[2023-06-29 21:39:35,466] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:39:35,470] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:39:35,470] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f63819f-cdc6-431a-b022-4eeba2978deb/dqc_reference
[2023-06-29 21:39:36,648] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:39:36,649] [INFO] Task started: Prodigal
[2023-06-29 21:39:36,649] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1f04785-8b1c-47e4-bf25-06873b87a333/GCA_946482005.1_SRR12181053_bin.8_metawrap_v1.3.0_MAG_genomic.fna.gz | prodigal -d GCA_946482005.1_SRR12181053_bin.8_metawrap_v1.3.0_MAG_genomic.fna/cds.fna -a GCA_946482005.1_SRR12181053_bin.8_metawrap_v1.3.0_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:39:41,040] [INFO] Task succeeded: Prodigal
[2023-06-29 21:39:41,040] [INFO] Task started: HMMsearch
[2023-06-29 21:39:41,040] [INFO] Running command: hmmsearch --tblout GCA_946482005.1_SRR12181053_bin.8_metawrap_v1.3.0_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f63819f-cdc6-431a-b022-4eeba2978deb/dqc_reference/reference_markers.hmm GCA_946482005.1_SRR12181053_bin.8_metawrap_v1.3.0_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:39:41,247] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:39:41,248] [INFO] Found 6/6 markers.
[2023-06-29 21:39:41,269] [INFO] Query marker FASTA was written to GCA_946482005.1_SRR12181053_bin.8_metawrap_v1.3.0_MAG_genomic.fna/markers.fasta
[2023-06-29 21:39:41,270] [INFO] Task started: Blastn
[2023-06-29 21:39:41,270] [INFO] Running command: blastn -query GCA_946482005.1_SRR12181053_bin.8_metawrap_v1.3.0_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f63819f-cdc6-431a-b022-4eeba2978deb/dqc_reference/reference_markers.fasta -out GCA_946482005.1_SRR12181053_bin.8_metawrap_v1.3.0_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:39:41,929] [INFO] Task succeeded: Blastn
[2023-06-29 21:39:41,933] [INFO] Selected 11 target genomes.
[2023-06-29 21:39:41,933] [INFO] Target genome list was writen to GCA_946482005.1_SRR12181053_bin.8_metawrap_v1.3.0_MAG_genomic.fna/target_genomes.txt
[2023-06-29 21:39:41,935] [INFO] Task started: fastANI
[2023-06-29 21:39:41,935] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1f04785-8b1c-47e4-bf25-06873b87a333/GCA_946482005.1_SRR12181053_bin.8_metawrap_v1.3.0_MAG_genomic.fna.gz --refList GCA_946482005.1_SRR12181053_bin.8_metawrap_v1.3.0_MAG_genomic.fna/target_genomes.txt --output GCA_946482005.1_SRR12181053_bin.8_metawrap_v1.3.0_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:39:49,369] [INFO] Task succeeded: fastANI
[2023-06-29 21:39:49,369] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f63819f-cdc6-431a-b022-4eeba2978deb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:39:49,370] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f63819f-cdc6-431a-b022-4eeba2978deb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:39:49,376] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:39:49,376] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 21:39:49,376] [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
Gilliamella apicola	strain=wkB1	GCA_000599985.1	1196095	1196095	suspected-type	True	89.8024	571	819	95	below_threshold
Gilliamella apicola	strain=DSM 104097	GCA_003201455.1	1196095	1196095	suspected-type	True	89.7254	557	819	95	below_threshold
Gilliamella apis	strain=NO3	GCA_002142155.1	1970738	1970738	type	True	82.9895	460	819	95	below_threshold
Gilliamella bombicola	strain=R-53248	GCA_900094945.1	1798182	1798182	type	True	79.8694	352	819	95	below_threshold
Gilliamella intestini	strain=R-53144	GCA_900094935.1	1798183	1798183	type	True	79.608	334	819	95	below_threshold
Frischella japonica	strain=Ac13	GCA_014489845.1	2741544	2741544	type	True	77.5687	159	819	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 21:39:49,378] [INFO] DFAST Taxonomy check result was written to GCA_946482005.1_SRR12181053_bin.8_metawrap_v1.3.0_MAG_genomic.fna/tc_result.tsv
[2023-06-29 21:39:49,378] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:39:49,379] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:39:49,379] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f63819f-cdc6-431a-b022-4eeba2978deb/dqc_reference/checkm_data
[2023-06-29 21:39:49,380] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:39:49,404] [INFO] Task started: CheckM
[2023-06-29 21:39:49,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_946482005.1_SRR12181053_bin.8_metawrap_v1.3.0_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_946482005.1_SRR12181053_bin.8_metawrap_v1.3.0_MAG_genomic.fna/checkm_input GCA_946482005.1_SRR12181053_bin.8_metawrap_v1.3.0_MAG_genomic.fna/checkm_result
[2023-06-29 21:40:09,110] [INFO] Task succeeded: CheckM
[2023-06-29 21:40:09,111] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 21:40:09,128] [INFO] ===== Completeness check finished =====
[2023-06-29 21:40:09,129] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:40:09,129] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_946482005.1_SRR12181053_bin.8_metawrap_v1.3.0_MAG_genomic.fna/markers.fasta)
[2023-06-29 21:40:09,129] [INFO] Task started: Blastn
[2023-06-29 21:40:09,129] [INFO] Running command: blastn -query GCA_946482005.1_SRR12181053_bin.8_metawrap_v1.3.0_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f63819f-cdc6-431a-b022-4eeba2978deb/dqc_reference/reference_markers_gtdb.fasta -out GCA_946482005.1_SRR12181053_bin.8_metawrap_v1.3.0_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:40:10,138] [INFO] Task succeeded: Blastn
[2023-06-29 21:40:10,142] [INFO] Selected 16 target genomes.
[2023-06-29 21:40:10,142] [INFO] Target genome list was writen to GCA_946482005.1_SRR12181053_bin.8_metawrap_v1.3.0_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:40:10,155] [INFO] Task started: fastANI
[2023-06-29 21:40:10,156] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1f04785-8b1c-47e4-bf25-06873b87a333/GCA_946482005.1_SRR12181053_bin.8_metawrap_v1.3.0_MAG_genomic.fna.gz --refList GCA_946482005.1_SRR12181053_bin.8_metawrap_v1.3.0_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_946482005.1_SRR12181053_bin.8_metawrap_v1.3.0_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:40:18,704] [INFO] Task succeeded: fastANI
[2023-06-29 21:40:18,717] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 21:40:18,717] [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_001693435.1	s__Gilliamella apicola_N	92.156	562	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	97.54	96.32	0.92	0.89	19	-
GCF_000599985.1	s__Gilliamella apicola	89.8024	571	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	98.05	97.62	0.94	0.91	21	-
GCF_003202915.1	s__Gilliamella apicola_Q	88.4989	596	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	95.60	95.60	0.89	0.89	2	-
GCF_002142215.1	s__Gilliamella sp002142215	84.1279	496	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	97.95	96.09	0.93	0.88	3	-
GCF_002142155.1	s__Gilliamella apis	82.9809	461	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	98.52	97.64	0.94	0.89	26	-
GCF_003202775.1	s__Gilliamella apis_A	82.2019	498	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	98.23	95.38	0.94	0.89	9	-
GCF_001693745.1	s__Gilliamella apicola_E	81.9246	452	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	97.90	97.90	0.90	0.90	2	-
GCF_001693755.1	s__Gilliamella apicola_F	79.9626	385	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	98.98	98.98	0.93	0.93	2	-
GCF_900103255.1	s__Gilliamella bombi	79.8854	353	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	97.07	95.43	0.85	0.80	12	-
GCF_900094945.1	s__Gilliamella bombicola	79.8754	352	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	98.14	97.05	0.94	0.93	3	-
GCF_900103085.1	s__Gilliamella mensalis	79.7688	337	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900094935.1	s__Gilliamella intestini	79.6227	333	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001690525.1	s__Gilliamella apicola_H	79.5321	346	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	95.50	95.50	0.87	0.87	2	-
GCF_001690275.1	s__Gilliamella apicola_C	79.3714	348	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	97.79	96.31	0.88	0.82	9	-
GCF_001690195.1	s__Gilliamella apicola_L	79.1643	351	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 21:40:18,719] [INFO] GTDB search result was written to GCA_946482005.1_SRR12181053_bin.8_metawrap_v1.3.0_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 21:40:18,720] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:40:18,723] [INFO] DFAST_QC result json was written to GCA_946482005.1_SRR12181053_bin.8_metawrap_v1.3.0_MAG_genomic.fna/dqc_result.json
[2023-06-29 21:40:18,723] [INFO] DFAST_QC completed!
[2023-06-29 21:40:18,723] [INFO] Total running time: 0h0m43s