[2024-01-24 12:22:27,654] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:27,657] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:27,657] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b7c6a6d-cf0d-4f2f-9e00-a3586faa6fde/dqc_reference
[2024-01-24 12:22:29,112] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:29,115] [INFO] Task started: Prodigal
[2024-01-24 12:22:29,117] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c22c8e6-b4ac-4548-9667-d7db2ac52f53/GCF_000430705.1_ASM43070v1_genomic.fna.gz | prodigal -d GCF_000430705.1_ASM43070v1_genomic.fna/cds.fna -a GCF_000430705.1_ASM43070v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:44,282] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:44,283] [INFO] Task started: HMMsearch
[2024-01-24 12:22:44,283] [INFO] Running command: hmmsearch --tblout GCF_000430705.1_ASM43070v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b7c6a6d-cf0d-4f2f-9e00-a3586faa6fde/dqc_reference/reference_markers.hmm GCF_000430705.1_ASM43070v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:44,609] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:44,611] [INFO] Found 6/6 markers.
[2024-01-24 12:22:44,654] [INFO] Query marker FASTA was written to GCF_000430705.1_ASM43070v1_genomic.fna/markers.fasta
[2024-01-24 12:22:44,655] [INFO] Task started: Blastn
[2024-01-24 12:22:44,655] [INFO] Running command: blastn -query GCF_000430705.1_ASM43070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b7c6a6d-cf0d-4f2f-9e00-a3586faa6fde/dqc_reference/reference_markers.fasta -out GCF_000430705.1_ASM43070v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:45,532] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:45,537] [INFO] Selected 29 target genomes.
[2024-01-24 12:22:45,537] [INFO] Target genome list was writen to GCF_000430705.1_ASM43070v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:45,544] [INFO] Task started: fastANI
[2024-01-24 12:22:45,544] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c22c8e6-b4ac-4548-9667-d7db2ac52f53/GCF_000430705.1_ASM43070v1_genomic.fna.gz --refList GCF_000430705.1_ASM43070v1_genomic.fna/target_genomes.txt --output GCF_000430705.1_ASM43070v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:09,213] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:09,213] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b7c6a6d-cf0d-4f2f-9e00-a3586faa6fde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:09,214] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b7c6a6d-cf0d-4f2f-9e00-a3586faa6fde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:09,236] [INFO] Found 29 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:09,237] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:09,237] [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
Arthrobacter castelli	strain=DSM 16402	GCA_000430705.1	271431	271431	type	True	100.0	1501	1505	95	conclusive
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	77.9732	311	1505	95	below_threshold
Arthrobacter yangruifuii	strain=785	GCA_009192775.1	2606616	2606616	type	True	77.7174	231	1505	95	below_threshold
Arthrobacter gallicola	strain=Sa2CUA1	GCA_014836775.1	2762225	2762225	type	True	77.6921	248	1505	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	77.658	203	1505	95	below_threshold
Arthrobacter gandavensis	strain=JCM 13316	GCA_009192735.1	169960	169960	type	True	77.5749	226	1505	95	below_threshold
Arthrobacter citreus	strain=DSM 20133	GCA_009192745.1	1670	1670	type	True	77.5116	223	1505	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	77.4763	262	1505	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	77.443	265	1505	95	below_threshold
Arthrobacter luteolus	strain=DSM 13067	GCA_008973725.1	98672	98672	type	True	77.4384	239	1505	95	below_threshold
Pseudarthrobacter sulfonivorans	strain=ALL	GCA_014712225.1	121292	121292	type	True	77.3982	212	1505	95	below_threshold
Pseudarthrobacter enclensis	strain=NIO-1008	GCA_001457025.1	993070	993070	type	True	77.363	251	1505	95	below_threshold
Arthrobacter luteolus	strain=NBRC 107841	GCA_001552075.1	98672	98672	type	True	77.3605	248	1505	95	below_threshold
Pseudarthrobacter enclensis	strain=NIO-1008	GCA_900094675.1	993070	993070	type	True	77.3408	253	1505	95	below_threshold
Arthrobacter cupressi	strain=DSM 24664	GCA_013409905.1	1045773	1045773	type	True	77.2712	242	1505	95	below_threshold
Arthrobacter crusticola	strain=SLN-3	GCA_004357995.1	2547960	2547960	type	True	77.2461	237	1505	95	below_threshold
Pseudarthrobacter scleromae	strain=CGMCC 1.3601	GCA_014644515.1	158897	158897	type	True	77.2	230	1505	95	below_threshold
Pseudarthrobacter chlorophenolicus	strain=A6	GCA_000022025.1	85085	85085	type	True	77.1849	248	1505	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	77.1775	214	1505	95	below_threshold
Arthrobacter cupressi	strain=CGMCC 1.10783	GCA_900099975.1	1045773	1045773	type	True	77.1696	247	1505	95	below_threshold
Pseudarthrobacter chlorophenolicus	strain=A6	GCA_900104315.1	85085	85085	type	True	77.152	252	1505	95	below_threshold
Arthrobacter tumbae	strain=DSM 16406	GCA_016907495.1	163874	163874	type	True	77.0709	188	1505	95	below_threshold
Sinomonas atrocyanea	strain=CGMCC 1.1891	GCA_014644475.1	37927	37927	type	True	76.8647	215	1505	95	below_threshold
Zhihengliuella salsuginis	strain=KCTC 19466	GCA_014651715.1	578222	578222	type	True	76.7623	207	1505	95	below_threshold
Streptomyces fumanus	strain=JCM 4477	GCA_014655295.1	67302	67302	type	True	75.7967	163	1505	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	75.7905	136	1505	95	below_threshold
Streptomyces yokosukanensis	strain=DSM 40224	GCA_001514035.1	67386	67386	type	True	75.6417	178	1505	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	75.5875	140	1505	95	below_threshold
Actinomadura harenae	strain=NEAU-Ht49	GCA_003696215.1	2483351	2483351	type	True	75.4813	140	1505	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:09,239] [INFO] DFAST Taxonomy check result was written to GCF_000430705.1_ASM43070v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:09,241] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:09,241] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:09,241] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b7c6a6d-cf0d-4f2f-9e00-a3586faa6fde/dqc_reference/checkm_data
[2024-01-24 12:23:09,242] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:09,288] [INFO] Task started: CheckM
[2024-01-24 12:23:09,288] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000430705.1_ASM43070v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000430705.1_ASM43070v1_genomic.fna/checkm_input GCF_000430705.1_ASM43070v1_genomic.fna/checkm_result
[2024-01-24 12:23:53,100] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:53,102] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:53,123] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:53,124] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:53,124] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000430705.1_ASM43070v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:53,125] [INFO] Task started: Blastn
[2024-01-24 12:23:53,125] [INFO] Running command: blastn -query GCF_000430705.1_ASM43070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b7c6a6d-cf0d-4f2f-9e00-a3586faa6fde/dqc_reference/reference_markers_gtdb.fasta -out GCF_000430705.1_ASM43070v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:54,403] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:54,407] [INFO] Selected 23 target genomes.
[2024-01-24 12:23:54,408] [INFO] Target genome list was writen to GCF_000430705.1_ASM43070v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:54,455] [INFO] Task started: fastANI
[2024-01-24 12:23:54,455] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c22c8e6-b4ac-4548-9667-d7db2ac52f53/GCF_000430705.1_ASM43070v1_genomic.fna.gz --refList GCF_000430705.1_ASM43070v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000430705.1_ASM43070v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:11,254] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:11,276] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:11,276] [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_000430705.1	s__Arthrobacter_C castelli	100.0	1501	1505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000520495.1	s__Arthrobacter_C sp000520495	79.0233	511	1505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395835.1	s__Arthrobacter_F mobilis	77.9814	309	1505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000328305.2	s__Arthrobacter_F crystallopoietes_A	77.9145	280	1505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428365.1	s__Arthrobacter_I sp001428365	77.8264	266	1505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004000035.1	s__Arthrobacter_F sulfonylureivorans	77.7588	284	1505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007858535.1	s__Arthrobacter_I sp007858535	77.7175	267	1505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531425.1	s__DKR-5 sp018531425	77.6941	285	1505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__DKR-5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013359735.1	s__Arthrobacter_I sp013359735	77.6233	270	1505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005047635.1	s__Arthrobacter_F sp005047635	77.5869	291	1505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016405885.1	s__Arthrobacter_D sp016405885	77.4233	228	1505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001457025.1	s__Pseudarthrobacter enclensis	77.3739	250	1505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	98.10	96.20	0.95	0.91	3	-
GCA_003602285.1	s__Arthrobacter_D sp003602285	77.3611	247	1505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	95.90	95.90	0.84	0.84	2	-
GCF_003946885.1	s__Specibacter cremeus	77.2635	258	1505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004357995.1	s__Arthrobacter_D crusticola	77.2508	235	1505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679325.1	s__Arthrobacter_I sp007679325	77.2299	244	1505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374905.1	s__Pseudarthrobacter sp000374905	77.189	231	1505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	98.45	96.91	0.92	0.90	5	-
GCF_008580665.1	s__Zafaria cholistanensis	77.1819	217	1505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zafaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099975.1	s__Arthrobacter_G cupressi	77.1696	247	1505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018613875.1	s__Arthrobacter sp018613875	77.1387	203	1505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003115775.1	s__Cellulomonas sp003115775	76.0712	99	1505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364275.1	s__Spirillospora sp013364275	75.676	150	1505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188445.1	s__Spirillospora meyerae	75.5789	141	1505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:11,278] [INFO] GTDB search result was written to GCF_000430705.1_ASM43070v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:11,279] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:11,284] [INFO] DFAST_QC result json was written to GCF_000430705.1_ASM43070v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:11,285] [INFO] DFAST_QC completed!
[2024-01-24 12:24:11,285] [INFO] Total running time: 0h1m44s