[2023-06-19 02:25:26,307] [INFO] DFAST_QC pipeline started.
[2023-06-19 02:25:26,311] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 02:25:26,312] [INFO] DQC Reference Directory: /var/lib/cwl/stg9922a993-719c-41fc-8061-6a0c89562623/dqc_reference
[2023-06-19 02:25:28,476] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 02:25:28,477] [INFO] Task started: Prodigal
[2023-06-19 02:25:28,478] [INFO] Running command: gunzip -c /var/lib/cwl/stg64d1bdbf-34ad-4de8-8783-c73e78c6b7c4/GCA_915062845.1_SRR1045093_bin.2_metaWRAP_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_915062845.1_SRR1045093_bin.2_metaWRAP_v1.1_MAG_genomic.fna/cds.fna -a GCA_915062845.1_SRR1045093_bin.2_metaWRAP_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 02:25:32,922] [INFO] Task succeeded: Prodigal
[2023-06-19 02:25:32,922] [INFO] Task started: HMMsearch
[2023-06-19 02:25:32,922] [INFO] Running command: hmmsearch --tblout GCA_915062845.1_SRR1045093_bin.2_metaWRAP_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9922a993-719c-41fc-8061-6a0c89562623/dqc_reference/reference_markers.hmm GCA_915062845.1_SRR1045093_bin.2_metaWRAP_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-19 02:25:33,150] [INFO] Task succeeded: HMMsearch
[2023-06-19 02:25:33,151] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg64d1bdbf-34ad-4de8-8783-c73e78c6b7c4/GCA_915062845.1_SRR1045093_bin.2_metaWRAP_v1.1_MAG_genomic.fna.gz]
[2023-06-19 02:25:33,169] [INFO] Query marker FASTA was written to GCA_915062845.1_SRR1045093_bin.2_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-19 02:25:33,169] [INFO] Task started: Blastn
[2023-06-19 02:25:33,169] [INFO] Running command: blastn -query GCA_915062845.1_SRR1045093_bin.2_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9922a993-719c-41fc-8061-6a0c89562623/dqc_reference/reference_markers.fasta -out GCA_915062845.1_SRR1045093_bin.2_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:25:33,796] [INFO] Task succeeded: Blastn
[2023-06-19 02:25:33,800] [INFO] Selected 15 target genomes.
[2023-06-19 02:25:33,800] [INFO] Target genome list was writen to GCA_915062845.1_SRR1045093_bin.2_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-19 02:25:33,803] [INFO] Task started: fastANI
[2023-06-19 02:25:33,803] [INFO] Running command: fastANI --query /var/lib/cwl/stg64d1bdbf-34ad-4de8-8783-c73e78c6b7c4/GCA_915062845.1_SRR1045093_bin.2_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_915062845.1_SRR1045093_bin.2_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_915062845.1_SRR1045093_bin.2_metaWRAP_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 02:25:41,856] [INFO] Task succeeded: fastANI
[2023-06-19 02:25:41,857] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9922a993-719c-41fc-8061-6a0c89562623/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 02:25:41,857] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9922a993-719c-41fc-8061-6a0c89562623/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 02:25:41,870] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2023-06-19 02:25:41,870] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-06-19 02:25:41,870] [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
Kingella oralis	strain=ATCC 51147	GCA_000160435.1	505	505	type	True	95.5446	382	407	95	inconclusive
Kingella oralis	strain=DSM 18271	GCA_014054985.1	505	505	type	True	95.4518	384	407	95	inconclusive
Kingella bonacorsii	strain=Marseille-Q4569	GCA_016623605.1	2796361	2796361	type	True	95.366	384	407	95	inconclusive
Neisseria bacilliformis	strain=DSM 23338	GCA_014055025.1	267212	267212	type	True	78.5977	167	407	95	below_threshold
Neisseria bacilliformis	strain=ATCC BAA-1200	GCA_000194925.1	267212	267212	type	True	78.5846	166	407	95	below_threshold
Kingella denitrificans	strain=FDAARGOS_1060	GCA_016127355.1	502	502	type	True	78.5673	168	407	95	below_threshold
Kingella denitrificans	strain=ATCC 33394	GCA_000190695.1	502	502	type	True	78.5442	167	407	95	below_threshold
Kingella potus	strain=NCTC13336	GCA_900451175.1	265175	265175	type	True	77.8389	141	407	95	below_threshold
Kingella potus	strain=3/SID/1128	GCA_022870985.1	265175	265175	type	True	77.8344	143	407	95	below_threshold
Alysiella crassa	strain=S6	GCA_022871045.1	153491	153491	type	True	77.5484	165	407	95	below_threshold
Alysiella crassa	strain=DSM 2578	GCA_000745955.1	153491	153491	type	True	77.5145	162	407	95	below_threshold
Uruburuella suis	strain=DSM 17474	GCA_004341385.1	252130	252130	type	True	77.362	118	407	95	below_threshold
Uruburuella suis	strain=1258/02	GCA_022870845.1	252130	252130	type	True	77.3432	121	407	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	76.9927	100	407	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	76.8108	102	407	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 02:25:41,872] [INFO] DFAST Taxonomy check result was written to GCA_915062845.1_SRR1045093_bin.2_metaWRAP_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-19 02:25:41,873] [INFO] ===== Taxonomy check completed =====
[2023-06-19 02:25:41,873] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 02:25:41,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9922a993-719c-41fc-8061-6a0c89562623/dqc_reference/checkm_data
[2023-06-19 02:25:41,875] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 02:25:41,895] [INFO] Task started: CheckM
[2023-06-19 02:25:41,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_915062845.1_SRR1045093_bin.2_metaWRAP_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_915062845.1_SRR1045093_bin.2_metaWRAP_v1.1_MAG_genomic.fna/checkm_input GCA_915062845.1_SRR1045093_bin.2_metaWRAP_v1.1_MAG_genomic.fna/checkm_result
[2023-06-19 02:26:00,789] [INFO] Task succeeded: CheckM
[2023-06-19 02:26:00,790] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 02:26:00,805] [INFO] ===== Completeness check finished =====
[2023-06-19 02:26:00,806] [INFO] ===== Start GTDB Search =====
[2023-06-19 02:26:00,806] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_915062845.1_SRR1045093_bin.2_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-19 02:26:00,806] [INFO] Task started: Blastn
[2023-06-19 02:26:00,806] [INFO] Running command: blastn -query GCA_915062845.1_SRR1045093_bin.2_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9922a993-719c-41fc-8061-6a0c89562623/dqc_reference/reference_markers_gtdb.fasta -out GCA_915062845.1_SRR1045093_bin.2_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:26:01,682] [INFO] Task succeeded: Blastn
[2023-06-19 02:26:01,685] [INFO] Selected 16 target genomes.
[2023-06-19 02:26:01,685] [INFO] Target genome list was writen to GCA_915062845.1_SRR1045093_bin.2_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 02:26:01,696] [INFO] Task started: fastANI
[2023-06-19 02:26:01,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg64d1bdbf-34ad-4de8-8783-c73e78c6b7c4/GCA_915062845.1_SRR1045093_bin.2_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_915062845.1_SRR1045093_bin.2_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_915062845.1_SRR1045093_bin.2_metaWRAP_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 02:26:09,270] [INFO] Task succeeded: fastANI
[2023-06-19 02:26:09,284] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 02:26:09,284] [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_014054985.1	s__Kingella_B oralis	95.5062	383	407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_B	95.0	98.22	96.45	0.95	0.91	3	conclusive
GCA_905373195.1	s__Kingella_B oralis_A	90.1299	247	407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014055025.1	s__Neisseria bacilliformis	78.587	168	407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.33	96.96	0.94	0.89	4	-
GCF_000190695.1	s__Kingella_A denitrificans	78.5339	168	407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_A	95.0	98.63	96.04	0.97	0.93	4	-
GCF_900451175.1	s__Neisseria potus	77.8621	140	407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237445.1	s__Neisseria sp002237445	77.8266	141	407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.69	99.69	0.98	0.98	2	-
GCF_014054525.1	s__Alysiella filiformis	77.7284	160	407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella	95.0	99.98	99.98	1.00	1.00	2	-
GCA_905372165.1	s__CAJPNX01 sp905372165	77.5851	168	407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__CAJPNX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000751855.1	s__Kingella negevensis	77.5483	162	407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella	95.0	99.09	98.48	0.96	0.94	3	-
GCF_000745955.1	s__Alysiella crassa	77.4544	161	407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella	95.0	99.94	99.94	0.99	0.99	2	-
GCF_900187105.1	s__Eikenella corrodens	77.3721	111	407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	96.96	95.30	0.90	0.87	23	-
GCF_001648355.1	s__Eikenella longinqua	77.3193	135	407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990355.1	s__Eikenella corrodens_B	77.2371	128	407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014054725.1	s__Conchiformibius steedae	77.1505	122	407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Conchiformibius	95.0	98.09	96.18	0.94	0.87	3	-
GCF_000226875.1	s__Eikenella shayeganii	76.8301	102	407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	96.47	96.47	0.85	0.85	2	-
GCF_002108505.1	s__Neisseria dumasiana	76.773	102	407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.54	97.26	0.91	0.89	4	-
--------------------------------------------------------------------------------
[2023-06-19 02:26:09,286] [INFO] GTDB search result was written to GCA_915062845.1_SRR1045093_bin.2_metaWRAP_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-19 02:26:09,287] [INFO] ===== GTDB Search completed =====
[2023-06-19 02:26:09,290] [INFO] DFAST_QC result json was written to GCA_915062845.1_SRR1045093_bin.2_metaWRAP_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-19 02:26:09,291] [INFO] DFAST_QC completed!
[2023-06-19 02:26:09,291] [INFO] Total running time: 0h0m43s