[2023-06-13 03:34:47,431] [INFO] DFAST_QC pipeline started.
[2023-06-13 03:34:47,434] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 03:34:47,434] [INFO] DQC Reference Directory: /var/lib/cwl/stg772e47fa-bf1f-43d2-a7db-9e019336f522/dqc_reference
[2023-06-13 03:34:48,666] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 03:34:48,667] [INFO] Task started: Prodigal
[2023-06-13 03:34:48,667] [INFO] Running command: gunzip -c /var/lib/cwl/stgfdb0f509-2fd8-4e93-ab84-07edb4338f9f/GCA_938044335.1_ERR2198699_bin.55_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938044335.1_ERR2198699_bin.55_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938044335.1_ERR2198699_bin.55_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 03:34:53,127] [INFO] Task succeeded: Prodigal
[2023-06-13 03:34:53,128] [INFO] Task started: HMMsearch
[2023-06-13 03:34:53,128] [INFO] Running command: hmmsearch --tblout GCA_938044335.1_ERR2198699_bin.55_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg772e47fa-bf1f-43d2-a7db-9e019336f522/dqc_reference/reference_markers.hmm GCA_938044335.1_ERR2198699_bin.55_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 03:34:53,371] [INFO] Task succeeded: HMMsearch
[2023-06-13 03:34:53,373] [INFO] Found 6/6 markers.
[2023-06-13 03:34:53,398] [INFO] Query marker FASTA was written to GCA_938044335.1_ERR2198699_bin.55_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 03:34:53,398] [INFO] Task started: Blastn
[2023-06-13 03:34:53,398] [INFO] Running command: blastn -query GCA_938044335.1_ERR2198699_bin.55_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg772e47fa-bf1f-43d2-a7db-9e019336f522/dqc_reference/reference_markers.fasta -out GCA_938044335.1_ERR2198699_bin.55_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 03:34:53,981] [INFO] Task succeeded: Blastn
[2023-06-13 03:34:53,986] [INFO] Selected 14 target genomes.
[2023-06-13 03:34:53,986] [INFO] Target genome list was writen to GCA_938044335.1_ERR2198699_bin.55_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 03:34:53,990] [INFO] Task started: fastANI
[2023-06-13 03:34:53,990] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdb0f509-2fd8-4e93-ab84-07edb4338f9f/GCA_938044335.1_ERR2198699_bin.55_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938044335.1_ERR2198699_bin.55_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938044335.1_ERR2198699_bin.55_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 03:34:59,386] [INFO] Task succeeded: fastANI
[2023-06-13 03:34:59,386] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg772e47fa-bf1f-43d2-a7db-9e019336f522/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 03:34:59,387] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg772e47fa-bf1f-43d2-a7db-9e019336f522/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 03:34:59,399] [INFO] Found 5 fastANI hits (3 hits with ANI > threshold)
[2023-06-13 03:34:59,399] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 03:34:59,399] [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
Pediococcus acidilactici	strain=FDAARGOS_1133	GCA_016726765.1	1254	1254	neotype	True	98.6393	577	675	95	conclusive
Pediococcus acidilactici	strain=DSM 20284	GCA_000146325.1	1254	1254	neotype	True	98.6387	576	675	95	conclusive
Pediococcus acidilactici	strain=CCUG 32235	GCA_012396515.1	1254	1254	neotype	True	98.6275	578	675	95	conclusive
Pediococcus pentosaceus	strain=ATCC 33316	GCA_004354495.1	1255	1255	type	True	79.7395	178	675	95	below_threshold
Pediococcus pentosaceus	strain=FDAARGOS_1009	GCA_016127775.1	1255	1255	type	True	79.5885	176	675	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 03:34:59,401] [INFO] DFAST Taxonomy check result was written to GCA_938044335.1_ERR2198699_bin.55_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 03:34:59,402] [INFO] ===== Taxonomy check completed =====
[2023-06-13 03:34:59,402] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 03:34:59,402] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg772e47fa-bf1f-43d2-a7db-9e019336f522/dqc_reference/checkm_data
[2023-06-13 03:34:59,403] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 03:34:59,431] [INFO] Task started: CheckM
[2023-06-13 03:34:59,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938044335.1_ERR2198699_bin.55_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938044335.1_ERR2198699_bin.55_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938044335.1_ERR2198699_bin.55_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 03:35:19,857] [INFO] Task succeeded: CheckM
[2023-06-13 03:35:19,858] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 03:35:19,880] [INFO] ===== Completeness check finished =====
[2023-06-13 03:35:19,881] [INFO] ===== Start GTDB Search =====
[2023-06-13 03:35:19,881] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938044335.1_ERR2198699_bin.55_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 03:35:19,881] [INFO] Task started: Blastn
[2023-06-13 03:35:19,882] [INFO] Running command: blastn -query GCA_938044335.1_ERR2198699_bin.55_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg772e47fa-bf1f-43d2-a7db-9e019336f522/dqc_reference/reference_markers_gtdb.fasta -out GCA_938044335.1_ERR2198699_bin.55_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 03:35:20,636] [INFO] Task succeeded: Blastn
[2023-06-13 03:35:20,641] [INFO] Selected 18 target genomes.
[2023-06-13 03:35:20,641] [INFO] Target genome list was writen to GCA_938044335.1_ERR2198699_bin.55_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 03:35:20,648] [INFO] Task started: fastANI
[2023-06-13 03:35:20,648] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdb0f509-2fd8-4e93-ab84-07edb4338f9f/GCA_938044335.1_ERR2198699_bin.55_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938044335.1_ERR2198699_bin.55_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938044335.1_ERR2198699_bin.55_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 03:35:27,378] [INFO] Task succeeded: fastANI
[2023-06-13 03:35:27,390] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 03:35:27,390] [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_000146325.1	s__Pediococcus acidilactici	98.6387	576	675	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	97.64	96.71	0.89	0.81	172	conclusive
GCA_009809575.1	s__Pediococcus acidilactici_A	89.9745	542	675	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001437285.1	s__Pediococcus pentosaceus	79.5946	177	675	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	98.80	98.32	0.92	0.90	75	-
GCF_001437075.1	s__Pediococcus stilesii	79.1508	136	675	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	97.68	97.68	0.92	0.92	2	-
GCF_001437605.1	s__Pediococcus argentinicus	78.9509	77	675	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	99.99	99.98	0.98	0.97	3	-
GCF_001438655.1	s__Pediococcus cellicola	77.3535	51	675	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-13 03:35:27,392] [INFO] GTDB search result was written to GCA_938044335.1_ERR2198699_bin.55_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 03:35:27,392] [INFO] ===== GTDB Search completed =====
[2023-06-13 03:35:27,395] [INFO] DFAST_QC result json was written to GCA_938044335.1_ERR2198699_bin.55_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 03:35:27,395] [INFO] DFAST_QC completed!
[2023-06-13 03:35:27,396] [INFO] Total running time: 0h0m40s