-24 11:08:07,225] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:08:07,226] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016863155.1_ASM1686315v1_genomic.fna/markers.fasta)
[2024-01-24 11:08:07,226] [INFO] Task started: Blastn
[2024-01-24 11:08:07,226] [INFO] Running command: blastn -query GCF_016863155.1_ASM1686315v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd2849e4-25dc-48bc-98ed-18e3d0468caf/dqc_reference/reference_markers_gtdb.fasta -out GCF_016863155.1_ASM1686315v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:08:09,222] [INFO] Task succeeded: Blastn
[2024-01-24 11:08:09,226] [INFO] Selected 10 target genomes.
[2024-01-24 11:08:09,227] [INFO] Target genome list was writen to GCF_016863155.1_ASM1686315v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:08:09,244] [INFO] Task started: fastANI
[2024-01-24 11:08:09,245] [INFO] Running command: fastANI --query /var/lib/cwl/stg403fafda-c50d-474b-93f1-32a8f396a695/GCF_016863155.1_ASM1686315v1_genomic.fna.gz --refList GCF_016863155.1_ASM1686315v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016863155.1_ASM1686315v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:08:32,423] [INFO] Task succeeded: fastANI
[2024-01-24 11:08:32,436] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:08:32,436] [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_014648175.1	s__Planobispora rosea	99.9982	2734	2745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	99.82	99.64	0.97	0.95	3	conclusive
GCF_016863135.1	s__Planobispora longispora	92.2743	2223	2745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203605.1	s__Planomonospora_A venezuelensis	88.5268	1992	2745	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	88.2542	2019	2745	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_016863175.1	s__Planobispora siamensis	87.8593	2047	2745	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	87.7851	2044	2745	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	85.6676	1701	2745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002149035.1	s__Streptosporangium minutum	84.3003	1572	2745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	N/A	N/A	N/A	N/A	1	-
GCF_000024865.1	s__Streptosporangium roseum	84.2932	1731	2745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188345.1	s__Streptosporangium subroseum	83.1486	1559	2745	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	95.81	95.81	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:08:32,437] [INFO] GTDB search result was written to GCF_016863155.1_ASM1686315v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:08:32,438] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:08:32,441] [INFO] DFAST_QC result json was written to GCF_016863155.1_ASM1686315v1_genomic.fna/dqc_result.json
[2024-01-24 11:08:32,441] [INFO] DFAST_QC completed!
[2024-01-24 11:08:32,441] [INFO] Total running time: 0h2m58s