[2024-01-24 13:18:32,996] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:32,998] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:32,998] [INFO] DQC Reference Directory: /var/lib/cwl/stg692a08ee-c014-4edd-9dee-bee66057ee8c/dqc_reference
[2024-01-24 13:18:34,338] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:34,339] [INFO] Task started: Prodigal
[2024-01-24 13:18:34,339] [INFO] Running command: gunzip -c /var/lib/cwl/stgd99b968d-5352-4229-b2f0-7afd86f3bedb/GCF_014138665.1_ASM1413866v1_genomic.fna.gz | prodigal -d GCF_014138665.1_ASM1413866v1_genomic.fna/cds.fna -a GCF_014138665.1_ASM1413866v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:00,655] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:00,655] [INFO] Task started: HMMsearch
[2024-01-24 13:19:00,655] [INFO] Running command: hmmsearch --tblout GCF_014138665.1_ASM1413866v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg692a08ee-c014-4edd-9dee-bee66057ee8c/dqc_reference/reference_markers.hmm GCF_014138665.1_ASM1413866v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:01,090] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:01,092] [INFO] Found 6/6 markers.
[2024-01-24 13:19:01,182] [INFO] Query marker FASTA was written to GCF_014138665.1_ASM1413866v1_genomic.fna/markers.fasta
[2024-01-24 13:19:01,182] [INFO] Task started: Blastn
[2024-01-24 13:19:01,182] [INFO] Running command: blastn -query GCF_014138665.1_ASM1413866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg692a08ee-c014-4edd-9dee-bee66057ee8c/dqc_reference/reference_markers.fasta -out GCF_014138665.1_ASM1413866v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:02,598] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:02,608] [INFO] Selected 19 target genomes.
[2024-01-24 13:19:02,608] [INFO] Target genome list was writen to GCF_014138665.1_ASM1413866v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:02,614] [INFO] Task started: fastANI
[2024-01-24 13:19:02,615] [INFO] Running command: fastANI --query /var/lib/cwl/stgd99b968d-5352-4229-b2f0-7afd86f3bedb/GCF_014138665.1_ASM1413866v1_genomic.fna.gz --refList GCF_014138665.1_ASM1413866v1_genomic.fna/target_genomes.txt --output GCF_014138665.1_ASM1413866v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:49,966] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:49,967] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg692a08ee-c014-4edd-9dee-bee66057ee8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:49,967] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg692a08ee-c014-4edd-9dee-bee66057ee8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:49,987] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:19:49,988] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:19:49,988] [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 namibiensis	strain=DSM 44197	GCA_014138665.1	182080	182080	type	True	100.0	3233	3236	95	inconclusive
Actinomadura kijaniata	strain=NBRC 14229	GCA_001552175.1	46161	46161	type	True	97.3247	2831	3236	95	inconclusive
Actinomadura hibisca	strain=NBRC 15177	GCA_001552635.1	68565	68565	type	True	84.3724	1915	3236	95	below_threshold
Actinomadura macrotermitis	strain=RB68	GCA_009604375.1	2585200	2585200	type	True	83.1517	1813	3236	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	82.1954	1659	3236	95	below_threshold
Actinomadura rubrobrunea	strain=NBRC 15275	GCA_001552235.1	115335	115335	type	True	82.1267	1364	3236	95	below_threshold
Actinomadura logoneensis	strain=NEAU-G17	GCA_003428695.1	2293572	2293572	type	True	81.8065	1325	3236	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	81.7247	1806	3236	95	below_threshold
Actinomadura physcomitrii	strain=LD22	GCA_008923205.2	2650748	2650748	type	True	81.6245	1655	3236	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	81.5813	1709	3236	95	below_threshold
Actinomadura latina	strain=ATCC BAA-277	GCA_012396395.1	163603	163603	type	True	81.5231	1484	3236	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	81.2185	1702	3236	95	below_threshold
Actinomadura rudentiformis	strain=HMC1	GCA_008923185.1	359158	359158	type	True	81.2055	1734	3236	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	81.1617	1554	3236	95	below_threshold
Actinomadura roseirufa		GCA_900659635.1	2094049	2094049	type	True	81.106	1433	3236	95	below_threshold
Actinomadura rifamycini	strain=DSM 43936	GCA_000425065.1	31962	31962	type	True	80.9771	1641	3236	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	80.5454	1342	3236	95	below_threshold
Streptosporangium violaceochromogenes	strain=JCM 3281	GCA_014654615.1	46188	46188	type	True	77.771	829	3236	95	below_threshold
Brevibacterium album	strain=DSM 18261	GCA_000426445.1	417948	417948	type	True	75.5055	313	3236	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:49,990] [INFO] DFAST Taxonomy check result was written to GCF_014138665.1_ASM1413866v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:49,990] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:49,990] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:49,991] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg692a08ee-c014-4edd-9dee-bee66057ee8c/dqc_reference/checkm_data
[2024-01-24 13:19:49,992] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:50,084] [INFO] Task started: CheckM
[2024-01-24 13:19:50,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014138665.1_ASM1413866v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014138665.1_ASM1413866v1_genomic.fna/checkm_input GCF_014138665.1_ASM1413866v1_genomic.fna/checkm_result
[2024-01-24 13:21:49,515] [INFO] Task succeeded: CheckM
[2024-01-24 13:21:49,516] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:21:49,541] [INFO] ===== Completeness check finished =====
[2024-01-24 13:21:49,542] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:21:49,542] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014138665.1_ASM1413866v1_genomic.fna/markers.fasta)
[2024-01-24 13:21:49,543] [INFO] Task started: Blastn
[2024-01-24 13:21:49,543] [INFO] Running command: blastn -query GCF_014138665.1_ASM1413866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg692a08ee-c014-4edd-9dee-bee66057ee8c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014138665.1_ASM1413866v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:51,856] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:51,859] [INFO] Selected 21 target genomes.
[2024-01-24 13:21:51,860] [INFO] Target genome list was writen to GCF_014138665.1_ASM1413866v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:21:51,913] [INFO] Task started: fastANI
[2024-01-24 13:21:51,913] [INFO] Running command: fastANI --query /var/lib/cwl/stgd99b968d-5352-4229-b2f0-7afd86f3bedb/GCF_014138665.1_ASM1413866v1_genomic.fna.gz --refList GCF_014138665.1_ASM1413866v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014138665.1_ASM1413866v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:43,184] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:43,204] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:43,204] [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_001552175.1	s__Spirillospora kijaniata	97.3247	2831	3236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	97.32	97.32	0.88	0.88	2	conclusive
GCF_001552635.1	s__Spirillospora hibisca	84.4181	1907	3236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009604375.1	s__Spirillospora macrotermitis	83.1418	1814	3236	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	82.0712	1425	3236	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_009793335.1	s__Spirillospora sp009793335	81.9482	1884	3236	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	81.6754	1639	3236	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	81.603	1707	3236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013211575.1	s__Spirillospora verrucosospora	81.5896	1841	3236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.82	95.82	0.89	0.89	2	-
GCF_900659615.1	s__Spirillospora fibrosa	81.5437	1675	3236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409365.1	s__Spirillospora luteofluorescens	81.4788	1709	3236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552195.1	s__Spirillospora latina	81.4659	1517	3236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.98	99.98	0.98	0.98	2	-
GCF_000374305.1	s__Spirillospora flavalba	81.3424	1425	3236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008923185.1	s__Spirillospora rudentiformis	81.245	1721	3236	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	81.1657	1556	3236	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	81.1214	1430	3236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348535.1	s__Spirillospora sp004348535	81.0759	1386	3236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425065.1	s__Spirillospora rifamycini	80.9308	1654	3236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.13	99.13	0.92	0.92	2	-
GCF_014654615.1	s__Streptosporangium violaceochromogenes	77.7557	835	3236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017565405.1	s__Allobranchiibius sp017565405	76.6019	342	3236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Allobranchiibius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213575.1	s__R-H-3 sp016213575	75.9077	672	3236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__R-H-3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426445.1	s__Brevibacterium album	75.4952	316	3236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:43,206] [INFO] GTDB search result was written to GCF_014138665.1_ASM1413866v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:43,207] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:43,211] [INFO] DFAST_QC result json was written to GCF_014138665.1_ASM1413866v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:43,211] [INFO] DFAST_QC completed!
[2024-01-24 13:22:43,211] [INFO] Total running time: 0h4m10s