[2024-01-25 19:52:05,666] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:52:05,667] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:52:05,668] [INFO] DQC Reference Directory: /var/lib/cwl/stgee8913d0-9699-4e6c-ad8e-9bac5e732337/dqc_reference
[2024-01-25 19:52:06,808] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:52:06,808] [INFO] Task started: Prodigal
[2024-01-25 19:52:06,809] [INFO] Running command: gunzip -c /var/lib/cwl/stge60e7eed-e7dc-4c38-8e7c-62d7830fa0ca/GCF_009604375.1_ASM960437v1_genomic.fna.gz | prodigal -d GCF_009604375.1_ASM960437v1_genomic.fna/cds.fna -a GCF_009604375.1_ASM960437v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:52:27,139] [INFO] Task succeeded: Prodigal
[2024-01-25 19:52:27,139] [INFO] Task started: HMMsearch
[2024-01-25 19:52:27,139] [INFO] Running command: hmmsearch --tblout GCF_009604375.1_ASM960437v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee8913d0-9699-4e6c-ad8e-9bac5e732337/dqc_reference/reference_markers.hmm GCF_009604375.1_ASM960437v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:52:27,492] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:52:27,493] [INFO] Found 6/6 markers.
[2024-01-25 19:52:27,557] [INFO] Query marker FASTA was written to GCF_009604375.1_ASM960437v1_genomic.fna/markers.fasta
[2024-01-25 19:52:27,557] [INFO] Task started: Blastn
[2024-01-25 19:52:27,557] [INFO] Running command: blastn -query GCF_009604375.1_ASM960437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee8913d0-9699-4e6c-ad8e-9bac5e732337/dqc_reference/reference_markers.fasta -out GCF_009604375.1_ASM960437v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:28,854] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:28,856] [INFO] Selected 16 target genomes.
[2024-01-25 19:52:28,857] [INFO] Target genome list was writen to GCF_009604375.1_ASM960437v1_genomic.fna/target_genomes.txt
[2024-01-25 19:52:28,875] [INFO] Task started: fastANI
[2024-01-25 19:52:28,876] [INFO] Running command: fastANI --query /var/lib/cwl/stge60e7eed-e7dc-4c38-8e7c-62d7830fa0ca/GCF_009604375.1_ASM960437v1_genomic.fna.gz --refList GCF_009604375.1_ASM960437v1_genomic.fna/target_genomes.txt --output GCF_009604375.1_ASM960437v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:53:12,505] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:12,506] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee8913d0-9699-4e6c-ad8e-9bac5e732337/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:53:12,506] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee8913d0-9699-4e6c-ad8e-9bac5e732337/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:53:12,516] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:53:12,516] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:53:12,516] [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 macrotermitis	strain=RB68	GCA_009604375.1	2585200	2585200	type	True	100.0	2841	2841	95	conclusive
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	85.1012	1712	2841	95	below_threshold
Actinomadura hibisca	strain=NBRC 15177	GCA_001552635.1	68565	68565	type	True	84.2261	1758	2841	95	below_threshold
Actinomadura kijaniata	strain=NBRC 14229	GCA_001552175.1	46161	46161	type	True	83.2864	1752	2841	95	below_threshold
Actinomadura namibiensis	strain=DSM 44197	GCA_014138665.1	182080	182080	type	True	83.1944	1818	2841	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	82.7414	1770	2841	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	82.6709	1642	2841	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	82.6019	1728	2841	95	below_threshold
Actinomadura rubrobrunea	strain=NBRC 15275	GCA_001552235.1	115335	115335	type	True	82.2894	1279	2841	95	below_threshold
Actinomadura rubrisoli	strain=H3C3	GCA_004349215.1	2530368	2530368	type	True	82.2315	1479	2841	95	below_threshold
Actinomadura darangshiensis	strain=DSM 45941	GCA_004349235.1	705336	705336	type	True	82.2266	1451	2841	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	82.1719	1411	2841	95	below_threshold
Actinomadura madurae	strain=DSM 43067	GCA_900115095.1	1993	1993	type	True	82.1631	1575	2841	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	81.9576	1628	2841	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	81.9458	1537	2841	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	81.0379	1303	2841	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:53:12,518] [INFO] DFAST Taxonomy check result was written to GCF_009604375.1_ASM960437v1_genomic.fna/tc_result.tsv
[2024-01-25 19:53:12,518] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:53:12,518] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:53:12,518] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee8913d0-9699-4e6c-ad8e-9bac5e732337/dqc_reference/checkm_data
[2024-01-25 19:53:12,519] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:53:12,593] [INFO] Task started: CheckM
[2024-01-25 19:53:12,594] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009604375.1_ASM960437v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009604375.1_ASM960437v1_genomic.fna/checkm_input GCF_009604375.1_ASM960437v1_genomic.fna/checkm_result
[2024-01-25 19:54:35,674] [INFO] Task succeeded: CheckM
[2024-01-25 19:54:35,677] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.26%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2024-01-25 19:54:35,705] [INFO] ===== Completeness check finished =====
[2024-01-25 19:54:35,705] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:54:35,706] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009604375.1_ASM960437v1_genomic.fna/markers.fasta)
[2024-01-25 19:54:35,706] [INFO] Task started: Blastn
[2024-01-25 19:54:35,706] [INFO] Running command: blastn -query GCF_009604375.1_ASM960437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee8913d0-9699-4e6c-ad8e-9bac5e732337/dqc_reference/reference_markers_gtdb.fasta -out GCF_009604375.1_ASM960437v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:37,887] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:37,889] [INFO] Selected 16 target genomes.
[2024-01-25 19:54:37,890] [INFO] Target genome list was writen to GCF_009604375.1_ASM960437v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:54:37,906] [INFO] Task started: fastANI
[2024-01-25 19:54:37,907] [INFO] Running command: fastANI --query /var/lib/cwl/stge60e7eed-e7dc-4c38-8e7c-62d7830fa0ca/GCF_009604375.1_ASM960437v1_genomic.fna.gz --refList GCF_009604375.1_ASM960437v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009604375.1_ASM960437v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:55:22,969] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:22,979] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:55:22,980] [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_009604375.1	s__Spirillospora macrotermitis	100.0	2841	2841	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_001552635.1	s__Spirillospora hibisca	84.2155	1759	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552175.1	s__Spirillospora kijaniata	83.3013	1750	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	97.32	97.32	0.88	0.88	2	-
GCF_013211575.1	s__Spirillospora verrucosospora	82.8034	1767	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.82	95.82	0.89	0.89	2	-
GCF_009793335.1	s__Spirillospora sp009793335	82.7382	1771	2841	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	82.6209	1653	2841	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	82.5963	1727	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.12	95.12	0.83	0.83	2	-
GCF_013372625.1	s__Spirillospora sp013372625	82.4327	1296	2841	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	82.3695	1640	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003001795.1	s__Actinomadura_B viridilutea	82.2495	1325	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_B	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004349215.1	s__Spirillospora rubrisoli	82.2439	1477	2841	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	82.1997	1456	2841	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	82.1687	1412	2841	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	82.1274	1582	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.34	99.27	0.95	0.95	3	-
GCF_900659635.1	s__Spirillospora roseirufa	81.8403	1422	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696215.1	s__Spirillospora harenae	81.7316	1488	2841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:55:22,981] [INFO] GTDB search result was written to GCF_009604375.1_ASM960437v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:55:22,982] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:55:22,985] [INFO] DFAST_QC result json was written to GCF_009604375.1_ASM960437v1_genomic.fna/dqc_result.json
[2024-01-25 19:55:22,985] [INFO] DFAST_QC completed!
[2024-01-25 19:55:22,985] [INFO] Total running time: 0h3m17s