[2024-01-24 14:39:02,887] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:02,889] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:02,889] [INFO] DQC Reference Directory: /var/lib/cwl/stg6088b611-71d4-4d17-b8b6-89786ba93f86/dqc_reference
[2024-01-24 14:39:04,291] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:04,292] [INFO] Task started: Prodigal
[2024-01-24 14:39:04,292] [INFO] Running command: gunzip -c /var/lib/cwl/stg30230bc4-4395-4efe-b6a9-e4397709cab0/GCF_018881545.1_ASM1888154v1_genomic.fna.gz | prodigal -d GCF_018881545.1_ASM1888154v1_genomic.fna/cds.fna -a GCF_018881545.1_ASM1888154v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:09,292] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:09,293] [INFO] Task started: HMMsearch
[2024-01-24 14:39:09,293] [INFO] Running command: hmmsearch --tblout GCF_018881545.1_ASM1888154v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6088b611-71d4-4d17-b8b6-89786ba93f86/dqc_reference/reference_markers.hmm GCF_018881545.1_ASM1888154v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:09,506] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:09,508] [INFO] Found 6/6 markers.
[2024-01-24 14:39:09,533] [INFO] Query marker FASTA was written to GCF_018881545.1_ASM1888154v1_genomic.fna/markers.fasta
[2024-01-24 14:39:09,534] [INFO] Task started: Blastn
[2024-01-24 14:39:09,534] [INFO] Running command: blastn -query GCF_018881545.1_ASM1888154v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6088b611-71d4-4d17-b8b6-89786ba93f86/dqc_reference/reference_markers.fasta -out GCF_018881545.1_ASM1888154v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:10,865] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:10,868] [INFO] Selected 13 target genomes.
[2024-01-24 14:39:10,869] [INFO] Target genome list was writen to GCF_018881545.1_ASM1888154v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:10,906] [INFO] Task started: fastANI
[2024-01-24 14:39:10,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg30230bc4-4395-4efe-b6a9-e4397709cab0/GCF_018881545.1_ASM1888154v1_genomic.fna.gz --refList GCF_018881545.1_ASM1888154v1_genomic.fna/target_genomes.txt --output GCF_018881545.1_ASM1888154v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:16,743] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:16,743] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6088b611-71d4-4d17-b8b6-89786ba93f86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:16,743] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6088b611-71d4-4d17-b8b6-89786ba93f86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:16,790] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:16,790] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:16,790] [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 alcilacus	strain=UK-Pondora-W15	GCA_018881545.1	1819739	1819739	type	True	100.0	674	674	95	conclusive
Polynucleobacter hirudinilacicola	strain=MWH-EgelM1-30-B4	GCA_002192535.1	1743166	1743166	type	True	81.3838	413	674	95	below_threshold
Polynucleobacter parvulilacunae	strain=Ross1-W9	GCA_018881715.1	1855631	1855631	type	True	81.2133	351	674	95	below_threshold
Polynucleobacter ibericus	strain=es-MAR-2	GCA_018687955.1	1819725	1819725	type	True	80.9385	366	674	95	below_threshold
Polynucleobacter asymbioticus	strain=QLW-P1DMWA-1	GCA_000016345.1	576611	576611	type	True	80.8478	323	674	95	below_threshold
Polynucleobacter nymphae	strain=AP-Mumm-500A-B3	GCA_018882155.1	2081043	2081043	type	True	80.7617	405	674	95	below_threshold
Polynucleobacter campilacus	strain=MWH-Feld-100	GCA_002206625.1	1743163	1743163	type	True	80.6761	390	674	95	below_threshold
Polynucleobacter yangtzensis	strain=MWH-JaK3	GCA_001595965.1	1743159	1743159	type	True	80.6587	363	674	95	below_threshold
Polynucleobacter wuianus	strain=QLW-P1FAT50C-4	GCA_001659725.1	1743168	1743168	type	True	80.5203	354	674	95	below_threshold
Polynucleobacter finlandensis	strain=MWH-Mekk-B1	GCA_018881755.1	1855894	1855894	type	True	80.0359	318	674	95	below_threshold
Polynucleobacter tropicus	strain=MWH-UH21B	GCA_013307225.1	1743174	1743174	type	True	79.6899	301	674	95	below_threshold
Polynucleobacter meluiroseus	strain=AP-Melu-1000-B4	GCA_900205755.1	1938814	1938814	type	True	79.4777	191	674	95	below_threshold
Polynucleobacter paneuropaeus	strain=MG-25-Pas1-D2	GCA_003261235.1	2527775	2527775	type	True	79.3421	231	674	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:16,793] [INFO] DFAST Taxonomy check result was written to GCF_018881545.1_ASM1888154v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:16,793] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:16,794] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:16,794] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6088b611-71d4-4d17-b8b6-89786ba93f86/dqc_reference/checkm_data
[2024-01-24 14:39:16,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:16,823] [INFO] Task started: CheckM
[2024-01-24 14:39:16,823] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018881545.1_ASM1888154v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018881545.1_ASM1888154v1_genomic.fna/checkm_input GCF_018881545.1_ASM1888154v1_genomic.fna/checkm_result
[2024-01-24 14:39:40,817] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:40,818] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:40,842] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:40,843] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:40,843] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018881545.1_ASM1888154v1_genomic.fna/markers.fasta)
[2024-01-24 14:39:40,843] [INFO] Task started: Blastn
[2024-01-24 14:39:40,843] [INFO] Running command: blastn -query GCF_018881545.1_ASM1888154v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6088b611-71d4-4d17-b8b6-89786ba93f86/dqc_reference/reference_markers_gtdb.fasta -out GCF_018881545.1_ASM1888154v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:41,780] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:41,784] [INFO] Selected 18 target genomes.
[2024-01-24 14:39:41,784] [INFO] Target genome list was writen to GCF_018881545.1_ASM1888154v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:41,797] [INFO] Task started: fastANI
[2024-01-24 14:39:41,797] [INFO] Running command: fastANI --query /var/lib/cwl/stg30230bc4-4395-4efe-b6a9-e4397709cab0/GCF_018881545.1_ASM1888154v1_genomic.fna.gz --refList GCF_018881545.1_ASM1888154v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018881545.1_ASM1888154v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:39:49,862] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:49,888] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:39:49,888] [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_018881545.1	s__Polynucleobacter sp018881545	100.0	674	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903843315.1	s__Polynucleobacter sp903843315	86.5787	432	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.21	99.08	0.85	0.77	17	-
GCF_002192535.1	s__Polynucleobacter hirudinilacicola	81.4008	412	674	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	81.3182	411	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881715.1	s__Polynucleobacter sp018881715	81.2133	351	674	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	81.1879	266	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882245.1	s__Polynucleobacter sp018882245	80.9885	335	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687955.1	s__Polynucleobacter sp018687955	80.9385	366	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018688315.1	s__Polynucleobacter sp018688315	80.9001	361	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687815.1	s__Polynucleobacter sp018687815	80.8636	364	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881635.1	s__Polynucleobacter sp018881635	80.8523	389	674	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	80.7617	405	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687355.1	s__Polynucleobacter sp018687355	80.7246	370	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002206625.1	s__Polynucleobacter campilacus	80.6761	390	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001659725.1	s__Polynucleobacter wuianus	80.5101	355	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.91	97.82	0.95	0.89	3	-
GCA_903900805.1	s__Polynucleobacter sp903900805	80.3362	346	674	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	79.9672	267	674	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900205755.1	s__Polynucleobacter meluiroseus	79.4642	192	674	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 14:39:49,890] [INFO] GTDB search result was written to GCF_018881545.1_ASM1888154v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:39:49,891] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:39:49,895] [INFO] DFAST_QC result json was written to GCF_018881545.1_ASM1888154v1_genomic.fna/dqc_result.json
[2024-01-24 14:39:49,895] [INFO] DFAST_QC completed!
[2024-01-24 14:39:49,895] [INFO] Total running time: 0h0m47s