[2024-01-24 12:53:36,252] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:36,254] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:36,254] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a249b9f-b621-420d-b658-07a4b592d55e/dqc_reference
[2024-01-24 12:53:37,561] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:37,561] [INFO] Task started: Prodigal
[2024-01-24 12:53:37,562] [INFO] Running command: gunzip -c /var/lib/cwl/stg736d327a-fe6a-49e0-9b73-c1ef2379ae1e/GCF_006538985.1_ASM653898v1_genomic.fna.gz | prodigal -d GCF_006538985.1_ASM653898v1_genomic.fna/cds.fna -a GCF_006538985.1_ASM653898v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:51,563] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:51,563] [INFO] Task started: HMMsearch
[2024-01-24 12:53:51,564] [INFO] Running command: hmmsearch --tblout GCF_006538985.1_ASM653898v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a249b9f-b621-420d-b658-07a4b592d55e/dqc_reference/reference_markers.hmm GCF_006538985.1_ASM653898v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:51,836] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:51,838] [INFO] Found 6/6 markers.
[2024-01-24 12:53:51,880] [INFO] Query marker FASTA was written to GCF_006538985.1_ASM653898v1_genomic.fna/markers.fasta
[2024-01-24 12:53:51,881] [INFO] Task started: Blastn
[2024-01-24 12:53:51,881] [INFO] Running command: blastn -query GCF_006538985.1_ASM653898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a249b9f-b621-420d-b658-07a4b592d55e/dqc_reference/reference_markers.fasta -out GCF_006538985.1_ASM653898v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:52,788] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:52,791] [INFO] Selected 11 target genomes.
[2024-01-24 12:53:52,792] [INFO] Target genome list was writen to GCF_006538985.1_ASM653898v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:52,800] [INFO] Task started: fastANI
[2024-01-24 12:53:52,800] [INFO] Running command: fastANI --query /var/lib/cwl/stg736d327a-fe6a-49e0-9b73-c1ef2379ae1e/GCF_006538985.1_ASM653898v1_genomic.fna.gz --refList GCF_006538985.1_ASM653898v1_genomic.fna/target_genomes.txt --output GCF_006538985.1_ASM653898v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:01,899] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:01,900] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a249b9f-b621-420d-b658-07a4b592d55e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:01,900] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a249b9f-b621-420d-b658-07a4b592d55e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:01,914] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:01,915] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:01,915] [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
Paenarthrobacter aurescens	strain=NBRC 12136	GCA_006538985.1	43663	43663	type	True	100.0	1404	1407	95	conclusive
Paenarthrobacter histidinolovorans	strain=JCM 2520	GCA_014647595.1	43664	43664	type	True	83.8766	1039	1407	95	below_threshold
Paenarthrobacter nicotinovorans	strain=JCM 3874	GCA_014648735.1	29320	29320	suspected-type	True	83.6616	1008	1407	95	below_threshold
Paenarthrobacter nicotinovorans	strain=ATCC 49919	GCA_021919345.1	29320	29320	suspected-type	True	83.6208	1021	1407	95	below_threshold
Paenarthrobacter nicotinovorans	strain=DSM 420	GCA_017876445.1	29320	29320	suspected-type	True	83.5856	1024	1407	95	below_threshold
Paenarthrobacter ilicis	strain=DSM 20138	GCA_016907545.1	43665	43665	type	True	82.8646	915	1407	95	below_threshold
Arthrobacter celericrescens	strain=NEAU-SA2	GCA_003614925.1	2320851	2320851	type	True	80.3783	626	1407	95	below_threshold
Arthrobacter ulcerisalmonis		GCA_900609065.1	2483813	2483813	type	True	79.3314	452	1407	95	below_threshold
Arthrobacter pullicola	strain=Sa2BUA2	GCA_014836875.1	2762224	2762224	type	True	78.3231	236	1407	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	78.231	238	1407	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	78.1719	237	1407	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:01,917] [INFO] DFAST Taxonomy check result was written to GCF_006538985.1_ASM653898v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:01,918] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:01,918] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:01,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a249b9f-b621-420d-b658-07a4b592d55e/dqc_reference/checkm_data
[2024-01-24 12:54:01,919] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:01,959] [INFO] Task started: CheckM
[2024-01-24 12:54:01,959] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006538985.1_ASM653898v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006538985.1_ASM653898v1_genomic.fna/checkm_input GCF_006538985.1_ASM653898v1_genomic.fna/checkm_result
[2024-01-24 12:54:43,800] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:43,801] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:43,817] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:43,818] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:43,818] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006538985.1_ASM653898v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:43,818] [INFO] Task started: Blastn
[2024-01-24 12:54:43,818] [INFO] Running command: blastn -query GCF_006538985.1_ASM653898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a249b9f-b621-420d-b658-07a4b592d55e/dqc_reference/reference_markers_gtdb.fasta -out GCF_006538985.1_ASM653898v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:45,114] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:45,118] [INFO] Selected 13 target genomes.
[2024-01-24 12:54:45,118] [INFO] Target genome list was writen to GCF_006538985.1_ASM653898v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:45,139] [INFO] Task started: fastANI
[2024-01-24 12:54:45,139] [INFO] Running command: fastANI --query /var/lib/cwl/stg736d327a-fe6a-49e0-9b73-c1ef2379ae1e/GCF_006538985.1_ASM653898v1_genomic.fna.gz --refList GCF_006538985.1_ASM653898v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006538985.1_ASM653898v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:59,318] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:59,333] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:59,333] [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_006538985.1	s__Paenarthrobacter aurescens	100.0	1404	1407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001512285.1	s__Paenarthrobacter sp001512285	88.2922	1206	1407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613695.1	s__Paenarthrobacter sp018613695	87.9159	1177	1407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979775.1	s__Paenarthrobacter sp002979775	87.759	1237	1407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000526335.1	s__Paenarthrobacter sp000526335	87.6642	1217	1407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506065.1	s__Paenarthrobacter sp902506065	87.38	1194	1407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	98.37	98.37	0.91	0.91	2	-
GCF_006964045.1	s__Paenarthrobacter sp006964045	87.1214	1147	1407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	98.36	98.36	0.86	0.86	2	-
GCF_000014925.1	s__Paenarthrobacter aurescens_A	86.3252	1181	1407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	98.88	98.80	0.86	0.86	3	-
GCF_000281065.1	s__Paenarthrobacter sp000281065	86.2513	1125	1407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106835.1	s__Paenarthrobacter sp900106835	85.1105	1087	1407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	98.81	98.81	0.92	0.92	2	-
GCF_017357425.1	s__Paenarthrobacter sp017357425	84.9476	1097	1407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902706295.1	s__Paenarthrobacter sp902706295	84.8399	1081	1407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007786235.1	s__Paenarthrobacter nitroguajacolicus_A	84.4498	1060	1407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:59,335] [INFO] GTDB search result was written to GCF_006538985.1_ASM653898v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:59,335] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:59,339] [INFO] DFAST_QC result json was written to GCF_006538985.1_ASM653898v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:59,339] [INFO] DFAST_QC completed!
[2024-01-24 12:54:59,339] [INFO] Total running time: 0h1m23s