[2024-01-24 15:18:26,547] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:26,549] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:26,549] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc2c1351-847a-4c1d-a954-7b4a7c7ec8a4/dqc_reference
[2024-01-24 15:18:27,992] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:27,993] [INFO] Task started: Prodigal
[2024-01-24 15:18:27,993] [INFO] Running command: gunzip -c /var/lib/cwl/stg28eec2fe-fd7d-40a4-be4a-773e1f265835/GCF_002206625.1_ASM220662v1_genomic.fna.gz | prodigal -d GCF_002206625.1_ASM220662v1_genomic.fna/cds.fna -a GCF_002206625.1_ASM220662v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:32,992] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:32,993] [INFO] Task started: HMMsearch
[2024-01-24 15:18:32,993] [INFO] Running command: hmmsearch --tblout GCF_002206625.1_ASM220662v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc2c1351-847a-4c1d-a954-7b4a7c7ec8a4/dqc_reference/reference_markers.hmm GCF_002206625.1_ASM220662v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:33,307] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:33,309] [INFO] Found 6/6 markers.
[2024-01-24 15:18:33,328] [INFO] Query marker FASTA was written to GCF_002206625.1_ASM220662v1_genomic.fna/markers.fasta
[2024-01-24 15:18:33,329] [INFO] Task started: Blastn
[2024-01-24 15:18:33,329] [INFO] Running command: blastn -query GCF_002206625.1_ASM220662v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc2c1351-847a-4c1d-a954-7b4a7c7ec8a4/dqc_reference/reference_markers.fasta -out GCF_002206625.1_ASM220662v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:33,926] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:33,929] [INFO] Selected 13 target genomes.
[2024-01-24 15:18:33,930] [INFO] Target genome list was writen to GCF_002206625.1_ASM220662v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:33,953] [INFO] Task started: fastANI
[2024-01-24 15:18:33,954] [INFO] Running command: fastANI --query /var/lib/cwl/stg28eec2fe-fd7d-40a4-be4a-773e1f265835/GCF_002206625.1_ASM220662v1_genomic.fna.gz --refList GCF_002206625.1_ASM220662v1_genomic.fna/target_genomes.txt --output GCF_002206625.1_ASM220662v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:39,782] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:39,783] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc2c1351-847a-4c1d-a954-7b4a7c7ec8a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:39,783] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc2c1351-847a-4c1d-a954-7b4a7c7ec8a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:39,794] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:39,794] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:39,794] [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 campilacus	strain=MWH-Feld-100	GCA_002206625.1	1743163	1743163	type	True	100.0	655	655	95	conclusive
Polynucleobacter nymphae	strain=AP-Mumm-500A-B3	GCA_018882155.1	2081043	2081043	type	True	85.2263	541	655	95	below_threshold
Polynucleobacter hirudinilacicola	strain=MWH-EgelM1-30-B4	GCA_002192535.1	1743166	1743166	type	True	83.262	473	655	95	below_threshold
Polynucleobacter parvulilacunae	strain=Ross1-W9	GCA_018881715.1	1855631	1855631	type	True	80.8928	353	655	95	below_threshold
Polynucleobacter yangtzensis	strain=MWH-JaK3	GCA_001595965.1	1743159	1743159	type	True	80.8698	363	655	95	below_threshold
Polynucleobacter ibericus	strain=es-MAR-2	GCA_018687955.1	1819725	1819725	type	True	80.859	354	655	95	below_threshold
Polynucleobacter alcilacus	strain=UK-Pondora-W15	GCA_018881545.1	1819739	1819739	type	True	80.6397	389	655	95	below_threshold
Polynucleobacter asymbioticus	strain=QLW-P1DMWA-1	GCA_000016345.1	576611	576611	type	True	80.4825	318	655	95	below_threshold
Polynucleobacter meluiroseus	strain=AP-Melu-1000-B4	GCA_900205755.1	1938814	1938814	type	True	80.0959	207	655	95	below_threshold
Polynucleobacter aenigmaticus	strain=MWH-K35W1	GCA_002206635.1	1743164	1743164	type	True	79.8558	276	655	95	below_threshold
Polynucleobacter bastaniensis	strain=AP-Basta-1000A-D1	GCA_018882205.1	2081039	2081039	type	True	79.7756	315	655	95	below_threshold
Polynucleobacter sphagniphilus	strain=MWH-Weng1-1	GCA_001953355.1	1743169	1743169	type	True	79.6941	232	655	95	below_threshold
Polynucleobacter brandtiae	strain=UB-Domo-W1	GCA_002797575.1	1938816	1938816	type	True	78.9583	209	655	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:39,796] [INFO] DFAST Taxonomy check result was written to GCF_002206625.1_ASM220662v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:39,796] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:39,796] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:39,797] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc2c1351-847a-4c1d-a954-7b4a7c7ec8a4/dqc_reference/checkm_data
[2024-01-24 15:18:39,797] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:39,821] [INFO] Task started: CheckM
[2024-01-24 15:18:39,821] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002206625.1_ASM220662v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002206625.1_ASM220662v1_genomic.fna/checkm_input GCF_002206625.1_ASM220662v1_genomic.fna/checkm_result
[2024-01-24 15:19:02,516] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:02,517] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:02,538] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:02,539] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:02,539] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002206625.1_ASM220662v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:02,540] [INFO] Task started: Blastn
[2024-01-24 15:19:02,540] [INFO] Running command: blastn -query GCF_002206625.1_ASM220662v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc2c1351-847a-4c1d-a954-7b4a7c7ec8a4/dqc_reference/reference_markers_gtdb.fasta -out GCF_002206625.1_ASM220662v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:03,386] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:03,390] [INFO] Selected 11 target genomes.
[2024-01-24 15:19:03,390] [INFO] Target genome list was writen to GCF_002206625.1_ASM220662v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:03,401] [INFO] Task started: fastANI
[2024-01-24 15:19:03,402] [INFO] Running command: fastANI --query /var/lib/cwl/stg28eec2fe-fd7d-40a4-be4a-773e1f265835/GCF_002206625.1_ASM220662v1_genomic.fna.gz --refList GCF_002206625.1_ASM220662v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002206625.1_ASM220662v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:08,618] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:08,628] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:08,628] [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_002206625.1	s__Polynucleobacter campilacus	100.0	655	655	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_018881635.1	s__Polynucleobacter sp018881635	92.8513	586	655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882155.1	s__Polynucleobacter sp018882155	85.2263	541	655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903900805.1	s__Polynucleobacter sp903900805	85.1581	470	655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903909925.1	s__Polynucleobacter sp903909925	84.6976	346	655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881855.1	s__Polynucleobacter sp018881855	83.3576	485	655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882465.1	s__Polynucleobacter sp018882465	83.3239	474	655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903995005.1	s__Polynucleobacter sp903995005	83.3153	308	655	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	83.2758	472	655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900096755.1	s__Polynucleobacter necessarius_K	80.7949	317	655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903843235.1	s__Polynucleobacter sp903843235	79.2784	201	655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.64	99.31	0.88	0.84	5	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:08,630] [INFO] GTDB search result was written to GCF_002206625.1_ASM220662v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:08,631] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:08,635] [INFO] DFAST_QC result json was written to GCF_002206625.1_ASM220662v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:08,636] [INFO] DFAST_QC completed!
[2024-01-24 15:19:08,636] [INFO] Total running time: 0h0m42s