[2024-01-24 10:47:06,543] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,547] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,547] [INFO] DQC Reference Directory: /var/lib/cwl/stg07250562-40f8-463e-a282-4d2be36cfa3f/dqc_reference
[2024-01-24 10:47:12,103] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,105] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,105] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb82a261-188c-41b0-90d2-7d9ad4f91a7e/GCF_019458805.1_ASM1945880v1_genomic.fna.gz | prodigal -d GCF_019458805.1_ASM1945880v1_genomic.fna/cds.fna -a GCF_019458805.1_ASM1945880v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:30,205] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:30,206] [INFO] Task started: HMMsearch
[2024-01-24 10:47:30,206] [INFO] Running command: hmmsearch --tblout GCF_019458805.1_ASM1945880v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07250562-40f8-463e-a282-4d2be36cfa3f/dqc_reference/reference_markers.hmm GCF_019458805.1_ASM1945880v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:30,605] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:30,608] [INFO] Found 6/6 markers.
[2024-01-24 10:47:30,669] [INFO] Query marker FASTA was written to GCF_019458805.1_ASM1945880v1_genomic.fna/markers.fasta
[2024-01-24 10:47:30,669] [INFO] Task started: Blastn
[2024-01-24 10:47:30,669] [INFO] Running command: blastn -query GCF_019458805.1_ASM1945880v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07250562-40f8-463e-a282-4d2be36cfa3f/dqc_reference/reference_markers.fasta -out GCF_019458805.1_ASM1945880v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:32,031] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:32,035] [INFO] Selected 21 target genomes.
[2024-01-24 10:47:32,036] [INFO] Target genome list was writen to GCF_019458805.1_ASM1945880v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:32,052] [INFO] Task started: fastANI
[2024-01-24 10:47:32,052] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb82a261-188c-41b0-90d2-7d9ad4f91a7e/GCF_019458805.1_ASM1945880v1_genomic.fna.gz --refList GCF_019458805.1_ASM1945880v1_genomic.fna/target_genomes.txt --output GCF_019458805.1_ASM1945880v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:29,247] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:29,248] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07250562-40f8-463e-a282-4d2be36cfa3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:29,248] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07250562-40f8-463e-a282-4d2be36cfa3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:29,264] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:29,264] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:29,264] [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 parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	100.0	2504	2504	95	conclusive
Actinomadura macrotermitis	strain=RB68	GCA_009604375.1	2585200	2585200	type	True	85.1554	1716	2504	95	below_threshold
Actinomadura hibisca	strain=NBRC 15177	GCA_001552635.1	68565	68565	type	True	83.2099	1648	2504	95	below_threshold
Actinomadura kijaniata	strain=NBRC 14229	GCA_001552175.1	46161	46161	type	True	82.2534	1617	2504	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	82.2104	1633	2504	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	82.21	1665	2504	95	below_threshold
Actinomadura namibiensis	strain=DSM 44197	GCA_014138665.1	182080	182080	type	True	82.1765	1676	2504	95	below_threshold
Actinomadura flavalba	strain=DSM 45200	GCA_000374305.1	1120938	1120938	type	True	82.1219	1376	2504	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	82.0676	1674	2504	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	82.0129	1525	2504	95	below_threshold
Actinomadura bangladeshensis	strain=DSM 45347	GCA_004348335.1	453573	453573	type	True	81.9293	1374	2504	95	below_threshold
Actinomadura atramentaria	strain=SF2197	GCA_000381885.1	1990	1990	type	True	81.9162	1382	2504	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	81.7554	1359	2504	95	below_threshold
Actinomadura rubteroloni	strain=RB29	GCA_002911665.1	1926885	1926885	type	True	81.7521	1286	2504	95	below_threshold
Actinomadura rayongensis	strain=DSM 102126	GCA_009831215.1	1429076	1429076	type	True	81.6814	1335	2504	95	below_threshold
Actinomadura madurae	strain=DSM 43067	GCA_900115095.1	1993	1993	type	True	81.6254	1549	2504	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	81.3814	1535	2504	95	below_threshold
Actinomadura rifamycini	strain=DSM 43936	GCA_000425065.1	31962	31962	type	True	81.294	1509	2504	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	81.1787	1449	2504	95	below_threshold
Actinomadura cremea	strain=JCM 3308	GCA_014648495.1	1991	1991	type	True	81.0989	1504	2504	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	80.6369	1240	2504	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:29,266] [INFO] DFAST Taxonomy check result was written to GCF_019458805.1_ASM1945880v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:29,266] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:29,266] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:29,266] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07250562-40f8-463e-a282-4d2be36cfa3f/dqc_reference/checkm_data
[2024-01-24 10:48:29,267] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:29,334] [INFO] Task started: CheckM
[2024-01-24 10:48:29,334] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019458805.1_ASM1945880v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019458805.1_ASM1945880v1_genomic.fna/checkm_input GCF_019458805.1_ASM1945880v1_genomic.fna/checkm_result
[2024-01-24 10:49:43,968] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:43,971] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:43,993] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:43,993] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:43,993] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019458805.1_ASM1945880v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:43,993] [INFO] Task started: Blastn
[2024-01-24 10:49:43,994] [INFO] Running command: blastn -query GCF_019458805.1_ASM1945880v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07250562-40f8-463e-a282-4d2be36cfa3f/dqc_reference/reference_markers_gtdb.fasta -out GCF_019458805.1_ASM1945880v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:46,166] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:46,169] [INFO] Selected 22 target genomes.
[2024-01-24 10:49:46,169] [INFO] Target genome list was writen to GCF_019458805.1_ASM1945880v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:46,183] [INFO] Task started: fastANI
[2024-01-24 10:49:46,183] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb82a261-188c-41b0-90d2-7d9ad4f91a7e/GCF_019458805.1_ASM1945880v1_genomic.fna.gz --refList GCF_019458805.1_ASM1945880v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019458805.1_ASM1945880v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:41,582] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:41,598] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:50:41,599] [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	85.2162	1706	2504	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552635.1	s__Spirillospora hibisca	83.1758	1654	2504	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	82.2991	1614	2504	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	82.2464	1617	2504	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	82.1639	1684	2504	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.82	95.82	0.89	0.89	2	-
GCF_000374305.1	s__Spirillospora flavalba	82.1613	1370	2504	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009793335.1	s__Spirillospora sp009793335	82.1608	1640	2504	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	82.0477	1600	2504	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	82.0171	1685	2504	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.12	95.12	0.83	0.83	2	-
GCF_900188445.1	s__Spirillospora meyerae	82.0074	1525	2504	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381885.1	s__Spirillospora atramentaria	81.8871	1386	2504	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	81.8465	1391	2504	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013372625.1	s__Spirillospora sp013372625	81.8412	1286	2504	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	81.7772	1530	2504	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	81.7735	1608	2504	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	81.7681	1355	2504	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009831215.1	s__Spirillospora rayongensis	81.676	1336	2504	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	81.6683	1533	2504	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	81.6584	1542	2504	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.34	99.27	0.95	0.95	3	-
GCF_002911665.1	s__Spirillospora rubteroloni	81.6473	1304	2504	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	81.279	1512	2504	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.13	99.13	0.92	0.92	2	-
GCA_003001795.1	s__Actinomadura_B viridilutea	81.2769	1311	2504	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_B	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:50:41,600] [INFO] GTDB search result was written to GCF_019458805.1_ASM1945880v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:41,601] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:41,623] [INFO] DFAST_QC result json was written to GCF_019458805.1_ASM1945880v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:41,623] [INFO] DFAST_QC completed!
[2024-01-24 10:50:41,623] [INFO] Total running time: 0h3m35s