[2023-06-18 18:31:01,521] [INFO] DFAST_QC pipeline started.
[2023-06-18 18:31:01,523] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 18:31:01,523] [INFO] DQC Reference Directory: /var/lib/cwl/stg0349903d-28f2-4341-a2d9-b6a376eb0a78/dqc_reference
[2023-06-18 18:31:02,869] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 18:31:02,869] [INFO] Task started: Prodigal
[2023-06-18 18:31:02,870] [INFO] Running command: gunzip -c /var/lib/cwl/stg31322730-c2c2-4c80-bfe2-ab82c9cd1ec9/GCA_018882695.1_ASM1888269v1_genomic.fna.gz | prodigal -d GCA_018882695.1_ASM1888269v1_genomic.fna/cds.fna -a GCA_018882695.1_ASM1888269v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 18:31:07,164] [INFO] Task succeeded: Prodigal
[2023-06-18 18:31:07,164] [INFO] Task started: HMMsearch
[2023-06-18 18:31:07,165] [INFO] Running command: hmmsearch --tblout GCA_018882695.1_ASM1888269v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0349903d-28f2-4341-a2d9-b6a376eb0a78/dqc_reference/reference_markers.hmm GCA_018882695.1_ASM1888269v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 18:31:07,430] [INFO] Task succeeded: HMMsearch
[2023-06-18 18:31:07,432] [INFO] Found 6/6 markers.
[2023-06-18 18:31:07,450] [INFO] Query marker FASTA was written to GCA_018882695.1_ASM1888269v1_genomic.fna/markers.fasta
[2023-06-18 18:31:07,451] [INFO] Task started: Blastn
[2023-06-18 18:31:07,451] [INFO] Running command: blastn -query GCA_018882695.1_ASM1888269v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0349903d-28f2-4341-a2d9-b6a376eb0a78/dqc_reference/reference_markers.fasta -out GCA_018882695.1_ASM1888269v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:31:08,101] [INFO] Task succeeded: Blastn
[2023-06-18 18:31:08,105] [INFO] Selected 16 target genomes.
[2023-06-18 18:31:08,106] [INFO] Target genome list was writen to GCA_018882695.1_ASM1888269v1_genomic.fna/target_genomes.txt
[2023-06-18 18:31:08,109] [INFO] Task started: fastANI
[2023-06-18 18:31:08,109] [INFO] Running command: fastANI --query /var/lib/cwl/stg31322730-c2c2-4c80-bfe2-ab82c9cd1ec9/GCA_018882695.1_ASM1888269v1_genomic.fna.gz --refList GCA_018882695.1_ASM1888269v1_genomic.fna/target_genomes.txt --output GCA_018882695.1_ASM1888269v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 18:31:15,059] [INFO] Task succeeded: fastANI
[2023-06-18 18:31:15,059] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0349903d-28f2-4341-a2d9-b6a376eb0a78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 18:31:15,060] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0349903d-28f2-4341-a2d9-b6a376eb0a78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 18:31:15,071] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 18:31:15,071] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 18:31:15,072] [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 acidiphobus	strain=MWH-PoolGreenA3	GCA_003065385.1	556053	556053	type	True	85.8054	446	512	95	below_threshold
Polynucleobacter difficilis	strain=AM-8B5	GCA_003065365.1	556054	556054	type	True	77.593	102	512	95	below_threshold
Polynucleobacter antarcticus	strain=LimPoW16	GCA_013307245.1	1743162	1743162	type	True	77.5393	87	512	95	below_threshold
Polynucleobacter paludilacus	strain=MWH-Mekk-C3	GCA_018687595.1	1855895	1855895	type	True	77.4954	89	512	95	below_threshold
Polynucleobacter parvulilacunae	strain=Ross1-W9	GCA_018881715.1	1855631	1855631	type	True	77.4591	79	512	95	below_threshold
Polynucleobacter alcilacus	strain=UK-Pondora-W15	GCA_018881545.1	1819739	1819739	type	True	77.2956	90	512	95	below_threshold
Polynucleobacter sphagniphilus	strain=MWH-Weng1-1	GCA_001953355.1	1743169	1743169	type	True	77.2696	83	512	95	below_threshold
Polynucleobacter nymphae	strain=AP-Mumm-500A-B3	GCA_018882155.1	2081043	2081043	type	True	77.2516	94	512	95	below_threshold
Polynucleobacter duraquae	strain=MWH-MoK4	GCA_000973625.1	1835254	1835254	type	True	77.2038	86	512	95	below_threshold
Polynucleobacter hirudinilacicola	strain=MWH-EgelM1-30-B4	GCA_002192535.1	1743166	1743166	type	True	77.1633	96	512	95	below_threshold
Polynucleobacter hallstattensis	strain=MWH-Hall10	GCA_018881835.1	1855586	1855586	type	True	77.1318	90	512	95	below_threshold
Polynucleobacter meluiroseus	strain=AP-Melu-1000-B4	GCA_900205755.1	1938814	1938814	type	True	77.0831	76	512	95	below_threshold
Polynucleobacter aenigmaticus	strain=MWH-K35W1	GCA_002206635.1	1743164	1743164	type	True	77.039	82	512	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 18:31:15,074] [INFO] DFAST Taxonomy check result was written to GCA_018882695.1_ASM1888269v1_genomic.fna/tc_result.tsv
[2023-06-18 18:31:15,074] [INFO] ===== Taxonomy check completed =====
[2023-06-18 18:31:15,074] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 18:31:15,075] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0349903d-28f2-4341-a2d9-b6a376eb0a78/dqc_reference/checkm_data
[2023-06-18 18:31:15,076] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 18:31:15,094] [INFO] Task started: CheckM
[2023-06-18 18:31:15,095] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018882695.1_ASM1888269v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018882695.1_ASM1888269v1_genomic.fna/checkm_input GCA_018882695.1_ASM1888269v1_genomic.fna/checkm_result
[2023-06-18 18:31:36,125] [INFO] Task succeeded: CheckM
[2023-06-18 18:31:36,126] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 18:31:36,157] [INFO] ===== Completeness check finished =====
[2023-06-18 18:31:36,157] [INFO] ===== Start GTDB Search =====
[2023-06-18 18:31:36,158] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018882695.1_ASM1888269v1_genomic.fna/markers.fasta)
[2023-06-18 18:31:36,158] [INFO] Task started: Blastn
[2023-06-18 18:31:36,158] [INFO] Running command: blastn -query GCA_018882695.1_ASM1888269v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0349903d-28f2-4341-a2d9-b6a376eb0a78/dqc_reference/reference_markers_gtdb.fasta -out GCA_018882695.1_ASM1888269v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:31:37,267] [INFO] Task succeeded: Blastn
[2023-06-18 18:31:37,272] [INFO] Selected 13 target genomes.
[2023-06-18 18:31:37,273] [INFO] Target genome list was writen to GCA_018882695.1_ASM1888269v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 18:31:37,278] [INFO] Task started: fastANI
[2023-06-18 18:31:37,278] [INFO] Running command: fastANI --query /var/lib/cwl/stg31322730-c2c2-4c80-bfe2-ab82c9cd1ec9/GCA_018882695.1_ASM1888269v1_genomic.fna.gz --refList GCA_018882695.1_ASM1888269v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018882695.1_ASM1888269v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 18:31:42,239] [INFO] Task succeeded: fastANI
[2023-06-18 18:31:42,253] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 18:31:42,254] [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_018687475.1	s__Polynucleobacter sp009928245	97.8307	498	512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	97.52	97.29	0.97	0.94	13	conclusive
GCA_016867965.1	s__Polynucleobacter sp016867965	94.6176	399	512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003065385.1	s__Polynucleobacter acidiphobus	85.8054	446	512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002359975.1	s__Polynucleobacter sp002359975	79.4535	123	512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.53	97.93	0.70	0.67	7	-
GCA_009924985.1	s__Polynucleobacter sp009924985	78.5758	165	512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292975.1	s__Polynucleobacter sp002292975	78.3652	205	512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.75	98.63	0.92	0.90	4	-
GCF_018882055.1	s__Polynucleobacter sp018882055	77.5218	91	512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018688095.1	s__Polynucleobacter sp018688095	77.4658	91	512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881575.1	s__Polynucleobacter sp018881575	77.3153	89	512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002192535.1	s__Polynucleobacter hirudinilacicola	77.1633	96	512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882295.1	s__Polynucleobacter sp018882295	77.1361	83	512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016462905.1	s__Polynucleobacter sp016462905	77.0374	101	512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882085.1	s__Polynucleobacter sp018882085	76.904	104	512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 18:31:42,256] [INFO] GTDB search result was written to GCA_018882695.1_ASM1888269v1_genomic.fna/result_gtdb.tsv
[2023-06-18 18:31:42,256] [INFO] ===== GTDB Search completed =====
[2023-06-18 18:31:42,260] [INFO] DFAST_QC result json was written to GCA_018882695.1_ASM1888269v1_genomic.fna/dqc_result.json
[2023-06-18 18:31:42,260] [INFO] DFAST_QC completed!
[2023-06-18 18:31:42,260] [INFO] Total running time: 0h0m41s