[2024-01-24 14:22:29,809] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:29,811] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:29,811] [INFO] DQC Reference Directory: /var/lib/cwl/stg944eae1e-ffff-4494-a4d8-b91314212c60/dqc_reference
[2024-01-24 14:22:31,161] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:31,161] [INFO] Task started: Prodigal
[2024-01-24 14:22:31,162] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d52caea-6db7-47cf-b06e-142a2a125818/GCF_003289645.1_ASM328964v1_genomic.fna.gz | prodigal -d GCF_003289645.1_ASM328964v1_genomic.fna/cds.fna -a GCF_003289645.1_ASM328964v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:53,729] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:53,729] [INFO] Task started: HMMsearch
[2024-01-24 14:22:53,730] [INFO] Running command: hmmsearch --tblout GCF_003289645.1_ASM328964v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg944eae1e-ffff-4494-a4d8-b91314212c60/dqc_reference/reference_markers.hmm GCF_003289645.1_ASM328964v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:54,037] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:54,039] [INFO] Found 6/6 markers.
[2024-01-24 14:22:54,103] [INFO] Query marker FASTA was written to GCF_003289645.1_ASM328964v1_genomic.fna/markers.fasta
[2024-01-24 14:22:54,103] [INFO] Task started: Blastn
[2024-01-24 14:22:54,104] [INFO] Running command: blastn -query GCF_003289645.1_ASM328964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg944eae1e-ffff-4494-a4d8-b91314212c60/dqc_reference/reference_markers.fasta -out GCF_003289645.1_ASM328964v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:55,446] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:55,449] [INFO] Selected 24 target genomes.
[2024-01-24 14:22:55,450] [INFO] Target genome list was writen to GCF_003289645.1_ASM328964v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:55,454] [INFO] Task started: fastANI
[2024-01-24 14:22:55,454] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d52caea-6db7-47cf-b06e-142a2a125818/GCF_003289645.1_ASM328964v1_genomic.fna.gz --refList GCF_003289645.1_ASM328964v1_genomic.fna/target_genomes.txt --output GCF_003289645.1_ASM328964v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:37,212] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:37,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg944eae1e-ffff-4494-a4d8-b91314212c60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:37,212] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg944eae1e-ffff-4494-a4d8-b91314212c60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:37,229] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:23:37,230] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:23:37,230] [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
Thermomonospora echinospora	strain=DSM 43163	GCA_900108175.1	1992	1992	type	True	81.7131	1405	2482	95	below_threshold
Thermomonospora umbrina	strain=DSM 43927	GCA_003386555.1	111806	111806	type	True	80.6665	1104	2482	95	below_threshold
Actinomadura viridis	strain=DSM 43175	GCA_015751755.1	58110	58110	type	True	80.6228	1289	2482	95	below_threshold
Thermomonospora catenispora	strain=3-22-3	GCA_006363815.1	2493090	2493090	type	True	80.591	1051	2482	95	below_threshold
Actinomadura coerulea	strain=DSM 43675	GCA_014208105.1	46159	46159	type	True	80.0993	1187	2482	95	below_threshold
Actinomadura citrea	strain=DSM 43461	GCA_013409045.1	46158	46158	type	True	80.0432	1202	2482	95	below_threshold
Actinomadura bangladeshensis	strain=DSM 45347	GCA_004348335.1	453573	453573	type	True	80.01	1107	2482	95	below_threshold
Actinomadura coerulea	strain=JCM 3320	GCA_014648535.1	46159	46159	type	True	80.0091	1188	2482	95	below_threshold
Actinomadura physcomitrii	strain=LD22	GCA_008923205.2	2650748	2650748	type	True	79.995	1257	2482	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	79.9845	1221	2482	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	79.8735	1112	2482	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	79.8332	1233	2482	95	below_threshold
Actinomadura cremea	strain=JCM 3308	GCA_014648495.1	1991	1991	type	True	79.8232	1217	2482	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	79.8205	1190	2482	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	79.719	1280	2482	95	below_threshold
Actinomadura roseirufa		GCA_900659635.1	2094049	2094049	type	True	79.7114	1063	2482	95	below_threshold
Actinomadura algeriensis	strain=DSM 46744	GCA_014873935.1	1679523	1679523	type	True	79.692	1212	2482	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	79.6857	1087	2482	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	79.6624	1270	2482	95	below_threshold
Actinomadura decatromicini	strain=CYP1-5	GCA_008121305.1	2604572	2604572	type	True	79.374	1144	2482	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	79.2289	976	2482	95	below_threshold
Actinoallomurus purpureus	strain=KCTC 19541	GCA_024055795.1	478114	478114	type	True	78.8021	896	2482	95	below_threshold
Actinoallomurus spadix	strain=KCTC 9252	GCA_024055725.1	79912	79912	type	True	78.6523	953	2482	95	below_threshold
Actinoallomurus bryophytorum	strain=DSM 102200	GCA_006716425.1	1490222	1490222	type	True	78.4995	915	2482	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:37,231] [INFO] DFAST Taxonomy check result was written to GCF_003289645.1_ASM328964v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:37,232] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:37,232] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:37,232] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg944eae1e-ffff-4494-a4d8-b91314212c60/dqc_reference/checkm_data
[2024-01-24 14:23:37,233] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:37,297] [INFO] Task started: CheckM
[2024-01-24 14:23:37,297] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003289645.1_ASM328964v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003289645.1_ASM328964v1_genomic.fna/checkm_input GCF_003289645.1_ASM328964v1_genomic.fna/checkm_result
[2024-01-24 14:24:47,599] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:47,600] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:47,618] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:47,618] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:47,618] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003289645.1_ASM328964v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:47,618] [INFO] Task started: Blastn
[2024-01-24 14:24:47,619] [INFO] Running command: blastn -query GCF_003289645.1_ASM328964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg944eae1e-ffff-4494-a4d8-b91314212c60/dqc_reference/reference_markers_gtdb.fasta -out GCF_003289645.1_ASM328964v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:49,624] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:49,628] [INFO] Selected 21 target genomes.
[2024-01-24 14:24:49,628] [INFO] Target genome list was writen to GCF_003289645.1_ASM328964v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:49,671] [INFO] Task started: fastANI
[2024-01-24 14:24:49,671] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d52caea-6db7-47cf-b06e-142a2a125818/GCF_003289645.1_ASM328964v1_genomic.fna.gz --refList GCF_003289645.1_ASM328964v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003289645.1_ASM328964v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:25:28,726] [INFO] Task succeeded: fastANI
[2024-01-24 14:25:28,742] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:25:28,742] [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_003289645.1	s__Actinomadura_D craniellae	100.0	2480	2482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900108175.1	s__Thermomonospora echinospora	81.7428	1400	2482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003589885.1	s__Thermomonospora amylolytica	81.1044	1255	2482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	98.39	98.39	0.92	0.92	2	-
GCF_003386555.1	s__Thermomonospora umbrina	80.631	1110	2482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006363815.1	s__Thermomonospora catenispora	80.6154	1048	2482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015751755.1	s__Spirillospora viridis	80.6146	1291	2482	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	80.4596	1089	2482	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_014208105.1	s__Spirillospora coerulea	80.0841	1190	2482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004348335.1	s__Spirillospora bangladeshensis	80.0576	1097	2482	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	80.017	1251	2482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718255.1	s__Spirillospora albida	79.9887	1006	2482	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	79.9759	1206	2482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008824145.1	s__Spirillospora sp008824145	79.9435	1267	2482	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	79.9037	1107	2482	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	79.829	1249	2482	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	79.7706	1247	2482	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	79.7463	1056	2482	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	79.6862	1210	2482	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	79.657	1271	2482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.12	95.12	0.83	0.83	2	-
GCF_014323705.1	s__Actinomadura_C alba	79.4974	988	2482	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_014323665.1	s__Actinomadura_C sp014323665	79.4014	910	2482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:25:28,744] [INFO] GTDB search result was written to GCF_003289645.1_ASM328964v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:25:28,744] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:25:28,749] [INFO] DFAST_QC result json was written to GCF_003289645.1_ASM328964v1_genomic.fna/dqc_result.json
[2024-01-24 14:25:28,749] [INFO] DFAST_QC completed!
[2024-01-24 14:25:28,749] [INFO] Total running time: 0h2m59s