[2024-01-24 13:17:13,720] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:13,723] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:13,723] [INFO] DQC Reference Directory: /var/lib/cwl/stg28bb07f5-e6b0-4ae0-afe4-e21f02f6e362/dqc_reference
[2024-01-24 13:17:15,056] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:15,057] [INFO] Task started: Prodigal
[2024-01-24 13:17:15,057] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb65fea6-9109-4eeb-901e-f437f3f3ed9a/GCF_018882205.1_ASM1888220v1_genomic.fna.gz | prodigal -d GCF_018882205.1_ASM1888220v1_genomic.fna/cds.fna -a GCF_018882205.1_ASM1888220v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:20,346] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:20,347] [INFO] Task started: HMMsearch
[2024-01-24 13:17:20,347] [INFO] Running command: hmmsearch --tblout GCF_018882205.1_ASM1888220v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28bb07f5-e6b0-4ae0-afe4-e21f02f6e362/dqc_reference/reference_markers.hmm GCF_018882205.1_ASM1888220v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:20,605] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:20,607] [INFO] Found 6/6 markers.
[2024-01-24 13:17:20,635] [INFO] Query marker FASTA was written to GCF_018882205.1_ASM1888220v1_genomic.fna/markers.fasta
[2024-01-24 13:17:20,635] [INFO] Task started: Blastn
[2024-01-24 13:17:20,636] [INFO] Running command: blastn -query GCF_018882205.1_ASM1888220v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28bb07f5-e6b0-4ae0-afe4-e21f02f6e362/dqc_reference/reference_markers.fasta -out GCF_018882205.1_ASM1888220v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:21,349] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:21,355] [INFO] Selected 9 target genomes.
[2024-01-24 13:17:21,355] [INFO] Target genome list was writen to GCF_018882205.1_ASM1888220v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:21,363] [INFO] Task started: fastANI
[2024-01-24 13:17:21,363] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb65fea6-9109-4eeb-901e-f437f3f3ed9a/GCF_018882205.1_ASM1888220v1_genomic.fna.gz --refList GCF_018882205.1_ASM1888220v1_genomic.fna/target_genomes.txt --output GCF_018882205.1_ASM1888220v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:26,094] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:26,095] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28bb07f5-e6b0-4ae0-afe4-e21f02f6e362/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:26,096] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28bb07f5-e6b0-4ae0-afe4-e21f02f6e362/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:26,109] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:26,109] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:26,109] [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
Polynucleobacter bastaniensis	strain=AP-Basta-1000A-D1	GCA_018882205.1	2081039	2081039	type	True	100.0	709	710	95	conclusive
Polynucleobacter corsicus	strain=AP-Melu-1000-A1	GCA_018688255.1	2081042	2081042	type	True	90.6914	567	710	95	below_threshold
Polynucleobacter hallstattensis	strain=MWH-Hall10	GCA_018881835.1	1855586	1855586	type	True	88.8064	607	710	95	below_threshold
Polynucleobacter duraquae	strain=MWH-MoK4	GCA_000973625.1	1835254	1835254	type	True	88.5352	585	710	95	below_threshold
Polynucleobacter arcticus	strain=UK-Long2-W17	GCA_013307205.1	1743165	1743165	type	True	82.0535	433	710	95	below_threshold
Polynucleobacter aenigmaticus	strain=MWH-K35W1	GCA_002206635.1	1743164	1743164	type	True	81.9069	436	710	95	below_threshold
Polynucleobacter sinensis	strain=MWH-HuW1	GCA_001595985.1	1743157	1743157	type	True	80.7004	349	710	95	below_threshold
Polynucleobacter parvulilacunae	strain=Ross1-W9	GCA_018881715.1	1855631	1855631	type	True	80.2683	295	710	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:26,111] [INFO] DFAST Taxonomy check result was written to GCF_018882205.1_ASM1888220v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:26,112] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:26,112] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:26,112] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28bb07f5-e6b0-4ae0-afe4-e21f02f6e362/dqc_reference/checkm_data
[2024-01-24 13:17:26,113] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:26,145] [INFO] Task started: CheckM
[2024-01-24 13:17:26,146] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018882205.1_ASM1888220v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018882205.1_ASM1888220v1_genomic.fna/checkm_input GCF_018882205.1_ASM1888220v1_genomic.fna/checkm_result
[2024-01-24 13:17:49,192] [INFO] Task succeeded: CheckM
[2024-01-24 13:17:49,193] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:17:49,213] [INFO] ===== Completeness check finished =====
[2024-01-24 13:17:49,214] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:17:49,214] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018882205.1_ASM1888220v1_genomic.fna/markers.fasta)
[2024-01-24 13:17:49,215] [INFO] Task started: Blastn
[2024-01-24 13:17:49,215] [INFO] Running command: blastn -query GCF_018882205.1_ASM1888220v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28bb07f5-e6b0-4ae0-afe4-e21f02f6e362/dqc_reference/reference_markers_gtdb.fasta -out GCF_018882205.1_ASM1888220v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:50,219] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:50,222] [INFO] Selected 8 target genomes.
[2024-01-24 13:17:50,222] [INFO] Target genome list was writen to GCF_018882205.1_ASM1888220v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:17:50,234] [INFO] Task started: fastANI
[2024-01-24 13:17:50,235] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb65fea6-9109-4eeb-901e-f437f3f3ed9a/GCF_018882205.1_ASM1888220v1_genomic.fna.gz --refList GCF_018882205.1_ASM1888220v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018882205.1_ASM1888220v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:17:54,322] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:54,342] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:17:54,343] [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_018882205.1	s__Polynucleobacter sp018882205	100.0	709	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018688355.1	s__Polynucleobacter sp018688355	91.4326	579	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018688155.1	s__Polynucleobacter sp018688155	91.1439	587	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018688255.1	s__Polynucleobacter sp018688255	90.6914	567	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687755.1	s__Polynucleobacter sp018687755	88.9552	557	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881835.1	s__Polynucleobacter sp018881835	88.8064	607	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000973625.1	s__Polynucleobacter duraquae	88.5352	585	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687675.1	s__Polynucleobacter sp018687675	88.4487	586	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:17:54,345] [INFO] GTDB search result was written to GCF_018882205.1_ASM1888220v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:17:54,346] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:17:54,349] [INFO] DFAST_QC result json was written to GCF_018882205.1_ASM1888220v1_genomic.fna/dqc_result.json
[2024-01-24 13:17:54,350] [INFO] DFAST_QC completed!
[2024-01-24 13:17:54,350] [INFO] Total running time: 0h0m41s