[2024-01-24 13:25:28,349] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:28,351] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:28,351] [INFO] DQC Reference Directory: /var/lib/cwl/stga69073d3-4d3a-4095-9fc0-083afd4d8ba0/dqc_reference
[2024-01-24 13:25:29,790] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:29,791] [INFO] Task started: Prodigal
[2024-01-24 13:25:29,791] [INFO] Running command: gunzip -c /var/lib/cwl/stg58ef98f6-f169-4d95-856c-d174a340554e/GCF_000025965.1_ASM2596v1_genomic.fna.gz | prodigal -d GCF_000025965.1_ASM2596v1_genomic.fna/cds.fna -a GCF_000025965.1_ASM2596v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:44,082] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:44,083] [INFO] Task started: HMMsearch
[2024-01-24 13:25:44,083] [INFO] Running command: hmmsearch --tblout GCF_000025965.1_ASM2596v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga69073d3-4d3a-4095-9fc0-083afd4d8ba0/dqc_reference/reference_markers.hmm GCF_000025965.1_ASM2596v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:44,395] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:44,396] [INFO] Found 6/6 markers.
[2024-01-24 13:25:44,442] [INFO] Query marker FASTA was written to GCF_000025965.1_ASM2596v1_genomic.fna/markers.fasta
[2024-01-24 13:25:44,442] [INFO] Task started: Blastn
[2024-01-24 13:25:44,443] [INFO] Running command: blastn -query GCF_000025965.1_ASM2596v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga69073d3-4d3a-4095-9fc0-083afd4d8ba0/dqc_reference/reference_markers.fasta -out GCF_000025965.1_ASM2596v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:45,425] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:45,432] [INFO] Selected 9 target genomes.
[2024-01-24 13:25:45,432] [INFO] Target genome list was writen to GCF_000025965.1_ASM2596v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:45,437] [INFO] Task started: fastANI
[2024-01-24 13:25:45,437] [INFO] Running command: fastANI --query /var/lib/cwl/stg58ef98f6-f169-4d95-856c-d174a340554e/GCF_000025965.1_ASM2596v1_genomic.fna.gz --refList GCF_000025965.1_ASM2596v1_genomic.fna/target_genomes.txt --output GCF_000025965.1_ASM2596v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:55,776] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:55,777] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga69073d3-4d3a-4095-9fc0-083afd4d8ba0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:55,778] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga69073d3-4d3a-4095-9fc0-083afd4d8ba0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:55,788] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:25:55,788] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:55,788] [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
Aromatoleum aromaticum	strain=EbN1	GCA_000025965.1	551760	551760	type	True	100.0	1573	1575	95	conclusive
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	93.3082	1079	1575	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	92.5629	1075	1575	95	below_threshold
Aromatoleum bremense	strain=PbN1	GCA_017894365.1	76115	76115	type	True	92.5345	1042	1575	95	below_threshold
Aromatoleum bremense	strain=PbN1	GCA_012910925.1	76115	76115	type	True	92.4434	998	1575	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	82.3212	730	1575	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	78.4236	388	1575	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.8802	367	1575	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:55,789] [INFO] DFAST Taxonomy check result was written to GCF_000025965.1_ASM2596v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:55,790] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:55,790] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:55,790] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga69073d3-4d3a-4095-9fc0-083afd4d8ba0/dqc_reference/checkm_data
[2024-01-24 13:25:55,791] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:55,837] [INFO] Task started: CheckM
[2024-01-24 13:25:55,838] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000025965.1_ASM2596v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000025965.1_ASM2596v1_genomic.fna/checkm_input GCF_000025965.1_ASM2596v1_genomic.fna/checkm_result
[2024-01-24 13:26:43,246] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:43,247] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:43,273] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:43,273] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:43,274] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000025965.1_ASM2596v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:43,274] [INFO] Task started: Blastn
[2024-01-24 13:26:43,274] [INFO] Running command: blastn -query GCF_000025965.1_ASM2596v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga69073d3-4d3a-4095-9fc0-083afd4d8ba0/dqc_reference/reference_markers_gtdb.fasta -out GCF_000025965.1_ASM2596v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:44,948] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:44,953] [INFO] Selected 6 target genomes.
[2024-01-24 13:26:44,953] [INFO] Target genome list was writen to GCF_000025965.1_ASM2596v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:44,963] [INFO] Task started: fastANI
[2024-01-24 13:26:44,963] [INFO] Running command: fastANI --query /var/lib/cwl/stg58ef98f6-f169-4d95-856c-d174a340554e/GCF_000025965.1_ASM2596v1_genomic.fna.gz --refList GCF_000025965.1_ASM2596v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000025965.1_ASM2596v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:52,029] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:52,040] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:52,041] [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_000025965.1	s__Aromatoleum aromaticum	100.0	1573	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	98.48	98.48	0.91	0.91	2	conclusive
GCF_012910785.1	s__Aromatoleum buckelii	93.2847	1058	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017894365.1	s__Aromatoleum bremense	92.5409	1047	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	99.97	99.97	1.00	1.00	2	-
GCF_012910705.1	s__Aromatoleum anaerobium	92.4655	1023	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001274695.1	s__Aromatoleum sp001274695	91.9604	1045	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:52,042] [INFO] GTDB search result was written to GCF_000025965.1_ASM2596v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:52,043] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:52,047] [INFO] DFAST_QC result json was written to GCF_000025965.1_ASM2596v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:52,047] [INFO] DFAST_QC completed!
[2024-01-24 13:26:52,047] [INFO] Total running time: 0h1m24s