[2024-01-25 17:37:35,605] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:37:35,609] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:37:35,610] [INFO] DQC Reference Directory: /var/lib/cwl/stg155c6348-e8b1-4580-baca-c68dd7fce013/dqc_reference
[2024-01-25 17:37:36,762] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:37:36,763] [INFO] Task started: Prodigal
[2024-01-25 17:37:36,763] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf76f454-4f22-48e6-81ba-6e9951249294/GCF_016907875.1_ASM1690787v1_genomic.fna.gz | prodigal -d GCF_016907875.1_ASM1690787v1_genomic.fna/cds.fna -a GCF_016907875.1_ASM1690787v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:37:45,304] [INFO] Task succeeded: Prodigal
[2024-01-25 17:37:45,305] [INFO] Task started: HMMsearch
[2024-01-25 17:37:45,305] [INFO] Running command: hmmsearch --tblout GCF_016907875.1_ASM1690787v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg155c6348-e8b1-4580-baca-c68dd7fce013/dqc_reference/reference_markers.hmm GCF_016907875.1_ASM1690787v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:37:45,523] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:37:45,525] [INFO] Found 6/6 markers.
[2024-01-25 17:37:45,552] [INFO] Query marker FASTA was written to GCF_016907875.1_ASM1690787v1_genomic.fna/markers.fasta
[2024-01-25 17:37:45,552] [INFO] Task started: Blastn
[2024-01-25 17:37:45,552] [INFO] Running command: blastn -query GCF_016907875.1_ASM1690787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg155c6348-e8b1-4580-baca-c68dd7fce013/dqc_reference/reference_markers.fasta -out GCF_016907875.1_ASM1690787v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:46,364] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:46,368] [INFO] Selected 25 target genomes.
[2024-01-25 17:37:46,368] [INFO] Target genome list was writen to GCF_016907875.1_ASM1690787v1_genomic.fna/target_genomes.txt
[2024-01-25 17:37:46,374] [INFO] Task started: fastANI
[2024-01-25 17:37:46,374] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf76f454-4f22-48e6-81ba-6e9951249294/GCF_016907875.1_ASM1690787v1_genomic.fna.gz --refList GCF_016907875.1_ASM1690787v1_genomic.fna/target_genomes.txt --output GCF_016907875.1_ASM1690787v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:38:03,074] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:03,075] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg155c6348-e8b1-4580-baca-c68dd7fce013/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:38:03,075] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg155c6348-e8b1-4580-baca-c68dd7fce013/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:38:03,088] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:38:03,089] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:38:03,089] [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 roseus	strain=DSM 14508	GCA_016907875.1	136274	136274	type	True	100.0	1024	1025	95	conclusive
Paenarthrobacter ilicis	strain=DSM 20138	GCA_016907545.1	43665	43665	type	True	77.9992	134	1025	95	below_threshold
Pseudarthrobacter phenanthrenivorans	strain=Sphe3	GCA_000189535.1	361575	361575	type	True	77.8853	124	1025	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	77.8233	152	1025	95	below_threshold
Arthrobacter crystallopoietes	strain=DSM 20117	GCA_002849715.1	37928	37928	type	True	77.6828	155	1025	95	below_threshold
Zhihengliuella halotolerans	strain=DSM 17364	GCA_004217565.1	370736	370736	type	True	77.6614	94	1025	95	below_threshold
Arthrobacter luteolus	strain=DSM 13067	GCA_008973725.1	98672	98672	type	True	77.5435	148	1025	95	below_threshold
Arthrobacter pullicola	strain=Sa2BUA2	GCA_014836875.1	2762224	2762224	type	True	77.4107	140	1025	95	below_threshold
Arthrobacter yangruifuii	strain=785	GCA_009192775.1	2606616	2606616	type	True	77.3559	145	1025	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	77.3424	147	1025	95	below_threshold
Arthrobacter citreus	strain=DSM 20133	GCA_009192745.1	1670	1670	type	True	77.3226	144	1025	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	77.3031	165	1025	95	below_threshold
Paeniglutamicibacter kerguelensis	strain=DSM 15797	GCA_017876535.1	254788	254788	type	True	77.2556	115	1025	95	below_threshold
Pseudarthrobacter sulfonivorans	strain=ALL	GCA_014712225.1	121292	121292	type	True	77.157	142	1025	95	below_threshold
Arthrobacter pascens	strain=DSM 20545	GCA_017052465.1	1677	1677	type	True	77.097	137	1025	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	77.0699	130	1025	95	below_threshold
Arthrobacter gallicola	strain=Sa2CUA1	GCA_014836775.1	2762225	2762225	type	True	77.0389	156	1025	95	below_threshold
Pseudarthrobacter enclensis	strain=NIO-1008	GCA_900094675.1	993070	993070	type	True	76.9846	152	1025	95	below_threshold
Arthrobacter terrae	strain=Z1-20	GCA_015708085.1	2935737	2935737	type	True	76.9798	93	1025	95	below_threshold
Pseudarthrobacter enclensis	strain=NIO-1008	GCA_001457025.1	993070	993070	type	True	76.9517	151	1025	95	below_threshold
Arthrobacter crusticola	strain=SLN-3	GCA_004357995.1	2547960	2547960	type	True	76.9491	128	1025	95	below_threshold
Sinomonas notoginsengisoli	strain=KCTC 29237	GCA_021554725.1	1457311	1457311	type	True	76.5145	94	1025	95	below_threshold
Occultella aeris	strain=CIP 111667	GCA_902703175.1	2761496	2761496	type	True	76.4003	51	1025	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:38:03,090] [INFO] DFAST Taxonomy check result was written to GCF_016907875.1_ASM1690787v1_genomic.fna/tc_result.tsv
[2024-01-25 17:38:03,091] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:38:03,091] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:38:03,091] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg155c6348-e8b1-4580-baca-c68dd7fce013/dqc_reference/checkm_data
[2024-01-25 17:38:03,092] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:38:03,123] [INFO] Task started: CheckM
[2024-01-25 17:38:03,123] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016907875.1_ASM1690787v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016907875.1_ASM1690787v1_genomic.fna/checkm_input GCF_016907875.1_ASM1690787v1_genomic.fna/checkm_result
[2024-01-25 17:38:31,142] [INFO] Task succeeded: CheckM
[2024-01-25 17:38:31,144] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:38:31,162] [INFO] ===== Completeness check finished =====
[2024-01-25 17:38:31,162] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:38:31,163] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016907875.1_ASM1690787v1_genomic.fna/markers.fasta)
[2024-01-25 17:38:31,163] [INFO] Task started: Blastn
[2024-01-25 17:38:31,163] [INFO] Running command: blastn -query GCF_016907875.1_ASM1690787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg155c6348-e8b1-4580-baca-c68dd7fce013/dqc_reference/reference_markers_gtdb.fasta -out GCF_016907875.1_ASM1690787v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:32,376] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:32,379] [INFO] Selected 30 target genomes.
[2024-01-25 17:38:32,379] [INFO] Target genome list was writen to GCF_016907875.1_ASM1690787v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:38:32,395] [INFO] Task started: fastANI
[2024-01-25 17:38:32,396] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf76f454-4f22-48e6-81ba-6e9951249294/GCF_016907875.1_ASM1690787v1_genomic.fna.gz --refList GCF_016907875.1_ASM1690787v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016907875.1_ASM1690787v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:38:50,696] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:50,709] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:38:50,710] [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_016907875.1	s__Arthrobacter_J roseus	100.0	1024	1025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_J	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018622995.1	s__Arthrobacter_B sp018622995	77.8233	152	1025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	99.13	98.27	0.96	0.92	3	-
GCF_005937985.2	s__Arthrobacter_I sp005937985	77.7038	155	1025	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_004217565.1	s__Zhihengliuella halotolerans	77.6591	94	1025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zhihengliuella	95.0	97.65	97.65	0.89	0.89	2	-
GCF_017368795.1	s__PO-11 sp017368795	77.6	135	1025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__PO-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422645.1	s__Arthrobacter_I sp001422645	77.5254	143	1025	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_900110595.1	s__Pseudarthrobacter sp900110595	77.4789	118	1025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	97.13	97.13	0.83	0.83	2	-
GCF_018613795.1	s__Arthrobacter sp018613795	77.4456	151	1025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506095.1	s__Pseudarthrobacter sp902506095	77.4253	129	1025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876535.1	s__Paeniglutamicibacter kerguelensis	77.4069	112	1025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836875.1	s__Arthrobacter_B sp014836875	77.3891	141	1025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019038615.1	s__Paenarthrobacter sp019038615	77.3855	128	1025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009192775.1	s__Arthrobacter_B yangruifuii	77.3559	145	1025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	97.52	97.52	0.93	0.93	2	-
GCF_013359735.1	s__Arthrobacter_I sp013359735	77.255	149	1025	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_003369445.1	s__Arthrobacter_G silvisoli	77.1476	132	1025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000876655.1	s__Arthrobacter_I sp000876655	77.131	141	1025	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_900016675.1	s__Arthrobacter_B saudimassiliensis	77.1127	165	1025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017052465.1	s__Arthrobacter pascens	77.0957	137	1025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395835.1	s__Arthrobacter_F mobilis	77.0745	128	1025	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_014836775.1	s__Arthrobacter_B sp014836775	77.0582	154	1025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613695.1	s__Paenarthrobacter sp018613695	77.0341	127	1025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016892645.1	s__Arthrobacter_H sp016892645	77.016	128	1025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634095.1	s__Arthrobacter_I oryzae	76.9928	151	1025	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_004357995.1	s__Arthrobacter_D crusticola	76.9511	127	1025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009728235.1	s__Arthrobacter_D sp009728235	76.8697	137	1025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:38:50,711] [INFO] GTDB search result was written to GCF_016907875.1_ASM1690787v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:38:50,712] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:38:50,716] [INFO] DFAST_QC result json was written to GCF_016907875.1_ASM1690787v1_genomic.fna/dqc_result.json
[2024-01-25 17:38:50,716] [INFO] DFAST_QC completed!
[2024-01-25 17:38:50,716] [INFO] Total running time: 0h1m15s