[2024-01-24 13:32:41,165] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:41,173] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:41,173] [INFO] DQC Reference Directory: /var/lib/cwl/stga87e4d60-a33e-4012-8464-cbb35a9183fa/dqc_reference
[2024-01-24 13:32:42,413] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:42,413] [INFO] Task started: Prodigal
[2024-01-24 13:32:42,413] [INFO] Running command: gunzip -c /var/lib/cwl/stg47b666d8-c899-4f12-a4e1-fe40e835bcc0/GCF_030811455.1_ASM3081145v1_genomic.fna.gz | prodigal -d GCF_030811455.1_ASM3081145v1_genomic.fna/cds.fna -a GCF_030811455.1_ASM3081145v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:12,458] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:12,459] [INFO] Task started: HMMsearch
[2024-01-24 13:33:12,459] [INFO] Running command: hmmsearch --tblout GCF_030811455.1_ASM3081145v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga87e4d60-a33e-4012-8464-cbb35a9183fa/dqc_reference/reference_markers.hmm GCF_030811455.1_ASM3081145v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:12,944] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:12,946] [INFO] Found 6/6 markers.
[2024-01-24 13:33:13,019] [INFO] Query marker FASTA was written to GCF_030811455.1_ASM3081145v1_genomic.fna/markers.fasta
[2024-01-24 13:33:13,020] [INFO] Task started: Blastn
[2024-01-24 13:33:13,020] [INFO] Running command: blastn -query GCF_030811455.1_ASM3081145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga87e4d60-a33e-4012-8464-cbb35a9183fa/dqc_reference/reference_markers.fasta -out GCF_030811455.1_ASM3081145v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:14,306] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:14,309] [INFO] Selected 19 target genomes.
[2024-01-24 13:33:14,309] [INFO] Target genome list was writen to GCF_030811455.1_ASM3081145v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:14,315] [INFO] Task started: fastANI
[2024-01-24 13:33:14,315] [INFO] Running command: fastANI --query /var/lib/cwl/stg47b666d8-c899-4f12-a4e1-fe40e835bcc0/GCF_030811455.1_ASM3081145v1_genomic.fna.gz --refList GCF_030811455.1_ASM3081145v1_genomic.fna/target_genomes.txt --output GCF_030811455.1_ASM3081145v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:54,958] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:54,959] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga87e4d60-a33e-4012-8464-cbb35a9183fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:54,959] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga87e4d60-a33e-4012-8464-cbb35a9183fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:54,971] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:33:54,971] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:33:54,971] [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 canum	strain=CGMCC 4.2126	GCA_900113865.1	324952	324952	type	True	86.1024	1896	3544	95	below_threshold
Streptosporangium roseum	strain=DSM 43021	GCA_000024865.1	2001	2001	type	True	86.0039	2044	3544	95	below_threshold
Streptosporangium minutum	strain=M26	GCA_002149035.1	569862	569862	type	True	85.8681	1814	3544	95	below_threshold
Streptosporangium album	strain=DSM 43023	GCA_014203795.1	47479	47479	type	True	85.2938	1826	3544	95	below_threshold
Streptosporangium amethystogenes	strain=NRRL B-2639	GCA_000721075.1	2002	2002	type	True	84.9704	1771	3544	95	below_threshold
Planobispora takensis	strain=NBRC 109077	GCA_016863195.1	1367882	1367882	type	True	83.3766	1644	3544	95	below_threshold
Streptosporangium sandarakinum	strain=DSM 45763	GCA_013409935.1	1260955	1260955	type	True	83.3763	1636	3544	95	below_threshold
Streptosporangium pseudovulgare	strain=JCM 3115	GCA_014648055.1	35765	35765	type	True	83.3022	1686	3544	95	below_threshold
Planobispora siamensis	strain=NBRC 107568	GCA_016863175.1	936338	936338	type	True	83.265	1648	3544	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	80.0059	942	3544	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	79.9112	1517	3544	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	79.907	1432	3544	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	79.7483	1491	3544	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	79.3097	1418	3544	95	below_threshold
Streptomyces fagopyri	strain=QMT-28	GCA_009498275.1	2662397	2662397	type	True	76.8061	656	3544	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	76.79	613	3544	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_003675955.1	1226757	1226757	type	True	76.5393	821	3544	95	below_threshold
Streptomyces atriruber	strain=NRRL B-24165	GCA_001418325.1	545121	545121	type	True	76.4899	622	3544	95	below_threshold
Streptomyces alanosinicus	strain=JCM 4714	GCA_014650595.1	68171	68171	type	True	76.3812	718	3544	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:54,973] [INFO] DFAST Taxonomy check result was written to GCF_030811455.1_ASM3081145v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:54,973] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:54,974] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:54,974] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga87e4d60-a33e-4012-8464-cbb35a9183fa/dqc_reference/checkm_data
[2024-01-24 13:33:54,975] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:55,070] [INFO] Task started: CheckM
[2024-01-24 13:33:55,070] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030811455.1_ASM3081145v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030811455.1_ASM3081145v1_genomic.fna/checkm_input GCF_030811455.1_ASM3081145v1_genomic.fna/checkm_result
[2024-01-24 13:35:47,456] [INFO] Task succeeded: CheckM
[2024-01-24 13:35:47,457] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.82%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:35:47,477] [INFO] ===== Completeness check finished =====
[2024-01-24 13:35:47,477] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:35:47,477] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030811455.1_ASM3081145v1_genomic.fna/markers.fasta)
[2024-01-24 13:35:47,478] [INFO] Task started: Blastn
[2024-01-24 13:35:47,478] [INFO] Running command: blastn -query GCF_030811455.1_ASM3081145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga87e4d60-a33e-4012-8464-cbb35a9183fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_030811455.1_ASM3081145v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:49,493] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:49,495] [INFO] Selected 15 target genomes.
[2024-01-24 13:35:49,496] [INFO] Target genome list was writen to GCF_030811455.1_ASM3081145v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:35:49,503] [INFO] Task started: fastANI
[2024-01-24 13:35:49,503] [INFO] Running command: fastANI --query /var/lib/cwl/stg47b666d8-c899-4f12-a4e1-fe40e835bcc0/GCF_030811455.1_ASM3081145v1_genomic.fna.gz --refList GCF_030811455.1_ASM3081145v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030811455.1_ASM3081145v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:36:20,010] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:20,020] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:36:20,020] [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_900188345.1	s__Streptosporangium subroseum	90.9855	2528	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	95.81	95.81	0.87	0.87	2	-
GCF_900113865.1	s__Streptosporangium canum	86.0746	1900	3544	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	86.0112	2041	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002149035.1	s__Streptosporangium minutum	85.8653	1814	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	N/A	N/A	N/A	N/A	1	-
GCF_014203795.1	s__Streptosporangium album	85.2969	1828	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721075.1	s__Streptosporangium amethystogenes	84.9944	1766	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015711605.1	s__Planomonospora_A sp015711605	83.5984	1587	3544	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_016863195.1	s__Planobispora takensis	83.3793	1644	3544	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	83.2962	1642	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCF_014648055.1	s__Streptosporangium pseudovulgare	83.2754	1692	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	96.6013	N/A	N/A	N/A	N/A	1	-
GCA_014647935.1	s__Planomonospora parontospora	83.2363	1619	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora	95.0	97.40	95.90	0.89	0.84	6	-
GCF_009498275.1	s__Streptomyces fagopyri	76.7821	658	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008042115.1	s__Streptomyces sp008042115	76.7416	689	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418325.1	s__Streptomyces atriruber	76.4729	630	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650595.1	s__Streptomyces alanosinicus	76.3867	720	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:36:20,022] [INFO] GTDB search result was written to GCF_030811455.1_ASM3081145v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:36:20,022] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:36:20,025] [INFO] DFAST_QC result json was written to GCF_030811455.1_ASM3081145v1_genomic.fna/dqc_result.json
[2024-01-24 13:36:20,025] [INFO] DFAST_QC completed!
[2024-01-24 13:36:20,025] [INFO] Total running time: 0h3m39s