[2024-01-24 11:06:04,661] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:06:04,662] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:06:04,662] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4ca2821-ad1f-4f2f-b04f-893e35ccdd02/dqc_reference
[2024-01-24 11:06:07,010] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:06:07,011] [INFO] Task started: Prodigal
[2024-01-24 11:06:07,011] [INFO] Running command: gunzip -c /var/lib/cwl/stg53416a15-1cb0-4677-a130-961cd69e2748/GCF_003072505.1_ASM307250v1_genomic.fna.gz | prodigal -d GCF_003072505.1_ASM307250v1_genomic.fna/cds.fna -a GCF_003072505.1_ASM307250v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:06:13,675] [INFO] Task succeeded: Prodigal
[2024-01-24 11:06:13,676] [INFO] Task started: HMMsearch
[2024-01-24 11:06:13,676] [INFO] Running command: hmmsearch --tblout GCF_003072505.1_ASM307250v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4ca2821-ad1f-4f2f-b04f-893e35ccdd02/dqc_reference/reference_markers.hmm GCF_003072505.1_ASM307250v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:06:13,937] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:06:13,938] [INFO] Found 6/6 markers.
[2024-01-24 11:06:13,965] [INFO] Query marker FASTA was written to GCF_003072505.1_ASM307250v1_genomic.fna/markers.fasta
[2024-01-24 11:06:13,965] [INFO] Task started: Blastn
[2024-01-24 11:06:13,965] [INFO] Running command: blastn -query GCF_003072505.1_ASM307250v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4ca2821-ad1f-4f2f-b04f-893e35ccdd02/dqc_reference/reference_markers.fasta -out GCF_003072505.1_ASM307250v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:14,560] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:14,564] [INFO] Selected 19 target genomes.
[2024-01-24 11:06:14,565] [INFO] Target genome list was writen to GCF_003072505.1_ASM307250v1_genomic.fna/target_genomes.txt
[2024-01-24 11:06:14,590] [INFO] Task started: fastANI
[2024-01-24 11:06:14,591] [INFO] Running command: fastANI --query /var/lib/cwl/stg53416a15-1cb0-4677-a130-961cd69e2748/GCF_003072505.1_ASM307250v1_genomic.fna.gz --refList GCF_003072505.1_ASM307250v1_genomic.fna/target_genomes.txt --output GCF_003072505.1_ASM307250v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:23,292] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:23,293] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4ca2821-ad1f-4f2f-b04f-893e35ccdd02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:23,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4ca2821-ad1f-4f2f-b04f-893e35ccdd02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:23,302] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:23,303] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:23,303] [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 rarus	strain=MT-CBb6A5	GCA_003072505.1	556055	556055	type	True	100.0	1051	1052	95	conclusive
Polynucleobacter kasalickyi	strain=VK13	GCA_900176405.1	1938817	1938817	type	True	80.2847	555	1052	95	below_threshold
Polynucleobacter victoriensis	strain=MWH-VicM1	GCA_900187875.1	2049319	2049319	type	True	77.6271	54	1052	95	below_threshold
Polynucleobacter corsicus	strain=AP-Melu-1000-A1	GCA_018688255.1	2081042	2081042	type	True	77.5169	53	1052	95	below_threshold
Polynucleobacter paludilacus	strain=MWH-Mekk-C3	GCA_018687595.1	1855895	1855895	type	True	77.1383	50	1052	95	below_threshold
Polynucleobacter hirudinilacicola	strain=MWH-EgelM1-30-B4	GCA_002192535.1	1743166	1743166	type	True	77.0935	52	1052	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:23,304] [INFO] DFAST Taxonomy check result was written to GCF_003072505.1_ASM307250v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:23,305] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:23,305] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:23,305] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4ca2821-ad1f-4f2f-b04f-893e35ccdd02/dqc_reference/checkm_data
[2024-01-24 11:06:23,306] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:23,340] [INFO] Task started: CheckM
[2024-01-24 11:06:23,340] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003072505.1_ASM307250v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003072505.1_ASM307250v1_genomic.fna/checkm_input GCF_003072505.1_ASM307250v1_genomic.fna/checkm_result
[2024-01-24 11:06:49,106] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:49,108] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:49,125] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:49,126] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:49,126] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003072505.1_ASM307250v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:49,126] [INFO] Task started: Blastn
[2024-01-24 11:06:49,126] [INFO] Running command: blastn -query GCF_003072505.1_ASM307250v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4ca2821-ad1f-4f2f-b04f-893e35ccdd02/dqc_reference/reference_markers_gtdb.fasta -out GCF_003072505.1_ASM307250v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:49,883] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:49,887] [INFO] Selected 18 target genomes.
[2024-01-24 11:06:49,887] [INFO] Target genome list was writen to GCF_003072505.1_ASM307250v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:49,919] [INFO] Task started: fastANI
[2024-01-24 11:06:49,919] [INFO] Running command: fastANI --query /var/lib/cwl/stg53416a15-1cb0-4677-a130-961cd69e2748/GCF_003072505.1_ASM307250v1_genomic.fna.gz --refList GCF_003072505.1_ASM307250v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003072505.1_ASM307250v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:59,025] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:59,042] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:59,042] [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_003072505.1	s__Polynucleobacter rarus	100.0	1051	1052	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_903889595.1	s__Polynucleobacter sp903889595	86.1441	641	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.49	99.49	0.84	0.84	2	-
GCF_900176405.1	s__Polynucleobacter sp900176405	80.2948	554	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.69	98.69	0.92	0.91	3	-
GCF_018688095.1	s__Polynucleobacter sp018688095	77.7224	52	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881655.1	s__Polynucleobacter sp001889925	77.6653	56	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	96.71	95.84	0.78	0.66	4	-
GCA_903867305.1	s__Polynucleobacter sp903867305	77.4821	137	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.81	99.77	0.91	0.90	6	-
GCF_018882405.1	s__Polynucleobacter sp018882405	77.4165	50	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903821995.1	s__Polynucleobacter sp903821995	77.4043	82	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.83	99.77	0.91	0.85	9	-
GCA_903871735.1	s__Polynucleobacter sp903871735	76.9991	101	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903875135.1	s__Polynucleobacter sp903875135	76.947	122	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.93	99.91	0.96	0.95	4	-
GCA_009927445.1	s__Polynucleobacter sp009927445	76.6001	112	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.27	99.27	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:59,043] [INFO] GTDB search result was written to GCF_003072505.1_ASM307250v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:59,043] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:59,046] [INFO] DFAST_QC result json was written to GCF_003072505.1_ASM307250v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:59,046] [INFO] DFAST_QC completed!
[2024-01-24 11:06:59,046] [INFO] Total running time: 0h0m54s