[2024-01-24 13:40:55,268] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:55,270] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:55,270] [INFO] DQC Reference Directory: /var/lib/cwl/stg54f42041-bc0e-4605-8efc-446599fbc5ae/dqc_reference
[2024-01-24 13:40:56,482] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:56,483] [INFO] Task started: Prodigal
[2024-01-24 13:40:56,483] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9d6239b-66da-4d3d-afc8-6cfc7e80cad3/GCF_001552215.1_ASM155221v1_genomic.fna.gz | prodigal -d GCF_001552215.1_ASM155221v1_genomic.fna/cds.fna -a GCF_001552215.1_ASM155221v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:20,369] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:20,369] [INFO] Task started: HMMsearch
[2024-01-24 13:41:20,369] [INFO] Running command: hmmsearch --tblout GCF_001552215.1_ASM155221v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54f42041-bc0e-4605-8efc-446599fbc5ae/dqc_reference/reference_markers.hmm GCF_001552215.1_ASM155221v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:20,805] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:20,806] [INFO] Found 6/6 markers.
[2024-01-24 13:41:20,869] [INFO] Query marker FASTA was written to GCF_001552215.1_ASM155221v1_genomic.fna/markers.fasta
[2024-01-24 13:41:20,870] [INFO] Task started: Blastn
[2024-01-24 13:41:20,870] [INFO] Running command: blastn -query GCF_001552215.1_ASM155221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54f42041-bc0e-4605-8efc-446599fbc5ae/dqc_reference/reference_markers.fasta -out GCF_001552215.1_ASM155221v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:22,119] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:22,122] [INFO] Selected 12 target genomes.
[2024-01-24 13:41:22,122] [INFO] Target genome list was writen to GCF_001552215.1_ASM155221v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:22,126] [INFO] Task started: fastANI
[2024-01-24 13:41:22,126] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9d6239b-66da-4d3d-afc8-6cfc7e80cad3/GCF_001552215.1_ASM155221v1_genomic.fna.gz --refList GCF_001552215.1_ASM155221v1_genomic.fna/target_genomes.txt --output GCF_001552215.1_ASM155221v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:50,564] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:50,565] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54f42041-bc0e-4605-8efc-446599fbc5ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:50,565] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54f42041-bc0e-4605-8efc-446599fbc5ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:50,573] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:50,573] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:50,573] [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 macra	strain=NBRC 14102	GCA_001552215.1	46164	46164	type	True	100.0	2987	2990	95	conclusive
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	89.6403	2319	2990	95	below_threshold
Actinomadura litoris	strain=NEAU-AAG5	GCA_009733595.1	2678616	2678616	type	True	85.9903	1948	2990	95	below_threshold
Actinomadura rubrisoli	strain=H3C3	GCA_004349215.1	2530368	2530368	type	True	85.7004	1812	2990	95	below_threshold
Actinomadura roseirufa		GCA_900659635.1	2094049	2094049	type	True	84.5024	1628	2990	95	below_threshold
Actinomadura madurae	strain=DSM 43067	GCA_900115095.1	1993	1993	type	True	83.7461	1729	2990	95	below_threshold
Actinomadura darangshiensis	strain=DSM 45941	GCA_004349235.1	705336	705336	type	True	83.701	1595	2990	95	below_threshold
Actinomadura bangladeshensis	strain=DSM 45347	GCA_004348335.1	453573	453573	type	True	83.6711	1468	2990	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	83.4534	1803	2990	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	82.9331	1593	2990	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	80.771	1405	2990	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	80.6014	1435	2990	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:50,574] [INFO] DFAST Taxonomy check result was written to GCF_001552215.1_ASM155221v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:50,575] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:50,575] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:50,575] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54f42041-bc0e-4605-8efc-446599fbc5ae/dqc_reference/checkm_data
[2024-01-24 13:41:50,576] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:50,655] [INFO] Task started: CheckM
[2024-01-24 13:41:50,655] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001552215.1_ASM155221v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001552215.1_ASM155221v1_genomic.fna/checkm_input GCF_001552215.1_ASM155221v1_genomic.fna/checkm_result
[2024-01-24 13:43:19,353] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:19,354] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.72%
Strain heterogeneity: 60.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:19,374] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:19,374] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:19,374] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001552215.1_ASM155221v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:19,374] [INFO] Task started: Blastn
[2024-01-24 13:43:19,374] [INFO] Running command: blastn -query GCF_001552215.1_ASM155221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54f42041-bc0e-4605-8efc-446599fbc5ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_001552215.1_ASM155221v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:21,388] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:21,391] [INFO] Selected 12 target genomes.
[2024-01-24 13:43:21,391] [INFO] Target genome list was writen to GCF_001552215.1_ASM155221v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:21,424] [INFO] Task started: fastANI
[2024-01-24 13:43:21,425] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9d6239b-66da-4d3d-afc8-6cfc7e80cad3/GCF_001552215.1_ASM155221v1_genomic.fna.gz --refList GCF_001552215.1_ASM155221v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001552215.1_ASM155221v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:50,165] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:50,173] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:50,173] [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_001552215.1	s__Spirillospora macra	100.0	2987	2990	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_009733595.1	s__Spirillospora litoris	86.0415	1940	2990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.22	99.22	0.97	0.97	2	-
GCF_004349215.1	s__Spirillospora rubrisoli	85.6723	1817	2990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900659635.1	s__Spirillospora roseirufa	84.5148	1626	2990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900659615.1	s__Spirillospora fibrosa	84.3612	1723	2990	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	83.7203	1735	2990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.34	99.27	0.95	0.95	3	-
GCF_004349235.1	s__Spirillospora darangshiensis	83.7151	1592	2990	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	83.7111	1709	2990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008923205.2	s__Spirillospora physcomitrii	83.6259	1661	2990	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	83.5014	1740	2990	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	83.466	1712	2990	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	83.4446	1765	2990	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 13:43:50,174] [INFO] GTDB search result was written to GCF_001552215.1_ASM155221v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:50,175] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:50,177] [INFO] DFAST_QC result json was written to GCF_001552215.1_ASM155221v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:50,177] [INFO] DFAST_QC completed!
[2024-01-24 13:43:50,178] [INFO] Total running time: 0h2m55s