[2023-06-29 14:42:13,534] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:42:13,536] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:42:13,536] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f452bd3-44c9-4719-b629-d665f759c551/dqc_reference
[2023-06-29 14:42:14,841] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:42:14,842] [INFO] Task started: Prodigal
[2023-06-29 14:42:14,842] [INFO] Running command: gunzip -c /var/lib/cwl/stg03b45e20-a84a-4dcb-8a44-039d87863768/GCA_910586795.1_MGBC140579_genomic.fna.gz | prodigal -d GCA_910586795.1_MGBC140579_genomic.fna/cds.fna -a GCA_910586795.1_MGBC140579_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:42:22,392] [INFO] Task succeeded: Prodigal
[2023-06-29 14:42:22,393] [INFO] Task started: HMMsearch
[2023-06-29 14:42:22,393] [INFO] Running command: hmmsearch --tblout GCA_910586795.1_MGBC140579_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f452bd3-44c9-4719-b629-d665f759c551/dqc_reference/reference_markers.hmm GCA_910586795.1_MGBC140579_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:42:22,649] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:42:22,650] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg03b45e20-a84a-4dcb-8a44-039d87863768/GCA_910586795.1_MGBC140579_genomic.fna.gz]
[2023-06-29 14:42:22,677] [INFO] Query marker FASTA was written to GCA_910586795.1_MGBC140579_genomic.fna/markers.fasta
[2023-06-29 14:42:22,677] [INFO] Task started: Blastn
[2023-06-29 14:42:22,678] [INFO] Running command: blastn -query GCA_910586795.1_MGBC140579_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f452bd3-44c9-4719-b629-d665f759c551/dqc_reference/reference_markers.fasta -out GCA_910586795.1_MGBC140579_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:42:23,263] [INFO] Task succeeded: Blastn
[2023-06-29 14:42:23,268] [INFO] Selected 20 target genomes.
[2023-06-29 14:42:23,268] [INFO] Target genome list was writen to GCA_910586795.1_MGBC140579_genomic.fna/target_genomes.txt
[2023-06-29 14:42:23,269] [INFO] Task started: fastANI
[2023-06-29 14:42:23,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg03b45e20-a84a-4dcb-8a44-039d87863768/GCA_910586795.1_MGBC140579_genomic.fna.gz --refList GCA_910586795.1_MGBC140579_genomic.fna/target_genomes.txt --output GCA_910586795.1_MGBC140579_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:42:37,173] [INFO] Task succeeded: fastANI
[2023-06-29 14:42:37,174] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f452bd3-44c9-4719-b629-d665f759c551/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:42:37,175] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f452bd3-44c9-4719-b629-d665f759c551/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:42:37,183] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:42:37,183] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:42:37,184] [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
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	76.3886	77	916	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	76.2169	82	916	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:42:37,187] [INFO] DFAST Taxonomy check result was written to GCA_910586795.1_MGBC140579_genomic.fna/tc_result.tsv
[2023-06-29 14:42:37,188] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:42:37,188] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:42:37,189] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f452bd3-44c9-4719-b629-d665f759c551/dqc_reference/checkm_data
[2023-06-29 14:42:37,191] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:42:37,225] [INFO] Task started: CheckM
[2023-06-29 14:42:37,225] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_910586795.1_MGBC140579_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_910586795.1_MGBC140579_genomic.fna/checkm_input GCA_910586795.1_MGBC140579_genomic.fna/checkm_result
[2023-06-29 14:43:05,435] [INFO] Task succeeded: CheckM
[2023-06-29 14:43:05,437] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:43:05,458] [INFO] ===== Completeness check finished =====
[2023-06-29 14:43:05,458] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:43:05,459] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_910586795.1_MGBC140579_genomic.fna/markers.fasta)
[2023-06-29 14:43:05,459] [INFO] Task started: Blastn
[2023-06-29 14:43:05,459] [INFO] Running command: blastn -query GCA_910586795.1_MGBC140579_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f452bd3-44c9-4719-b629-d665f759c551/dqc_reference/reference_markers_gtdb.fasta -out GCA_910586795.1_MGBC140579_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:43:06,241] [INFO] Task succeeded: Blastn
[2023-06-29 14:43:06,246] [INFO] Selected 14 target genomes.
[2023-06-29 14:43:06,247] [INFO] Target genome list was writen to GCA_910586795.1_MGBC140579_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:43:06,252] [INFO] Task started: fastANI
[2023-06-29 14:43:06,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg03b45e20-a84a-4dcb-8a44-039d87863768/GCA_910586795.1_MGBC140579_genomic.fna.gz --refList GCA_910586795.1_MGBC140579_genomic.fna/target_genomes_gtdb.txt --output GCA_910586795.1_MGBC140579_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:43:14,500] [INFO] Task succeeded: fastANI
[2023-06-29 14:43:14,513] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 14:43:14,514] [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
GCA_009774625.1	s__VSOB01 sp009774625	99.3925	798	916	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__VSOB01	95.0	99.49	99.49	0.87	0.87	2	conclusive
GCA_009774655.1	s__UBA3282 sp009774655	80.4432	92	916	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	98.36	98.36	0.78	0.78	2	-
GCA_910589075.1	s__VSOB01 sp910589075	80.1466	500	916	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__VSOB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587155.1	s__VSOB01 sp910587155	79.3961	440	916	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__VSOB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585205.1	s__VSOB01 sp910585205	78.8762	372	916	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__VSOB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585345.1	s__VSOB01 sp910585345	78.2312	309	916	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__VSOB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587635.1	s__VSOB01 sp910587635	77.9182	256	916	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__VSOB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017621975.1	s__VSOB01 sp017621975	77.6119	225	916	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__VSOB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578085.1	s__1XD8-76 sp910578085	76.4899	91	916	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD8-76	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587095.1	s__UBA3282 sp910587095	76.3955	68	916	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000436115.1	s__CAG-95 sp000436115	76.208	77	916	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	99.37	99.32	0.91	0.90	3	-
--------------------------------------------------------------------------------
[2023-06-29 14:43:14,516] [INFO] GTDB search result was written to GCA_910586795.1_MGBC140579_genomic.fna/result_gtdb.tsv
[2023-06-29 14:43:14,517] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:43:14,520] [INFO] DFAST_QC result json was written to GCA_910586795.1_MGBC140579_genomic.fna/dqc_result.json
[2023-06-29 14:43:14,520] [INFO] DFAST_QC completed!
[2023-06-29 14:43:14,520] [INFO] Total running time: 0h1m1s