[2024-01-24 14:42:02,903] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:42:02,910] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:42:02,910] [INFO] DQC Reference Directory: /var/lib/cwl/stg36012d02-afac-4779-90bc-191cc83373ec/dqc_reference
[2024-01-24 14:42:04,266] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:42:04,266] [INFO] Task started: Prodigal
[2024-01-24 14:42:04,267] [INFO] Running command: gunzip -c /var/lib/cwl/stg384d9a8e-10a6-4654-a989-e759a7da4cb0/GCF_007994735.1_ASM799473v1_genomic.fna.gz | prodigal -d GCF_007994735.1_ASM799473v1_genomic.fna/cds.fna -a GCF_007994735.1_ASM799473v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:42:12,173] [INFO] Task succeeded: Prodigal
[2024-01-24 14:42:12,173] [INFO] Task started: HMMsearch
[2024-01-24 14:42:12,174] [INFO] Running command: hmmsearch --tblout GCF_007994735.1_ASM799473v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36012d02-afac-4779-90bc-191cc83373ec/dqc_reference/reference_markers.hmm GCF_007994735.1_ASM799473v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:42:12,455] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:42:12,456] [INFO] Found 6/6 markers.
[2024-01-24 14:42:12,486] [INFO] Query marker FASTA was written to GCF_007994735.1_ASM799473v1_genomic.fna/markers.fasta
[2024-01-24 14:42:12,486] [INFO] Task started: Blastn
[2024-01-24 14:42:12,487] [INFO] Running command: blastn -query GCF_007994735.1_ASM799473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36012d02-afac-4779-90bc-191cc83373ec/dqc_reference/reference_markers.fasta -out GCF_007994735.1_ASM799473v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:13,643] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:13,646] [INFO] Selected 18 target genomes.
[2024-01-24 14:42:13,646] [INFO] Target genome list was writen to GCF_007994735.1_ASM799473v1_genomic.fna/target_genomes.txt
[2024-01-24 14:42:13,718] [INFO] Task started: fastANI
[2024-01-24 14:42:13,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg384d9a8e-10a6-4654-a989-e759a7da4cb0/GCF_007994735.1_ASM799473v1_genomic.fna.gz --refList GCF_007994735.1_ASM799473v1_genomic.fna/target_genomes.txt --output GCF_007994735.1_ASM799473v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:42:24,842] [INFO] Task succeeded: fastANI
[2024-01-24 14:42:24,842] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36012d02-afac-4779-90bc-191cc83373ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:42:24,843] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36012d02-afac-4779-90bc-191cc83373ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:42:24,856] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:42:24,856] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:42:24,857] [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
Nesterenkonia populi	strain=DSM 27959	GCA_007994735.1	1591087	1591087	type	True	100.0	848	849	95	conclusive
Nesterenkonia pannonica	strain=DSM 29786	GCA_019575955.1	1548602	1548602	type	True	81.5965	561	849	95	below_threshold
Nesterenkonia cremea	strain=CGMCC 1.15388	GCA_014642675.1	1882340	1882340	type	True	80.1966	428	849	95	below_threshold
Nesterenkonia lacusekhoensis	strain=DSM 12544	GCA_017876395.1	150832	150832	type	True	79.8971	389	849	95	below_threshold
Nesterenkonia alkaliphila	strain=F10	GCA_009758175.1	1463631	1463631	type	True	79.747	359	849	95	below_threshold
Nesterenkonia alkaliphila	strain=CGMCC 1.12781	GCA_014639295.1	1463631	1463631	type	True	79.686	371	849	95	below_threshold
Nesterenkonia ebinurensis	strain=MD2	GCA_008711175.1	2608252	2608252	type	True	79.5357	369	849	95	below_threshold
Nesterenkonia sedimenti	strain=MY13	GCA_012641515.1	1463632	1463632	type	True	79.3148	311	849	95	below_threshold
Nesterenkonia jeotgali	strain=DSM 19081	GCA_014138825.1	317018	317018	type	True	79.1838	363	849	95	below_threshold
Nesterenkonia sandarakina	strain=DSM 15664	GCA_013410215.1	272918	272918	type	True	79.0659	364	849	95	below_threshold
Nesterenkonia halotolerans	strain=DSM 15474	GCA_014874065.1	225325	225325	type	True	79.0526	323	849	95	below_threshold
Nesterenkonia muleiensis	strain=RB2	GCA_003600155.1	2282648	2282648	type	True	78.9546	342	849	95	below_threshold
Nesterenkonia massiliensis	strain=NP1	GCA_000455245.1	1232429	1232429	type	True	78.9086	298	849	95	below_threshold
Micrococcus luteus	strain=NCTC2665	GCA_900475555.1	1270	1270	type	True	78.4385	222	849	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	77.7471	154	849	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	77.6113	178	849	95	below_threshold
Occultella gossypii	strain=N2-46	GCA_019947135.1	2800820	2800820	type	True	76.5825	130	849	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.5528	115	849	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:42:24,858] [INFO] DFAST Taxonomy check result was written to GCF_007994735.1_ASM799473v1_genomic.fna/tc_result.tsv
[2024-01-24 14:42:24,859] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:42:24,859] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:42:24,859] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36012d02-afac-4779-90bc-191cc83373ec/dqc_reference/checkm_data
[2024-01-24 14:42:24,861] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:42:24,887] [INFO] Task started: CheckM
[2024-01-24 14:42:24,887] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007994735.1_ASM799473v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007994735.1_ASM799473v1_genomic.fna/checkm_input GCF_007994735.1_ASM799473v1_genomic.fna/checkm_result
[2024-01-24 14:42:54,392] [INFO] Task succeeded: CheckM
[2024-01-24 14:42:54,393] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:42:54,416] [INFO] ===== Completeness check finished =====
[2024-01-24 14:42:54,417] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:42:54,417] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007994735.1_ASM799473v1_genomic.fna/markers.fasta)
[2024-01-24 14:42:54,418] [INFO] Task started: Blastn
[2024-01-24 14:42:54,418] [INFO] Running command: blastn -query GCF_007994735.1_ASM799473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36012d02-afac-4779-90bc-191cc83373ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_007994735.1_ASM799473v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:55,942] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:55,946] [INFO] Selected 14 target genomes.
[2024-01-24 14:42:55,947] [INFO] Target genome list was writen to GCF_007994735.1_ASM799473v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:42:55,961] [INFO] Task started: fastANI
[2024-01-24 14:42:55,961] [INFO] Running command: fastANI --query /var/lib/cwl/stg384d9a8e-10a6-4654-a989-e759a7da4cb0/GCF_007994735.1_ASM799473v1_genomic.fna.gz --refList GCF_007994735.1_ASM799473v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007994735.1_ASM799473v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:43:04,254] [INFO] Task succeeded: fastANI
[2024-01-24 14:43:04,266] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:43:04,266] [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_007994735.1	s__Nesterenkonia populi	100.0	848	849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007922635.1	s__Nesterenkonia sp007922635	81.7341	563	849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642675.1	s__Nesterenkonia cremea	80.193	429	849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876395.1	s__Nesterenkonia lacusekhoensis	79.8975	388	849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009758175.1	s__Nesterenkonia alkaliphila	79.7469	359	849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013410745.1	s__Nesterenkonia xinjiangensis	79.374	352	849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001758425.2	s__Nesterenkonia sp001758425	79.3471	369	849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003175.1	s__Nesterenkonia sandarakina_A	79.3404	368	849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641515.1	s__Nesterenkonia sp012641515	79.2994	312	849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410215.1	s__Nesterenkonia sandarakina	79.0409	366	849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	97.10	97.05	0.88	0.86	3	-
GCF_014874065.1	s__Nesterenkonia halotolerans	79.0139	322	849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003600155.1	s__Nesterenkonia muleiensis	78.9416	343	849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455245.1	s__Nesterenkonia massiliensis	78.9077	298	849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003261175.1	s__Arthrobacter globiformis_A	77.5952	138	849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:43:04,268] [INFO] GTDB search result was written to GCF_007994735.1_ASM799473v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:43:04,269] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:43:04,272] [INFO] DFAST_QC result json was written to GCF_007994735.1_ASM799473v1_genomic.fna/dqc_result.json
[2024-01-24 14:43:04,273] [INFO] DFAST_QC completed!
[2024-01-24 14:43:04,273] [INFO] Total running time: 0h1m1s