[2023-06-05 18:59:01,261] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:59:01,264] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:59:01,264] [INFO] DQC Reference Directory: /var/lib/cwl/stg13f82aef-3949-4cde-8401-60fbfdbd3ce4/dqc_reference
[2023-06-05 18:59:02,436] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:59:02,437] [INFO] Task started: Prodigal
[2023-06-05 18:59:02,437] [INFO] Running command: gunzip -c /var/lib/cwl/stg38fe9997-6021-440e-9ebc-b616ed95ec8f/GCA_934229455.1_ERR7738606_bin.171_genomic.fna.gz | prodigal -d GCA_934229455.1_ERR7738606_bin.171_genomic.fna/cds.fna -a GCA_934229455.1_ERR7738606_bin.171_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:59:05,417] [INFO] Task succeeded: Prodigal
[2023-06-05 18:59:05,418] [INFO] Task started: HMMsearch
[2023-06-05 18:59:05,418] [INFO] Running command: hmmsearch --tblout GCA_934229455.1_ERR7738606_bin.171_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13f82aef-3949-4cde-8401-60fbfdbd3ce4/dqc_reference/reference_markers.hmm GCA_934229455.1_ERR7738606_bin.171_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:59:05,643] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:59:05,645] [INFO] Found 6/6 markers.
[2023-06-05 18:59:05,683] [INFO] Query marker FASTA was written to GCA_934229455.1_ERR7738606_bin.171_genomic.fna/markers.fasta
[2023-06-05 18:59:05,683] [INFO] Task started: Blastn
[2023-06-05 18:59:05,684] [INFO] Running command: blastn -query GCA_934229455.1_ERR7738606_bin.171_genomic.fna/markers.fasta -db /var/lib/cwl/stg13f82aef-3949-4cde-8401-60fbfdbd3ce4/dqc_reference/reference_markers.fasta -out GCA_934229455.1_ERR7738606_bin.171_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:59:06,308] [INFO] Task succeeded: Blastn
[2023-06-05 18:59:06,313] [INFO] Selected 11 target genomes.
[2023-06-05 18:59:06,313] [INFO] Target genome list was writen to GCA_934229455.1_ERR7738606_bin.171_genomic.fna/target_genomes.txt
[2023-06-05 18:59:06,319] [INFO] Task started: fastANI
[2023-06-05 18:59:06,320] [INFO] Running command: fastANI --query /var/lib/cwl/stg38fe9997-6021-440e-9ebc-b616ed95ec8f/GCA_934229455.1_ERR7738606_bin.171_genomic.fna.gz --refList GCA_934229455.1_ERR7738606_bin.171_genomic.fna/target_genomes.txt --output GCA_934229455.1_ERR7738606_bin.171_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:59:10,656] [INFO] Task succeeded: fastANI
[2023-06-05 18:59:10,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13f82aef-3949-4cde-8401-60fbfdbd3ce4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:59:10,658] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13f82aef-3949-4cde-8401-60fbfdbd3ce4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:59:10,670] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:59:10,670] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:59:10,670] [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
Streptococcus infantarius	strain=FDAARGOS_1019	GCA_016127275.1	102684	102684	type	True	94.5405	371	402	95	below_threshold
Streptococcus infantarius	strain=NCTC13760	GCA_900459445.1	102684	102684	type	True	94.5111	373	402	95	below_threshold
Streptococcus infantarius subsp. infantarius	strain=ATCC BAA-102	GCA_000154985.1	150054	102684	type	True	94.4795	366	402	95	below_threshold
Streptococcus lutetiensis	strain=FDAARGOS_1158	GCA_016725165.1	150055	150055	type	True	93.7018	369	402	95	below_threshold
Streptococcus lutetiensis	strain=NCTC13774	GCA_900475675.1	150055	150055	type	True	93.6499	364	402	95	below_threshold
Streptococcus lutetiensis	strain=FDAARGOS_1018	GCA_016403165.1	150055	150055	type	True	93.6073	363	402	95	below_threshold
Streptococcus vicugnae	strain=SL1232	GCA_016461705.1	2740579	2740579	type	True	89.5908	372	402	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:59:10,672] [INFO] DFAST Taxonomy check result was written to GCA_934229455.1_ERR7738606_bin.171_genomic.fna/tc_result.tsv
[2023-06-05 18:59:10,673] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:59:10,673] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:59:10,673] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13f82aef-3949-4cde-8401-60fbfdbd3ce4/dqc_reference/checkm_data
[2023-06-05 18:59:10,674] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:59:10,696] [INFO] Task started: CheckM
[2023-06-05 18:59:10,696] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934229455.1_ERR7738606_bin.171_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934229455.1_ERR7738606_bin.171_genomic.fna/checkm_input GCA_934229455.1_ERR7738606_bin.171_genomic.fna/checkm_result
[2023-06-05 18:59:27,926] [INFO] Task succeeded: CheckM
[2023-06-05 18:59:27,928] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.01%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:59:27,951] [INFO] ===== Completeness check finished =====
[2023-06-05 18:59:27,952] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:59:27,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934229455.1_ERR7738606_bin.171_genomic.fna/markers.fasta)
[2023-06-05 18:59:27,952] [INFO] Task started: Blastn
[2023-06-05 18:59:27,952] [INFO] Running command: blastn -query GCA_934229455.1_ERR7738606_bin.171_genomic.fna/markers.fasta -db /var/lib/cwl/stg13f82aef-3949-4cde-8401-60fbfdbd3ce4/dqc_reference/reference_markers_gtdb.fasta -out GCA_934229455.1_ERR7738606_bin.171_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:59:28,960] [INFO] Task succeeded: Blastn
[2023-06-05 18:59:28,965] [INFO] Selected 5 target genomes.
[2023-06-05 18:59:28,965] [INFO] Target genome list was writen to GCA_934229455.1_ERR7738606_bin.171_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:59:28,972] [INFO] Task started: fastANI
[2023-06-05 18:59:28,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg38fe9997-6021-440e-9ebc-b616ed95ec8f/GCA_934229455.1_ERR7738606_bin.171_genomic.fna.gz --refList GCA_934229455.1_ERR7738606_bin.171_genomic.fna/target_genomes_gtdb.txt --output GCA_934229455.1_ERR7738606_bin.171_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:59:30,924] [INFO] Task succeeded: fastANI
[2023-06-05 18:59:30,933] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:59:30,933] [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_900101445.1	s__Streptococcus equinus_B	97.7904	386	402	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.22	0.90	0.87	9	conclusive
GCF_000154985.1	s__Streptococcus infantarius	94.4795	366	402	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.67	95.30	0.89	0.82	24	-
GCF_900475675.1	s__Streptococcus lutetiensis	93.6499	364	402	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.21	95.22	0.92	0.85	50	-
GCF_900104225.1	s__Streptococcus equinus_D	89.8841	374	402	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016461705.1	s__Streptococcus vicugnae	89.5908	372	402	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.43	98.30	0.94	0.90	4	-
--------------------------------------------------------------------------------
[2023-06-05 18:59:30,936] [INFO] GTDB search result was written to GCA_934229455.1_ERR7738606_bin.171_genomic.fna/result_gtdb.tsv
[2023-06-05 18:59:30,937] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:59:30,941] [INFO] DFAST_QC result json was written to GCA_934229455.1_ERR7738606_bin.171_genomic.fna/dqc_result.json
[2023-06-05 18:59:30,941] [INFO] DFAST_QC completed!
[2023-06-05 18:59:30,941] [INFO] Total running time: 0h0m30s