[2024-01-24 13:49:00,191] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:00,193] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:00,194] [INFO] DQC Reference Directory: /var/lib/cwl/stg32cca12e-30e3-4bb1-ade4-1d00cff77549/dqc_reference
[2024-01-24 13:49:01,503] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,504] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,505] [INFO] Running command: gunzip -c /var/lib/cwl/stg513c8200-cb4b-4008-a2da-22f355cd4c28/GCF_010669225.1_ASM1066922v1_genomic.fna.gz | prodigal -d GCF_010669225.1_ASM1066922v1_genomic.fna/cds.fna -a GCF_010669225.1_ASM1066922v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:06,143] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:06,144] [INFO] Task started: HMMsearch
[2024-01-24 13:49:06,144] [INFO] Running command: hmmsearch --tblout GCF_010669225.1_ASM1066922v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32cca12e-30e3-4bb1-ade4-1d00cff77549/dqc_reference/reference_markers.hmm GCF_010669225.1_ASM1066922v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:06,390] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:06,391] [INFO] Found 6/6 markers.
[2024-01-24 13:49:06,418] [INFO] Query marker FASTA was written to GCF_010669225.1_ASM1066922v1_genomic.fna/markers.fasta
[2024-01-24 13:49:06,418] [INFO] Task started: Blastn
[2024-01-24 13:49:06,418] [INFO] Running command: blastn -query GCF_010669225.1_ASM1066922v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32cca12e-30e3-4bb1-ade4-1d00cff77549/dqc_reference/reference_markers.fasta -out GCF_010669225.1_ASM1066922v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:07,002] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:07,005] [INFO] Selected 15 target genomes.
[2024-01-24 13:49:07,006] [INFO] Target genome list was writen to GCF_010669225.1_ASM1066922v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:07,052] [INFO] Task started: fastANI
[2024-01-24 13:49:07,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg513c8200-cb4b-4008-a2da-22f355cd4c28/GCF_010669225.1_ASM1066922v1_genomic.fna.gz --refList GCF_010669225.1_ASM1066922v1_genomic.fna/target_genomes.txt --output GCF_010669225.1_ASM1066922v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:14,262] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:14,262] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32cca12e-30e3-4bb1-ade4-1d00cff77549/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:14,263] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32cca12e-30e3-4bb1-ade4-1d00cff77549/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:14,270] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:14,270] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:14,270] [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
Megamonas funiformis	strain=JCM 14723	GCA_010669225.1	437897	437897	type	True	100.0	855	855	95	conclusive
Megamonas funiformis	strain=YIT 11815	GCA_000245775.1	437897	437897	type	True	99.8963	842	855	95	conclusive
Megamonas hypermegale	strain=NCTC10570	GCA_900187035.1	158847	158847	type	True	82.0292	458	855	95	below_threshold
Megamonas hypermegale	strain=DSM 1672	GCA_000423385.1	158847	158847	type	True	81.5423	437	855	95	below_threshold
Pectinatus sottacetonis	strain=MB620	GCA_015732155.1	1002795	1002795	type	True	77.3888	81	855	95	below_threshold
Pectinatus brassicae	strain=DSM 24661	GCA_014201835.1	862415	862415	type	True	77.093	82	855	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:14,272] [INFO] DFAST Taxonomy check result was written to GCF_010669225.1_ASM1066922v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:14,273] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:14,273] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:14,273] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32cca12e-30e3-4bb1-ade4-1d00cff77549/dqc_reference/checkm_data
[2024-01-24 13:49:14,274] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:14,302] [INFO] Task started: CheckM
[2024-01-24 13:49:14,302] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010669225.1_ASM1066922v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010669225.1_ASM1066922v1_genomic.fna/checkm_input GCF_010669225.1_ASM1066922v1_genomic.fna/checkm_result
[2024-01-24 13:49:35,439] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:35,440] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:35,470] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:35,471] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:35,472] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010669225.1_ASM1066922v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:35,472] [INFO] Task started: Blastn
[2024-01-24 13:49:35,472] [INFO] Running command: blastn -query GCF_010669225.1_ASM1066922v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32cca12e-30e3-4bb1-ade4-1d00cff77549/dqc_reference/reference_markers_gtdb.fasta -out GCF_010669225.1_ASM1066922v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:36,179] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:36,184] [INFO] Selected 21 target genomes.
[2024-01-24 13:49:36,184] [INFO] Target genome list was writen to GCF_010669225.1_ASM1066922v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:36,226] [INFO] Task started: fastANI
[2024-01-24 13:49:36,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg513c8200-cb4b-4008-a2da-22f355cd4c28/GCF_010669225.1_ASM1066922v1_genomic.fna.gz --refList GCF_010669225.1_ASM1066922v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010669225.1_ASM1066922v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:44,040] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:44,052] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:44,052] [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_010669225.1	s__Megamonas funiformis	100.0	855	855	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Megamonas	95.0	97.89	97.23	0.89	0.80	26	conclusive
GCA_900556715.1	s__Megamonas sp900556715	93.1405	279	855	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Megamonas	95.0	99.82	99.65	0.90	0.83	3	-
GCF_900187035.1	s__Megamonas hypermegale	82.03	457	855	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Megamonas	95.0	98.37	97.31	0.90	0.84	6	-
GCA_002314325.1	s__Megamonas hypermegale_A	79.2988	187	855	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Megamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554895.1	s__Megamonas gallistercoris	78.1482	187	855	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Megamonas	95.0	98.29	98.29	0.76	0.76	2	-
GCA_902363205.1	s__CABIZH01 sp902363205	77.6514	64	855	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Massilibacillaceae;g__CABIZH01	95.0	97.61	97.54	0.87	0.81	4	-
GCF_015732155.1	s__Pectinatus sottacetonis	77.3632	80	855	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Pectinatus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:44,054] [INFO] GTDB search result was written to GCF_010669225.1_ASM1066922v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:44,054] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:44,057] [INFO] DFAST_QC result json was written to GCF_010669225.1_ASM1066922v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:44,057] [INFO] DFAST_QC completed!
[2024-01-24 13:49:44,057] [INFO] Total running time: 0h0m44s