[2024-01-24 14:06:05,662] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:05,664] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:05,664] [INFO] DQC Reference Directory: /var/lib/cwl/stg778be97c-2cfc-41ec-b2c7-1d1ad5f52d3b/dqc_reference
[2024-01-24 14:06:07,035] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:07,036] [INFO] Task started: Prodigal
[2024-01-24 14:06:07,036] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1745f88-c9bd-40ec-9d86-52f641a009b2/GCF_010993745.1_ASM1099374v1_genomic.fna.gz | prodigal -d GCF_010993745.1_ASM1099374v1_genomic.fna/cds.fna -a GCF_010993745.1_ASM1099374v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:34,186] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:34,187] [INFO] Task started: HMMsearch
[2024-01-24 14:06:34,187] [INFO] Running command: hmmsearch --tblout GCF_010993745.1_ASM1099374v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg778be97c-2cfc-41ec-b2c7-1d1ad5f52d3b/dqc_reference/reference_markers.hmm GCF_010993745.1_ASM1099374v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:34,610] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:34,611] [INFO] Found 6/6 markers.
[2024-01-24 14:06:34,681] [INFO] Query marker FASTA was written to GCF_010993745.1_ASM1099374v1_genomic.fna/markers.fasta
[2024-01-24 14:06:34,681] [INFO] Task started: Blastn
[2024-01-24 14:06:34,681] [INFO] Running command: blastn -query GCF_010993745.1_ASM1099374v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg778be97c-2cfc-41ec-b2c7-1d1ad5f52d3b/dqc_reference/reference_markers.fasta -out GCF_010993745.1_ASM1099374v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:35,951] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:35,963] [INFO] Selected 29 target genomes.
[2024-01-24 14:06:35,964] [INFO] Target genome list was writen to GCF_010993745.1_ASM1099374v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:35,984] [INFO] Task started: fastANI
[2024-01-24 14:06:35,984] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1745f88-c9bd-40ec-9d86-52f641a009b2/GCF_010993745.1_ASM1099374v1_genomic.fna.gz --refList GCF_010993745.1_ASM1099374v1_genomic.fna/target_genomes.txt --output GCF_010993745.1_ASM1099374v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:22,465] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:22,466] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg778be97c-2cfc-41ec-b2c7-1d1ad5f52d3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:22,466] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg778be97c-2cfc-41ec-b2c7-1d1ad5f52d3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:22,488] [INFO] Found 29 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:07:22,488] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:22,488] [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
Fodinicola acaciae	strain=GKU 173	GCA_010993745.1	2681555	2681555	type	True	100.0	2951	2952	95	conclusive
Amycolatopsis methanolica	strain=239	GCA_000739085.1	1814	1814	type	True	76.7205	589	2952	95	below_threshold
Amycolatopsis granulosa	strain=DSM 45669	GCA_011758745.1	185684	185684	type	True	76.7036	520	2952	95	below_threshold
Blastococcus litoris	strain=GP-S2-8	GCA_003075095.1	2171622	2171622	type	True	76.6851	442	2952	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	76.6159	549	2952	95	below_threshold
Geodermatophilus siccatus	strain=DSM 45419	GCA_900103785.1	1137991	1137991	type	True	76.6012	507	2952	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	76.5987	609	2952	95	below_threshold
Salinispora fenicalii	strain=CNT-569	GCA_000514815.1	1137263	1137263	type	True	76.5929	320	2952	95	below_threshold
Kutzneria kofuensis	strain=DSM 43851	GCA_014203355.1	103725	103725	type	True	76.5843	764	2952	95	below_threshold
Amycolatopsis thermoflava	strain=N1165	GCA_000473265.1	84480	84480	type	True	76.5691	653	2952	95	below_threshold
Actinokineospora cianjurensis	strain=DSM 45657	GCA_003663795.1	585224	585224	type	True	76.5598	482	2952	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	76.5577	690	2952	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	76.5449	598	2952	95	below_threshold
Blastococcus aggregatus	strain=DSM 4725	GCA_900221005.1	38502	38502	type	True	76.5402	440	2952	95	below_threshold
Cryptosporangium arvum	strain=DSM 44712	GCA_000585375.1	80871	80871	type	True	76.5322	697	2952	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	76.5137	609	2952	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	76.5115	715	2952	95	below_threshold
Cryptosporangium aurantiacum	strain=DSM 46144	GCA_900143005.1	134849	134849	type	True	76.4968	667	2952	95	below_threshold
Saccharothrix ecbatanensis	strain=DSM 45486	GCA_014205015.1	1105145	1105145	type	True	76.4643	553	2952	95	below_threshold
Cryptosporangium phraense	strain=A-T 5661	GCA_006912135.1	2593070	2593070	type	True	76.4494	667	2952	95	below_threshold
Kutzneria buriramensis	strain=DSM 45791	GCA_003387475.1	1045776	1045776	type	True	76.4135	857	2952	95	below_threshold
Actinokineospora fastidiosa	strain=JCM 3276	GCA_014648415.1	1816	1816	type	True	76.4025	560	2952	95	below_threshold
Klenkia taihuensis	strain=DSM 45962	GCA_900112525.1	1225127	1225127	type	True	76.3848	502	2952	95	below_threshold
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	76.3277	675	2952	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	76.3274	507	2952	95	below_threshold
Actinomadura physcomitrii	strain=LD22	GCA_008923205.2	2650748	2650748	type	True	76.2193	664	2952	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	76.1237	701	2952	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	76.1011	712	2952	95	below_threshold
Actinomycetospora corticicola	strain=DSM 45772	GCA_013409505.1	663602	663602	type	True	75.9687	452	2952	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:22,490] [INFO] DFAST Taxonomy check result was written to GCF_010993745.1_ASM1099374v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:22,491] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:22,491] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:22,491] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg778be97c-2cfc-41ec-b2c7-1d1ad5f52d3b/dqc_reference/checkm_data
[2024-01-24 14:07:22,492] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:22,572] [INFO] Task started: CheckM
[2024-01-24 14:07:22,573] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010993745.1_ASM1099374v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010993745.1_ASM1099374v1_genomic.fna/checkm_input GCF_010993745.1_ASM1099374v1_genomic.fna/checkm_result
[2024-01-24 14:08:45,552] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:45,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.94%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:45,582] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:45,583] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:45,583] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010993745.1_ASM1099374v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:45,584] [INFO] Task started: Blastn
[2024-01-24 14:08:45,584] [INFO] Running command: blastn -query GCF_010993745.1_ASM1099374v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg778be97c-2cfc-41ec-b2c7-1d1ad5f52d3b/dqc_reference/reference_markers_gtdb.fasta -out GCF_010993745.1_ASM1099374v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:47,492] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:47,496] [INFO] Selected 26 target genomes.
[2024-01-24 14:08:47,497] [INFO] Target genome list was writen to GCF_010993745.1_ASM1099374v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:47,518] [INFO] Task started: fastANI
[2024-01-24 14:08:47,518] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1745f88-c9bd-40ec-9d86-52f641a009b2/GCF_010993745.1_ASM1099374v1_genomic.fna.gz --refList GCF_010993745.1_ASM1099374v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010993745.1_ASM1099374v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:09:29,226] [INFO] Task succeeded: fastANI
[2024-01-24 14:09:29,250] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:09:29,251] [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_010993745.1	s__Fodinicola acaciae	100.0	2951	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__HKI-0501;g__Fodinicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_010993775.1	s__Fodinicola feengrottensis	80.3826	1416	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__HKI-0501;g__Fodinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075095.1	s__Blastococcus litoris	76.7046	438	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805565.1	s__CADCTP01 sp902805565	76.6999	490	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__CADCTP01;g__CADCTP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203355.1	s__Kutzneria kofuensis	76.6165	759	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012328925.1	s__Amycolatopsis acididurans	76.6139	512	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907655.1	s__Actinosynnema algeriensis	76.6027	588	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385215.1	s__Amycolatopsis thermalba	76.5795	614	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.72	99.30	0.96	0.93	4	-
GCF_014653945.1	s__Amycolatopsis deserti	76.574	632	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900221005.1	s__Blastococcus aggregatus	76.5607	437	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000585375.1	s__Cryptosporangium arvum	76.5499	702	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Cryptosporangiaceae;g__Cryptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016865425.1	s__Actinocatenispora thailandica	76.5179	746	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinocatenispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634935.1	s__Actinosynnema australiense	76.5043	612	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205015.1	s__Actinosynnema ecbatanense	76.5041	553	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143005.1	s__Cryptosporangium aurantiacum	76.5009	663	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Cryptosporangiaceae;g__Cryptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000231075.2	s__Amycolatopsis sp000231075	76.4851	669	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.4849	N/A	N/A	N/A	N/A	1	-
GCF_016464705.1	s__Saccharomonospora sp016464705	76.4846	495	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006912135.1	s__Cryptosporangium phraense	76.4437	668	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Cryptosporangiaceae;g__Cryptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648415.1	s__Actinokineospora fastidiosa	76.4033	560	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000306785.1	s__Modestobacter marinus_A	76.3966	516	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387475.1	s__Kutzneria buriramensis	76.3954	866	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112525.1	s__Klenkia taihuensis	76.3844	502	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Klenkia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014208095.1	s__Pseudonocardia eucalypti	76.3169	674	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002904335.1	s__Amycolatopsis sp002904335	76.2573	725	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280085.1	s__Actinosynnema sp001280085	76.2351	655	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953865.1	s__Amycolatopsis coloradensis	76.2264	486	2952	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:09:29,252] [INFO] GTDB search result was written to GCF_010993745.1_ASM1099374v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:09:29,253] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:09:29,258] [INFO] DFAST_QC result json was written to GCF_010993745.1_ASM1099374v1_genomic.fna/dqc_result.json
[2024-01-24 14:09:29,258] [INFO] DFAST_QC completed!
[2024-01-24 14:09:29,258] [INFO] Total running time: 0h3m24s