[2024-01-24 13:28:01,855] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:01,860] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:01,860] [INFO] DQC Reference Directory: /var/lib/cwl/stg0af1d182-9a00-476a-8f16-151cf02a1138/dqc_reference
[2024-01-24 13:28:03,218] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:03,219] [INFO] Task started: Prodigal
[2024-01-24 13:28:03,219] [INFO] Running command: gunzip -c /var/lib/cwl/stg78fa9bdc-1d39-4aa0-9db9-a3ab8dc66fd9/GCF_012910985.1_ASM1291098v1_genomic.fna.gz | prodigal -d GCF_012910985.1_ASM1291098v1_genomic.fna/cds.fna -a GCF_012910985.1_ASM1291098v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:18,913] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:18,914] [INFO] Task started: HMMsearch
[2024-01-24 13:28:18,914] [INFO] Running command: hmmsearch --tblout GCF_012910985.1_ASM1291098v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0af1d182-9a00-476a-8f16-151cf02a1138/dqc_reference/reference_markers.hmm GCF_012910985.1_ASM1291098v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:19,200] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:19,202] [INFO] Found 6/6 markers.
[2024-01-24 13:28:19,253] [INFO] Query marker FASTA was written to GCF_012910985.1_ASM1291098v1_genomic.fna/markers.fasta
[2024-01-24 13:28:19,253] [INFO] Task started: Blastn
[2024-01-24 13:28:19,253] [INFO] Running command: blastn -query GCF_012910985.1_ASM1291098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0af1d182-9a00-476a-8f16-151cf02a1138/dqc_reference/reference_markers.fasta -out GCF_012910985.1_ASM1291098v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:20,278] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:20,282] [INFO] Selected 11 target genomes.
[2024-01-24 13:28:20,282] [INFO] Target genome list was writen to GCF_012910985.1_ASM1291098v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:20,288] [INFO] Task started: fastANI
[2024-01-24 13:28:20,288] [INFO] Running command: fastANI --query /var/lib/cwl/stg78fa9bdc-1d39-4aa0-9db9-a3ab8dc66fd9/GCF_012910985.1_ASM1291098v1_genomic.fna.gz --refList GCF_012910985.1_ASM1291098v1_genomic.fna/target_genomes.txt --output GCF_012910985.1_ASM1291098v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:33,369] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:33,369] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0af1d182-9a00-476a-8f16-151cf02a1138/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:33,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0af1d182-9a00-476a-8f16-151cf02a1138/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:33,382] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:28:33,382] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:33,383] [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 petrolei	strain=ToN1	GCA_012910985.1	76116	76116	type	True	100.0	1709	1718	95	conclusive
Aromatoleum petrolei	strain=ToN1	GCA_017894385.1	76116	76116	type	True	99.9978	1718	1718	95	conclusive
Aromatoleum evansii	strain=KB740	GCA_012910805.1	59406	59406	type	True	91.4434	1265	1718	95	below_threshold
Aromatoleum toluclasticum	strain=MF63	GCA_000378245.1	92003	92003	type	True	89.0423	1260	1718	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	89.0196	1239	1718	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	88.9031	1188	1718	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	87.2561	1081	1718	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	81.8326	751	1718	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	81.7737	735	1718	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	78.9874	460	1718	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	77.9119	308	1718	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:33,384] [INFO] DFAST Taxonomy check result was written to GCF_012910985.1_ASM1291098v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:33,386] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:33,390] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:33,391] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0af1d182-9a00-476a-8f16-151cf02a1138/dqc_reference/checkm_data
[2024-01-24 13:28:33,392] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:33,443] [INFO] Task started: CheckM
[2024-01-24 13:28:33,444] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012910985.1_ASM1291098v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012910985.1_ASM1291098v1_genomic.fna/checkm_input GCF_012910985.1_ASM1291098v1_genomic.fna/checkm_result
[2024-01-24 13:29:25,216] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:25,217] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:25,233] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:25,234] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:25,234] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012910985.1_ASM1291098v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:25,234] [INFO] Task started: Blastn
[2024-01-24 13:29:25,235] [INFO] Running command: blastn -query GCF_012910985.1_ASM1291098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0af1d182-9a00-476a-8f16-151cf02a1138/dqc_reference/reference_markers_gtdb.fasta -out GCF_012910985.1_ASM1291098v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:27,182] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:27,185] [INFO] Selected 9 target genomes.
[2024-01-24 13:29:27,185] [INFO] Target genome list was writen to GCF_012910985.1_ASM1291098v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:27,198] [INFO] Task started: fastANI
[2024-01-24 13:29:27,198] [INFO] Running command: fastANI --query /var/lib/cwl/stg78fa9bdc-1d39-4aa0-9db9-a3ab8dc66fd9/GCF_012910985.1_ASM1291098v1_genomic.fna.gz --refList GCF_012910985.1_ASM1291098v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012910985.1_ASM1291098v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:38,484] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:38,492] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:38,492] [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_017894385.1	s__Aromatoleum petrolei	99.9978	1718	1718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_012910805.1	s__Aromatoleum evansii	91.4434	1265	1718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378245.1	s__Aromatoleum toluclasticum	89.0423	1260	1718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911005.1	s__Aromatoleum toluolicum	89.0137	1239	1718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156155.1	s__Aromatoleum tolulyticum	88.8966	1188	1718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014822185.1	s__Aromatoleum sp014822185	88.8121	1169	1718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001190925.1	s__Aromatoleum sp001190925	88.7266	1240	1718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910905.1	s__Aromatoleum toluvorans	87.2465	1081	1718	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003628555.1	s__Aromatoleum sp003628555	86.679	1055	1718	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 13:29:38,494] [INFO] GTDB search result was written to GCF_012910985.1_ASM1291098v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:38,495] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:38,498] [INFO] DFAST_QC result json was written to GCF_012910985.1_ASM1291098v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:38,498] [INFO] DFAST_QC completed!
[2024-01-24 13:29:38,498] [INFO] Total running time: 0h1m37s