[2024-01-24 13:42:57,517] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:42:57,519] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:42:57,519] [INFO] DQC Reference Directory: /var/lib/cwl/stgab2d1cf3-b488-4e24-ba8b-cdf307378004/dqc_reference
[2024-01-24 13:42:58,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:42:58,786] [INFO] Task started: Prodigal
[2024-01-24 13:42:58,787] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d4aee6e-2795-4c19-9b7a-87b85b856005/GCF_003751225.1_ASM375122v1_genomic.fna.gz | prodigal -d GCF_003751225.1_ASM375122v1_genomic.fna/cds.fna -a GCF_003751225.1_ASM375122v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:24,826] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:24,827] [INFO] Task started: HMMsearch
[2024-01-24 13:43:24,827] [INFO] Running command: hmmsearch --tblout GCF_003751225.1_ASM375122v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab2d1cf3-b488-4e24-ba8b-cdf307378004/dqc_reference/reference_markers.hmm GCF_003751225.1_ASM375122v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:25,202] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:25,204] [INFO] Found 6/6 markers.
[2024-01-24 13:43:25,280] [INFO] Query marker FASTA was written to GCF_003751225.1_ASM375122v1_genomic.fna/markers.fasta
[2024-01-24 13:43:25,281] [INFO] Task started: Blastn
[2024-01-24 13:43:25,281] [INFO] Running command: blastn -query GCF_003751225.1_ASM375122v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab2d1cf3-b488-4e24-ba8b-cdf307378004/dqc_reference/reference_markers.fasta -out GCF_003751225.1_ASM375122v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:26,620] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:26,624] [INFO] Selected 22 target genomes.
[2024-01-24 13:43:26,625] [INFO] Target genome list was writen to GCF_003751225.1_ASM375122v1_genomic.fna/target_genomes.txt
[2024-01-24 13:43:26,658] [INFO] Task started: fastANI
[2024-01-24 13:43:26,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d4aee6e-2795-4c19-9b7a-87b85b856005/GCF_003751225.1_ASM375122v1_genomic.fna.gz --refList GCF_003751225.1_ASM375122v1_genomic.fna/target_genomes.txt --output GCF_003751225.1_ASM375122v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:44:08,470] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:08,470] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab2d1cf3-b488-4e24-ba8b-cdf307378004/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:44:08,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab2d1cf3-b488-4e24-ba8b-cdf307378004/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:44:08,491] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:44:08,491] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:44:08,491] [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
Actinocorallia herbida	strain=DSM 44254	GCA_003751225.1	58109	58109	type	True	100.0	3262	3266	95	conclusive
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	78.552	1280	3266	95	below_threshold
Actinomadura logoneensis	strain=NEAU-G17	GCA_003428695.1	2293572	2293572	type	True	78.4219	948	3266	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	78.3849	1134	3266	95	below_threshold
Actinomadura rubrobrunea	strain=NBRC 15275	GCA_001552235.1	115335	115335	type	True	78.3081	943	3266	95	below_threshold
Actinomadura coerulea	strain=DSM 43675	GCA_014208105.1	46159	46159	type	True	78.2538	1145	3266	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	78.2375	1340	3266	95	below_threshold
Actinomadura coerulea	strain=JCM 3320	GCA_014648535.1	46159	46159	type	True	78.2323	1106	3266	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	78.2255	1199	3266	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	78.2227	1181	3266	95	below_threshold
Actinomadura harenae	strain=NEAU-Ht49	GCA_003696215.1	2483351	2483351	type	True	78.2207	1080	3266	95	below_threshold
Thermomonospora umbrina	strain=DSM 43927	GCA_003386555.1	111806	111806	type	True	78.2157	954	3266	95	below_threshold
Actinomadura kijaniata	strain=NBRC 14229	GCA_001552175.1	46161	46161	type	True	78.1932	1262	3266	95	below_threshold
Actinomadura oligospora	strain=ATCC 43269	GCA_000518265.1	111804	111804	type	True	78.1921	1141	3266	95	below_threshold
Actinomadura namibiensis	strain=DSM 44197	GCA_014138665.1	182080	182080	type	True	78.1847	1252	3266	95	below_threshold
Actinomadura algeriensis	strain=DSM 46744	GCA_014873935.1	1679523	1679523	type	True	78.1228	1216	3266	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	78.0442	1343	3266	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	77.9151	916	3266	95	below_threshold
Actinomadura roseirufa		GCA_900659635.1	2094049	2094049	type	True	77.8984	1038	3266	95	below_threshold
Actinoallomurus spadix	strain=KCTC 9252	GCA_024055725.1	79912	79912	type	True	77.5589	934	3266	95	below_threshold
Actinoallomurus purpureus	strain=KCTC 19541	GCA_024055795.1	478114	478114	type	True	77.4574	919	3266	95	below_threshold
Actinoallomurus bryophytorum	strain=DSM 102200	GCA_006716425.1	1490222	1490222	type	True	77.3343	900	3266	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:44:08,493] [INFO] DFAST Taxonomy check result was written to GCF_003751225.1_ASM375122v1_genomic.fna/tc_result.tsv
[2024-01-24 13:44:08,493] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:44:08,493] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:44:08,494] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab2d1cf3-b488-4e24-ba8b-cdf307378004/dqc_reference/checkm_data
[2024-01-24 13:44:08,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:44:08,585] [INFO] Task started: CheckM
[2024-01-24 13:44:08,586] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003751225.1_ASM375122v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003751225.1_ASM375122v1_genomic.fna/checkm_input GCF_003751225.1_ASM375122v1_genomic.fna/checkm_result
[2024-01-24 13:46:19,842] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:19,843] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:19,872] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:19,873] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:19,873] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003751225.1_ASM375122v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:19,873] [INFO] Task started: Blastn
[2024-01-24 13:46:19,873] [INFO] Running command: blastn -query GCF_003751225.1_ASM375122v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab2d1cf3-b488-4e24-ba8b-cdf307378004/dqc_reference/reference_markers_gtdb.fasta -out GCF_003751225.1_ASM375122v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:22,132] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:22,135] [INFO] Selected 19 target genomes.
[2024-01-24 13:46:22,136] [INFO] Target genome list was writen to GCF_003751225.1_ASM375122v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:22,154] [INFO] Task started: fastANI
[2024-01-24 13:46:22,154] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d4aee6e-2795-4c19-9b7a-87b85b856005/GCF_003751225.1_ASM375122v1_genomic.fna.gz --refList GCF_003751225.1_ASM375122v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003751225.1_ASM375122v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:02,569] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:02,584] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:02,585] [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_003751225.1	s__Actinocorallia herbida	100.0	3264	3266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinocorallia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002995495.1	s__Actinocorallia populi	81.532	1531	3266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinocorallia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552635.1	s__Spirillospora hibisca	78.4174	1189	3266	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	78.4066	1257	3266	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	78.371	1136	3266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014208105.1	s__Spirillospora coerulea	78.2849	1144	3266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003001795.1	s__Actinomadura_B viridilutea	78.2606	979	3266	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_003386555.1	s__Thermomonospora umbrina	78.2529	946	3266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017573545.1	s__Spirillospora nitritigenes	78.2415	1342	3266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.12	95.12	0.83	0.83	2	-
GCF_013211575.1	s__Spirillospora verrucosospora	78.2203	1340	3266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.82	95.82	0.89	0.89	2	-
GCF_003696215.1	s__Spirillospora harenae	78.2118	1081	3266	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	78.2037	1257	3266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	97.32	97.32	0.88	0.88	2	-
GCF_900659615.1	s__Spirillospora fibrosa	78.1938	1277	3266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518265.1	s__Spirillospora oligospora	78.1807	1149	3266	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	78.1284	1325	3266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873935.1	s__Spirillospora algeriensis	78.1257	1210	3266	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	77.9006	1040	3266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014323705.1	s__Actinomadura_C alba	77.613	825	3266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386285.1	s__Nocardiopsis sp003386285	76.8394	593	3266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:02,586] [INFO] GTDB search result was written to GCF_003751225.1_ASM375122v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:02,587] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:02,591] [INFO] DFAST_QC result json was written to GCF_003751225.1_ASM375122v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:02,591] [INFO] DFAST_QC completed!
[2024-01-24 13:47:02,591] [INFO] Total running time: 0h4m5s