[2024-01-24 12:44:43,637] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:43,639] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:43,640] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5482dcf-7431-46ff-ae0e-21603fb5bdc4/dqc_reference
[2024-01-24 12:44:44,948] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:44,949] [INFO] Task started: Prodigal
[2024-01-24 12:44:44,949] [INFO] Running command: gunzip -c /var/lib/cwl/stg880c1b40-b702-4024-86b1-93c59dad7ed4/GCF_017052465.1_ASM1705246v1_genomic.fna.gz | prodigal -d GCF_017052465.1_ASM1705246v1_genomic.fna/cds.fna -a GCF_017052465.1_ASM1705246v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:00,163] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:00,164] [INFO] Task started: HMMsearch
[2024-01-24 12:45:00,164] [INFO] Running command: hmmsearch --tblout GCF_017052465.1_ASM1705246v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5482dcf-7431-46ff-ae0e-21603fb5bdc4/dqc_reference/reference_markers.hmm GCF_017052465.1_ASM1705246v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:00,489] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:00,490] [INFO] Found 6/6 markers.
[2024-01-24 12:45:00,547] [INFO] Query marker FASTA was written to GCF_017052465.1_ASM1705246v1_genomic.fna/markers.fasta
[2024-01-24 12:45:00,547] [INFO] Task started: Blastn
[2024-01-24 12:45:00,547] [INFO] Running command: blastn -query GCF_017052465.1_ASM1705246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5482dcf-7431-46ff-ae0e-21603fb5bdc4/dqc_reference/reference_markers.fasta -out GCF_017052465.1_ASM1705246v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:01,663] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:01,667] [INFO] Selected 17 target genomes.
[2024-01-24 12:45:01,667] [INFO] Target genome list was writen to GCF_017052465.1_ASM1705246v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:01,675] [INFO] Task started: fastANI
[2024-01-24 12:45:01,675] [INFO] Running command: fastANI --query /var/lib/cwl/stg880c1b40-b702-4024-86b1-93c59dad7ed4/GCF_017052465.1_ASM1705246v1_genomic.fna.gz --refList GCF_017052465.1_ASM1705246v1_genomic.fna/target_genomes.txt --output GCF_017052465.1_ASM1705246v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:18,731] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:18,732] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5482dcf-7431-46ff-ae0e-21603fb5bdc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:18,733] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5482dcf-7431-46ff-ae0e-21603fb5bdc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:18,753] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:18,753] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:18,754] [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 pascens	strain=DSM 20545	GCA_017052465.1	1677	1677	type	True	100.0	1546	1552	95	conclusive
Arthrobacter globiformis	strain=NBRC 12137	GCA_000238915.2	1665	1665	type	True	83.5097	1024	1552	95	below_threshold
Arthrobacter ipis	strain=IA7	GCA_014694315.1	2716202	2716202	type	True	83.2243	1005	1552	95	below_threshold
Pseudarthrobacter psychrotolerans	strain=YJ56	GCA_009911795.1	2697569	2697569	type	True	81.6496	798	1552	95	below_threshold
Pseudarthrobacter sulfonivorans	strain=ALL	GCA_014712225.1	121292	121292	type	True	81.5955	777	1552	95	below_threshold
Pseudarthrobacter scleromae	strain=CGMCC 1.3601	GCA_014644515.1	158897	158897	type	True	81.3914	720	1552	95	below_threshold
Pseudarthrobacter polychromogenes	strain=CGMCC 1.1927	GCA_014644495.1	1676	1676	type	True	81.3325	730	1552	95	below_threshold
Pseudarthrobacter chlorophenolicus	strain=A6	GCA_900104315.1	85085	85085	type	True	81.2055	755	1552	95	below_threshold
Pseudarthrobacter chlorophenolicus	strain=A6	GCA_000022025.1	85085	85085	type	True	81.1564	756	1552	95	below_threshold
Arthrobacter celericrescens	strain=NEAU-SA2	GCA_003614925.1	2320851	2320851	type	True	80.9899	694	1552	95	below_threshold
Arthrobacter cupressi	strain=CGMCC 1.10783	GCA_900099975.1	1045773	1045773	type	True	80.9634	669	1552	95	below_threshold
Arthrobacter cupressi	strain=DSM 24664	GCA_013409905.1	1045773	1045773	type	True	80.9338	677	1552	95	below_threshold
Paenarthrobacter nicotinovorans	strain=ATCC 49919	GCA_021919345.1	29320	29320	suspected-type	True	80.1495	610	1552	95	below_threshold
Arthrobacter ulcerisalmonis		GCA_900609065.1	2483813	2483813	type	True	80.077	549	1552	95	below_threshold
Arthrobacter stackebrandtii	strain=DSM 16005	GCA_017876675.1	272161	272161	type	True	79.014	385	1552	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.8427	432	1552	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.8223	332	1552	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:18,755] [INFO] DFAST Taxonomy check result was written to GCF_017052465.1_ASM1705246v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:18,756] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:18,756] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:18,757] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5482dcf-7431-46ff-ae0e-21603fb5bdc4/dqc_reference/checkm_data
[2024-01-24 12:45:18,758] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:18,814] [INFO] Task started: CheckM
[2024-01-24 12:45:18,814] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017052465.1_ASM1705246v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017052465.1_ASM1705246v1_genomic.fna/checkm_input GCF_017052465.1_ASM1705246v1_genomic.fna/checkm_result
[2024-01-24 12:46:02,092] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:02,093] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:02,115] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:02,116] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:02,116] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017052465.1_ASM1705246v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:02,117] [INFO] Task started: Blastn
[2024-01-24 12:46:02,117] [INFO] Running command: blastn -query GCF_017052465.1_ASM1705246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5482dcf-7431-46ff-ae0e-21603fb5bdc4/dqc_reference/reference_markers_gtdb.fasta -out GCF_017052465.1_ASM1705246v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:03,679] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:03,683] [INFO] Selected 13 target genomes.
[2024-01-24 12:46:03,683] [INFO] Target genome list was writen to GCF_017052465.1_ASM1705246v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:03,699] [INFO] Task started: fastANI
[2024-01-24 12:46:03,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg880c1b40-b702-4024-86b1-93c59dad7ed4/GCF_017052465.1_ASM1705246v1_genomic.fna.gz --refList GCF_017052465.1_ASM1705246v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017052465.1_ASM1705246v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:18,032] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:18,055] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:18,056] [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_017052465.1	s__Arthrobacter pascens	100.0	1546	1552	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018613875.1	s__Arthrobacter sp018613875	85.5135	1020	1552	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613835.1	s__Arthrobacter sp018613835	85.0981	1079	1552	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428005.1	s__Arthrobacter sp001428005	85.0219	1093	1552	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929275.1	s__Arthrobacter sp002929275	84.8395	1035	1552	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002008315.2	s__Arthrobacter sp002008315	84.7789	1038	1552	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238915.1	s__Arthrobacter globiformis	83.4989	1025	1552	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002892795.1	s__Arthrobacter sp002892795	83.4825	1023	1552	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613795.1	s__Arthrobacter sp018613795	83.3723	980	1552	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423745.1	s__Arthrobacter_I sp001423745	82.3895	837	1552	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_000685965.1	s__Arthrobacter_I sp000685965	82.3648	868	1552	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_000876655.1	s__Arthrobacter_I sp000876655	82.2393	807	1552	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_000196235.1	s__Arthrobacter_I sp000196235	82.0964	835	1552	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	98.94	98.92	0.91	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:18,058] [INFO] GTDB search result was written to GCF_017052465.1_ASM1705246v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:18,058] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:18,062] [INFO] DFAST_QC result json was written to GCF_017052465.1_ASM1705246v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:18,062] [INFO] DFAST_QC completed!
[2024-01-24 12:46:18,062] [INFO] Total running time: 0h1m34s