[2023-06-13 10:10:45,184] [INFO] DFAST_QC pipeline started.
[2023-06-13 10:10:45,188] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 10:10:45,188] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ae20c4c-b151-4f59-9d12-a3cd5cedc838/dqc_reference
[2023-06-13 10:10:47,160] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 10:10:47,161] [INFO] Task started: Prodigal
[2023-06-13 10:10:47,162] [INFO] Running command: gunzip -c /var/lib/cwl/stgab0ee9fa-f14d-430a-a5c3-b69eb5290c6a/GCA_947449785.1_Jr-16oct17-161_genomic.fna.gz | prodigal -d GCA_947449785.1_Jr-16oct17-161_genomic.fna/cds.fna -a GCA_947449785.1_Jr-16oct17-161_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 10:10:51,755] [INFO] Task succeeded: Prodigal
[2023-06-13 10:10:51,757] [INFO] Task started: HMMsearch
[2023-06-13 10:10:51,757] [INFO] Running command: hmmsearch --tblout GCA_947449785.1_Jr-16oct17-161_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ae20c4c-b151-4f59-9d12-a3cd5cedc838/dqc_reference/reference_markers.hmm GCA_947449785.1_Jr-16oct17-161_genomic.fna/protein.faa > /dev/null
[2023-06-13 10:10:52,133] [INFO] Task succeeded: HMMsearch
[2023-06-13 10:10:52,135] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgab0ee9fa-f14d-430a-a5c3-b69eb5290c6a/GCA_947449785.1_Jr-16oct17-161_genomic.fna.gz]
[2023-06-13 10:10:52,156] [INFO] Query marker FASTA was written to GCA_947449785.1_Jr-16oct17-161_genomic.fna/markers.fasta
[2023-06-13 10:10:52,156] [INFO] Task started: Blastn
[2023-06-13 10:10:52,156] [INFO] Running command: blastn -query GCA_947449785.1_Jr-16oct17-161_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ae20c4c-b151-4f59-9d12-a3cd5cedc838/dqc_reference/reference_markers.fasta -out GCA_947449785.1_Jr-16oct17-161_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:10:52,782] [INFO] Task succeeded: Blastn
[2023-06-13 10:10:52,786] [INFO] Selected 14 target genomes.
[2023-06-13 10:10:52,786] [INFO] Target genome list was writen to GCA_947449785.1_Jr-16oct17-161_genomic.fna/target_genomes.txt
[2023-06-13 10:10:52,788] [INFO] Task started: fastANI
[2023-06-13 10:10:52,788] [INFO] Running command: fastANI --query /var/lib/cwl/stgab0ee9fa-f14d-430a-a5c3-b69eb5290c6a/GCA_947449785.1_Jr-16oct17-161_genomic.fna.gz --refList GCA_947449785.1_Jr-16oct17-161_genomic.fna/target_genomes.txt --output GCA_947449785.1_Jr-16oct17-161_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 10:10:59,038] [INFO] Task succeeded: fastANI
[2023-06-13 10:10:59,038] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ae20c4c-b151-4f59-9d12-a3cd5cedc838/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 10:10:59,039] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ae20c4c-b151-4f59-9d12-a3cd5cedc838/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 10:10:59,051] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 10:10:59,051] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 10:10:59,051] [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 finlandensis	strain=MWH-Mekk-B1	GCA_018881755.1	1855894	1855894	type	True	80.2641	311	569	95	below_threshold
Polynucleobacter corsicus	strain=AP-Melu-1000-A1	GCA_018688255.1	2081042	2081042	type	True	78.7965	191	569	95	below_threshold
Polynucleobacter aenigmaticus	strain=MWH-K35W1	GCA_002206635.1	1743164	1743164	type	True	78.7354	187	569	95	below_threshold
Polynucleobacter wuianus	strain=QLW-P1FAT50C-4	GCA_001659725.1	1743168	1743168	type	True	78.6727	210	569	95	below_threshold
Polynucleobacter hirudinilacicola	strain=MWH-EgelM1-30-B4	GCA_002192535.1	1743166	1743166	type	True	78.5433	210	569	95	below_threshold
Polynucleobacter alcilacus	strain=UK-Pondora-W15	GCA_018881545.1	1819739	1819739	type	True	78.5188	198	569	95	below_threshold
Polynucleobacter arcticus	strain=UK-Long2-W17	GCA_013307205.1	1743165	1743165	type	True	78.4625	183	569	95	below_threshold
Polynucleobacter ibericus	strain=es-MAR-2	GCA_018687955.1	1819725	1819725	type	True	78.4466	192	569	95	below_threshold
Polynucleobacter campilacus	strain=MWH-Feld-100	GCA_002206625.1	1743163	1743163	type	True	78.3055	188	569	95	below_threshold
Polynucleobacter hallstattensis	strain=MWH-Hall10	GCA_018881835.1	1855586	1855586	type	True	78.1888	194	569	95	below_threshold
Polynucleobacter tropicus	strain=MWH-UH21B	GCA_013307225.1	1743174	1743174	type	True	78.1706	179	569	95	below_threshold
Polynucleobacter bastaniensis	strain=AP-Basta-1000A-D1	GCA_018882205.1	2081039	2081039	type	True	78.1452	185	569	95	below_threshold
Polynucleobacter paludilacus	strain=MWH-Mekk-C3	GCA_018687595.1	1855895	1855895	type	True	77.8257	140	569	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 10:10:59,053] [INFO] DFAST Taxonomy check result was written to GCA_947449785.1_Jr-16oct17-161_genomic.fna/tc_result.tsv
[2023-06-13 10:10:59,054] [INFO] ===== Taxonomy check completed =====
[2023-06-13 10:10:59,054] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 10:10:59,054] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ae20c4c-b151-4f59-9d12-a3cd5cedc838/dqc_reference/checkm_data
[2023-06-13 10:10:59,055] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 10:10:59,080] [INFO] Task started: CheckM
[2023-06-13 10:10:59,080] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947449785.1_Jr-16oct17-161_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947449785.1_Jr-16oct17-161_genomic.fna/checkm_input GCA_947449785.1_Jr-16oct17-161_genomic.fna/checkm_result
[2023-06-13 10:11:20,413] [INFO] Task succeeded: CheckM
[2023-06-13 10:11:20,415] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 10:11:20,435] [INFO] ===== Completeness check finished =====
[2023-06-13 10:11:20,435] [INFO] ===== Start GTDB Search =====
[2023-06-13 10:11:20,436] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947449785.1_Jr-16oct17-161_genomic.fna/markers.fasta)
[2023-06-13 10:11:20,436] [INFO] Task started: Blastn
[2023-06-13 10:11:20,436] [INFO] Running command: blastn -query GCA_947449785.1_Jr-16oct17-161_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ae20c4c-b151-4f59-9d12-a3cd5cedc838/dqc_reference/reference_markers_gtdb.fasta -out GCA_947449785.1_Jr-16oct17-161_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:11:21,241] [INFO] Task succeeded: Blastn
[2023-06-13 10:11:21,245] [INFO] Selected 21 target genomes.
[2023-06-13 10:11:21,246] [INFO] Target genome list was writen to GCA_947449785.1_Jr-16oct17-161_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 10:11:21,255] [INFO] Task started: fastANI
[2023-06-13 10:11:21,256] [INFO] Running command: fastANI --query /var/lib/cwl/stgab0ee9fa-f14d-430a-a5c3-b69eb5290c6a/GCA_947449785.1_Jr-16oct17-161_genomic.fna.gz --refList GCA_947449785.1_Jr-16oct17-161_genomic.fna/target_genomes_gtdb.txt --output GCA_947449785.1_Jr-16oct17-161_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 10:11:29,924] [INFO] Task succeeded: fastANI
[2023-06-13 10:11:29,945] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 10:11:29,945] [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_018881755.1	s__Polynucleobacter sp903953215	80.283	310	569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.19	97.38	0.93	0.86	15	-
GCF_018881925.1	s__Polynucleobacter sp903880555	79.7743	315	569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.13	99.10	0.89	0.87	4	-
GCA_903843235.1	s__Polynucleobacter sp903843235	79.7542	249	569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.64	99.31	0.88	0.84	5	-
GCA_903858445.1	s__Polynucleobacter sp903858445	79.3667	246	569	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	78.8507	196	569	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	78.7612	198	569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882405.1	s__Polynucleobacter sp018882405	78.7056	195	569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018688235.1	s__Polynucleobacter sp018688235	78.6544	185	569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000342265.1	s__Polynucleobacter sp000342265	78.6038	199	569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882365.1	s__Polynucleobacter sp018882365	78.5843	201	569	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	78.5433	210	569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882335.1	s__Polynucleobacter sp018882335	78.538	195	569	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	78.5235	203	569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882215.1	s__Polynucleobacter sp018882215	78.4717	203	569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	95.58	95.58	0.83	0.83	2	-
GCF_018687955.1	s__Polynucleobacter sp018687955	78.4466	192	569	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	78.3874	196	569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018688495.1	s__Polynucleobacter sp018688495	78.3723	198	569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	97.81	97.81	0.94	0.94	2	-
GCF_018881835.1	s__Polynucleobacter sp018881835	78.1888	194	569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 10:11:29,947] [INFO] GTDB search result was written to GCA_947449785.1_Jr-16oct17-161_genomic.fna/result_gtdb.tsv
[2023-06-13 10:11:29,948] [INFO] ===== GTDB Search completed =====
[2023-06-13 10:11:29,952] [INFO] DFAST_QC result json was written to GCA_947449785.1_Jr-16oct17-161_genomic.fna/dqc_result.json
[2023-06-13 10:11:29,952] [INFO] DFAST_QC completed!
[2023-06-13 10:11:29,952] [INFO] Total running time: 0h0m45s