[2024-01-24 13:40:42,637] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:42,638] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:42,639] [INFO] DQC Reference Directory: /var/lib/cwl/stg16d208d4-1a8c-42bc-9b4d-72e199457295/dqc_reference
[2024-01-24 13:40:43,988] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:43,989] [INFO] Task started: Prodigal
[2024-01-24 13:40:43,989] [INFO] Running command: gunzip -c /var/lib/cwl/stg391b198f-3a42-4412-bbe4-bcee249d717a/GCF_002909445.1_ASM290944v1_genomic.fna.gz | prodigal -d GCF_002909445.1_ASM290944v1_genomic.fna/cds.fna -a GCF_002909445.1_ASM290944v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:00,308] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:00,309] [INFO] Task started: HMMsearch
[2024-01-24 13:41:00,309] [INFO] Running command: hmmsearch --tblout GCF_002909445.1_ASM290944v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16d208d4-1a8c-42bc-9b4d-72e199457295/dqc_reference/reference_markers.hmm GCF_002909445.1_ASM290944v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:00,589] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:00,590] [INFO] Found 6/6 markers.
[2024-01-24 13:41:00,633] [INFO] Query marker FASTA was written to GCF_002909445.1_ASM290944v1_genomic.fna/markers.fasta
[2024-01-24 13:41:00,634] [INFO] Task started: Blastn
[2024-01-24 13:41:00,634] [INFO] Running command: blastn -query GCF_002909445.1_ASM290944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16d208d4-1a8c-42bc-9b4d-72e199457295/dqc_reference/reference_markers.fasta -out GCF_002909445.1_ASM290944v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:01,547] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:01,550] [INFO] Selected 13 target genomes.
[2024-01-24 13:41:01,551] [INFO] Target genome list was writen to GCF_002909445.1_ASM290944v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:01,556] [INFO] Task started: fastANI
[2024-01-24 13:41:01,557] [INFO] Running command: fastANI --query /var/lib/cwl/stg391b198f-3a42-4412-bbe4-bcee249d717a/GCF_002909445.1_ASM290944v1_genomic.fna.gz --refList GCF_002909445.1_ASM290944v1_genomic.fna/target_genomes.txt --output GCF_002909445.1_ASM290944v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:12,352] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:12,353] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16d208d4-1a8c-42bc-9b4d-72e199457295/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:12,353] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16d208d4-1a8c-42bc-9b4d-72e199457295/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:12,368] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:12,368] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:12,368] [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 glacialis	strain=HLT2-12-2	GCA_002909445.1	1664	1664	type	True	100.0	1458	1459	95	conclusive
Arthrobacter alpinus	strain=DSM 22274	GCA_900105965.1	656366	656366	suspected-type	True	82.1464	777	1459	95	below_threshold
Arthrobacter stackebrandtii	strain=DSM 16005	GCA_017876675.1	272161	272161	type	True	81.2346	731	1459	95	below_threshold
Arthrobacter psychrolactophilus	strain=B7	GCA_003219795.1	92442	92442	type	True	80.9442	646	1459	95	below_threshold
Arthrobacter psychrochitiniphilus	strain=DSM 23143	GCA_013408645.1	291045	291045	type	True	80.458	606	1459	95	below_threshold
Arthrobacter livingstonensis	strain=LI2	GCA_003219815.1	670078	670078	type	True	80.4417	667	1459	95	below_threshold
Arthrobacter wenxiniae	strain=AETb3-4	GCA_013376105.1	2713570	2713570	type	True	80.4389	614	1459	95	below_threshold
Arthrobacter psychrochitiniphilus	strain=GP3	GCA_003185915.1	291045	291045	type	True	80.4255	616	1459	95	below_threshold
Arthrobacter dokdonellae		GCA_003268655.1	2211210	2211210	type	True	79.9705	604	1459	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	78.8991	235	1459	95	below_threshold
Arthrobacter cryoconiti	strain=Cr6-08	GCA_020905375.1	748907	748907	type	True	78.7767	349	1459	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	78.0424	275	1459	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	77.976	280	1459	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:12,370] [INFO] DFAST Taxonomy check result was written to GCF_002909445.1_ASM290944v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:12,370] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:12,371] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:12,371] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16d208d4-1a8c-42bc-9b4d-72e199457295/dqc_reference/checkm_data
[2024-01-24 13:41:12,372] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:12,414] [INFO] Task started: CheckM
[2024-01-24 13:41:12,414] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002909445.1_ASM290944v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002909445.1_ASM290944v1_genomic.fna/checkm_input GCF_002909445.1_ASM290944v1_genomic.fna/checkm_result
[2024-01-24 13:42:01,456] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:01,458] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:01,485] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:01,486] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:01,486] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002909445.1_ASM290944v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:01,487] [INFO] Task started: Blastn
[2024-01-24 13:42:01,487] [INFO] Running command: blastn -query GCF_002909445.1_ASM290944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16d208d4-1a8c-42bc-9b4d-72e199457295/dqc_reference/reference_markers_gtdb.fasta -out GCF_002909445.1_ASM290944v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:02,794] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:02,798] [INFO] Selected 12 target genomes.
[2024-01-24 13:42:02,798] [INFO] Target genome list was writen to GCF_002909445.1_ASM290944v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:02,813] [INFO] Task started: fastANI
[2024-01-24 13:42:02,813] [INFO] Running command: fastANI --query /var/lib/cwl/stg391b198f-3a42-4412-bbe4-bcee249d717a/GCF_002909445.1_ASM290944v1_genomic.fna.gz --refList GCF_002909445.1_ASM290944v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002909445.1_ASM290944v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:13,713] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:13,728] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:13,728] [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_002909445.1	s__Specibacter glacialis	100.0	1458	1459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	99.29	99.29	0.92	0.92	2	conclusive
GCF_900105965.1	s__Specibacter alpinus	82.1394	778	1459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	96.92	96.92	0.91	0.91	2	-
GCF_002929705.1	s__Specibacter sp002929705	81.4393	749	1459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000785535.1	s__Specibacter sp000785535	81.2641	749	1459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929305.1	s__Specibacter sp002929305	81.2263	676	1459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876675.1	s__Specibacter stackebrandtii	81.2219	733	1459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820535.1	s__Specibacter sp016820535	81.1014	703	1459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001281315.1	s__Specibacter sp001281315	80.951	728	1459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003219795.1	s__Specibacter psychrolactophilus	80.9442	646	1459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001294625.1	s__Specibacter alpinus_A	80.5056	645	1459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	99.52	99.48	0.93	0.92	3	-
GCF_003219815.1	s__Specibacter livingstonensis	80.4201	670	1459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013376095.1	s__Specibacter sp013376095	80.1909	605	1459	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:13,730] [INFO] GTDB search result was written to GCF_002909445.1_ASM290944v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:13,730] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:13,734] [INFO] DFAST_QC result json was written to GCF_002909445.1_ASM290944v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:13,734] [INFO] DFAST_QC completed!
[2024-01-24 13:42:13,734] [INFO] Total running time: 0h1m31s