[2024-01-24 13:49:30,723] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:30,725] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:30,725] [INFO] DQC Reference Directory: /var/lib/cwl/stga829faae-8ba7-4238-ba62-f1bd0338657e/dqc_reference
[2024-01-24 13:49:32,068] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:32,069] [INFO] Task started: Prodigal
[2024-01-24 13:49:32,069] [INFO] Running command: gunzip -c /var/lib/cwl/stg62fc122f-874b-4b5d-946e-551b990bfa0b/GCF_001552155.1_ASM155215v1_genomic.fna.gz | prodigal -d GCF_001552155.1_ASM155215v1_genomic.fna/cds.fna -a GCF_001552155.1_ASM155215v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:51,119] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:51,120] [INFO] Task started: HMMsearch
[2024-01-24 13:49:51,120] [INFO] Running command: hmmsearch --tblout GCF_001552155.1_ASM155215v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga829faae-8ba7-4238-ba62-f1bd0338657e/dqc_reference/reference_markers.hmm GCF_001552155.1_ASM155215v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:51,578] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:51,580] [INFO] Found 6/6 markers.
[2024-01-24 13:49:51,642] [INFO] Query marker FASTA was written to GCF_001552155.1_ASM155215v1_genomic.fna/markers.fasta
[2024-01-24 13:49:51,643] [INFO] Task started: Blastn
[2024-01-24 13:49:51,643] [INFO] Running command: blastn -query GCF_001552155.1_ASM155215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga829faae-8ba7-4238-ba62-f1bd0338657e/dqc_reference/reference_markers.fasta -out GCF_001552155.1_ASM155215v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:52,948] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:52,952] [INFO] Selected 16 target genomes.
[2024-01-24 13:49:52,952] [INFO] Target genome list was writen to GCF_001552155.1_ASM155215v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:52,965] [INFO] Task started: fastANI
[2024-01-24 13:49:52,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg62fc122f-874b-4b5d-946e-551b990bfa0b/GCF_001552155.1_ASM155215v1_genomic.fna.gz --refList GCF_001552155.1_ASM155215v1_genomic.fna/target_genomes.txt --output GCF_001552155.1_ASM155215v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:27,635] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:27,635] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga829faae-8ba7-4238-ba62-f1bd0338657e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:27,636] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga829faae-8ba7-4238-ba62-f1bd0338657e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:27,649] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:27,649] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:27,649] [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 formosensis	strain=NBRC 14204	GCA_001552155.1	60706	60706	type	True	100.0	2178	2195	95	conclusive
Actinomadura latina	strain=ATCC BAA-277	GCA_012396395.1	163603	163603	type	True	89.038	1577	2195	95	below_threshold
Actinomadura latina	strain=NBRC 106108	GCA_001552195.1	163603	163603	type	True	88.962	1592	2195	95	below_threshold
Actinomadura bangladeshensis	strain=DSM 45347	GCA_004348335.1	453573	453573	type	True	88.4122	1486	2195	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	88.0226	1386	2195	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	87.887	1593	2195	95	below_threshold
Actinomadura madurae	strain=DSM 43067	GCA_900115095.1	1993	1993	type	True	86.9112	1600	2195	95	below_threshold
Actinomadura coerulea	strain=JCM 3320	GCA_014648535.1	46159	46159	type	True	86.9085	1518	2195	95	below_threshold
Actinomadura coerulea	strain=DSM 43675	GCA_014208105.1	46159	46159	type	True	86.8366	1541	2195	95	below_threshold
Actinomadura mexicana	strain=DSM 44485	GCA_900188105.1	134959	134959	type	True	86.7541	1555	2195	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	84.9528	1333	2195	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	84.7785	1453	2195	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	84.7061	1548	2195	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	83.935	1423	2195	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	81.6725	1242	2195	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	81.3297	1224	2195	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:27,651] [INFO] DFAST Taxonomy check result was written to GCF_001552155.1_ASM155215v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:27,652] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:27,652] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:27,652] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga829faae-8ba7-4238-ba62-f1bd0338657e/dqc_reference/checkm_data
[2024-01-24 13:50:27,654] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:27,724] [INFO] Task started: CheckM
[2024-01-24 13:50:27,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001552155.1_ASM155215v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001552155.1_ASM155215v1_genomic.fna/checkm_input GCF_001552155.1_ASM155215v1_genomic.fna/checkm_result
[2024-01-24 13:51:24,239] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:24,241] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:24,268] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:24,268] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:24,269] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001552155.1_ASM155215v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:24,269] [INFO] Task started: Blastn
[2024-01-24 13:51:24,269] [INFO] Running command: blastn -query GCF_001552155.1_ASM155215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga829faae-8ba7-4238-ba62-f1bd0338657e/dqc_reference/reference_markers_gtdb.fasta -out GCF_001552155.1_ASM155215v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:26,269] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:26,274] [INFO] Selected 15 target genomes.
[2024-01-24 13:51:26,274] [INFO] Target genome list was writen to GCF_001552155.1_ASM155215v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:26,307] [INFO] Task started: fastANI
[2024-01-24 13:51:26,307] [INFO] Running command: fastANI --query /var/lib/cwl/stg62fc122f-874b-4b5d-946e-551b990bfa0b/GCF_001552155.1_ASM155215v1_genomic.fna.gz --refList GCF_001552155.1_ASM155215v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001552155.1_ASM155215v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:57,330] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:57,347] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:57,348] [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_001552155.1	s__Spirillospora formosensis	100.0	2178	2195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_001552195.1	s__Spirillospora latina	88.9732	1590	2195	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	88.6638	1415	2195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348335.1	s__Spirillospora bangladeshensis	88.4405	1483	2195	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	88.1034	1649	2195	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	87.9944	1388	2195	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	87.8693	1596	2195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349235.1	s__Spirillospora darangshiensis	87.1719	1463	2195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008327685.1	s__Spirillospora sp008327685	86.9347	1645	2195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115095.1	s__Spirillospora madurae	86.9161	1600	2195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.34	99.27	0.95	0.95	3	-
GCF_013409365.1	s__Spirillospora luteofluorescens	86.747	1597	2195	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	86.7426	1554	2195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006547145.1	s__Spirillospora sp006547145	86.5294	1600	2195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349245.1	s__Spirillospora sp004349245	86.086	1380	2195	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	84.788	1451	2195	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:57,350] [INFO] GTDB search result was written to GCF_001552155.1_ASM155215v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:57,350] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:57,354] [INFO] DFAST_QC result json was written to GCF_001552155.1_ASM155215v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:57,355] [INFO] DFAST_QC completed!
[2024-01-24 13:51:57,355] [INFO] Total running time: 0h2m27s