[2024-01-24 13:09:51,806] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:51,808] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:51,808] [INFO] DQC Reference Directory: /var/lib/cwl/stg1919e2d8-f943-4fcf-bd0d-ebf6893a8cbc/dqc_reference
[2024-01-24 13:09:53,173] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:53,174] [INFO] Task started: Prodigal
[2024-01-24 13:09:53,175] [INFO] Running command: gunzip -c /var/lib/cwl/stg48b1a74c-c163-4b64-b3e7-3163b844813d/GCF_004348335.1_ASM434833v1_genomic.fna.gz | prodigal -d GCF_004348335.1_ASM434833v1_genomic.fna/cds.fna -a GCF_004348335.1_ASM434833v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:14,763] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:14,763] [INFO] Task started: HMMsearch
[2024-01-24 13:10:14,763] [INFO] Running command: hmmsearch --tblout GCF_004348335.1_ASM434833v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1919e2d8-f943-4fcf-bd0d-ebf6893a8cbc/dqc_reference/reference_markers.hmm GCF_004348335.1_ASM434833v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:15,164] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:15,166] [INFO] Found 6/6 markers.
[2024-01-24 13:10:15,255] [INFO] Query marker FASTA was written to GCF_004348335.1_ASM434833v1_genomic.fna/markers.fasta
[2024-01-24 13:10:15,255] [INFO] Task started: Blastn
[2024-01-24 13:10:15,255] [INFO] Running command: blastn -query GCF_004348335.1_ASM434833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1919e2d8-f943-4fcf-bd0d-ebf6893a8cbc/dqc_reference/reference_markers.fasta -out GCF_004348335.1_ASM434833v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:16,681] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:16,684] [INFO] Selected 15 target genomes.
[2024-01-24 13:10:16,684] [INFO] Target genome list was writen to GCF_004348335.1_ASM434833v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:16,690] [INFO] Task started: fastANI
[2024-01-24 13:10:16,690] [INFO] Running command: fastANI --query /var/lib/cwl/stg48b1a74c-c163-4b64-b3e7-3163b844813d/GCF_004348335.1_ASM434833v1_genomic.fna.gz --refList GCF_004348335.1_ASM434833v1_genomic.fna/target_genomes.txt --output GCF_004348335.1_ASM434833v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:54,403] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:54,404] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1919e2d8-f943-4fcf-bd0d-ebf6893a8cbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:54,404] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1919e2d8-f943-4fcf-bd0d-ebf6893a8cbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:54,416] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:54,416] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:54,416] [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
Actinomadura bangladeshensis	strain=DSM 45347	GCA_004348335.1	453573	453573	type	True	100.0	2568	2595	95	conclusive
Actinomadura latina	strain=NBRC 106108	GCA_001552195.1	163603	163603	type	True	91.0666	1918	2595	95	below_threshold
Actinomadura latina	strain=ATCC BAA-277	GCA_012396395.1	163603	163603	type	True	91.0144	1906	2595	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	89.8676	1727	2595	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	89.3324	1894	2595	95	below_threshold
Actinomadura formosensis	strain=NBRC 14204	GCA_001552155.1	60706	60706	type	True	88.3275	1507	2595	95	below_threshold
Actinomadura madurae	strain=DSM 43067	GCA_900115095.1	1993	1993	type	True	87.2193	1869	2595	95	below_threshold
Actinomadura mexicana	strain=DSM 44485	GCA_900188105.1	134959	134959	type	True	86.8669	1756	2595	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	85.1403	1653	2595	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	85.0903	1835	2595	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	85.0082	1797	2595	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	84.7271	1439	2595	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	83.8568	1480	2595	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	81.816	1400	2595	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	81.3507	1376	2595	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:54,418] [INFO] DFAST Taxonomy check result was written to GCF_004348335.1_ASM434833v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:54,418] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:54,418] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:54,418] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1919e2d8-f943-4fcf-bd0d-ebf6893a8cbc/dqc_reference/checkm_data
[2024-01-24 13:10:54,419] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:54,502] [INFO] Task started: CheckM
[2024-01-24 13:10:54,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004348335.1_ASM434833v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004348335.1_ASM434833v1_genomic.fna/checkm_input GCF_004348335.1_ASM434833v1_genomic.fna/checkm_result
[2024-01-24 13:11:59,395] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:59,396] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:59,420] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:59,421] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:59,421] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004348335.1_ASM434833v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:59,422] [INFO] Task started: Blastn
[2024-01-24 13:11:59,422] [INFO] Running command: blastn -query GCF_004348335.1_ASM434833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1919e2d8-f943-4fcf-bd0d-ebf6893a8cbc/dqc_reference/reference_markers_gtdb.fasta -out GCF_004348335.1_ASM434833v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:01,471] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:01,474] [INFO] Selected 11 target genomes.
[2024-01-24 13:12:01,474] [INFO] Target genome list was writen to GCF_004348335.1_ASM434833v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:12:01,481] [INFO] Task started: fastANI
[2024-01-24 13:12:01,482] [INFO] Running command: fastANI --query /var/lib/cwl/stg48b1a74c-c163-4b64-b3e7-3163b844813d/GCF_004348335.1_ASM434833v1_genomic.fna.gz --refList GCF_004348335.1_ASM434833v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004348335.1_ASM434833v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:12:28,170] [INFO] Task succeeded: fastANI
[2024-01-24 13:12:28,192] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:12:28,193] [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_004348335.1	s__Spirillospora bangladeshensis	100.0	2568	2595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001552195.1	s__Spirillospora latina	91.0407	1921	2595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.98	99.98	0.98	0.98	2	-
GCF_013372625.1	s__Spirillospora sp013372625	90.8285	1690	2595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364275.1	s__Spirillospora sp013364275	89.8589	2018	2595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005889745.1	s__Spirillospora geliboluensis	89.8528	1729	2595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188445.1	s__Spirillospora meyerae	89.3462	1892	2595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552155.1	s__Spirillospora formosensis	88.3591	1503	2595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.99	99.99	0.99	0.99	2	-
GCF_008327685.1	s__Spirillospora sp008327685	87.0941	1843	2595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188105.1	s__Spirillospora mexicana	86.8942	1753	2595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008923365.1	s__Spirillospora montaniterrae	85.1262	1654	2595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017573545.1	s__Spirillospora nitritigenes	85.1013	1833	2595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.12	95.12	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:12:28,195] [INFO] GTDB search result was written to GCF_004348335.1_ASM434833v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:12:28,196] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:12:28,200] [INFO] DFAST_QC result json was written to GCF_004348335.1_ASM434833v1_genomic.fna/dqc_result.json
[2024-01-24 13:12:28,200] [INFO] DFAST_QC completed!
[2024-01-24 13:12:28,200] [INFO] Total running time: 0h2m36s