[2023-06-08 12:31:39,102] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:31:39,105] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:31:39,106] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8e1af0f-313e-44be-abec-bd2b1501b7a7/dqc_reference
[2023-06-08 12:31:40,457] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:31:40,458] [INFO] Task started: Prodigal
[2023-06-08 12:31:40,458] [INFO] Running command: gunzip -c /var/lib/cwl/stg5bcf09e9-6dfe-44cb-b698-e36d284d8a06/GCA_947074365.1_SRR13169520_bin.1_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947074365.1_SRR13169520_bin.1_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947074365.1_SRR13169520_bin.1_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:31:44,663] [INFO] Task succeeded: Prodigal
[2023-06-08 12:31:44,663] [INFO] Task started: HMMsearch
[2023-06-08 12:31:44,663] [INFO] Running command: hmmsearch --tblout GCA_947074365.1_SRR13169520_bin.1_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8e1af0f-313e-44be-abec-bd2b1501b7a7/dqc_reference/reference_markers.hmm GCA_947074365.1_SRR13169520_bin.1_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:31:44,883] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:31:44,884] [INFO] Found 6/6 markers.
[2023-06-08 12:31:44,906] [INFO] Query marker FASTA was written to GCA_947074365.1_SRR13169520_bin.1_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 12:31:44,907] [INFO] Task started: Blastn
[2023-06-08 12:31:44,907] [INFO] Running command: blastn -query GCA_947074365.1_SRR13169520_bin.1_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8e1af0f-313e-44be-abec-bd2b1501b7a7/dqc_reference/reference_markers.fasta -out GCA_947074365.1_SRR13169520_bin.1_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:31:45,466] [INFO] Task succeeded: Blastn
[2023-06-08 12:31:45,470] [INFO] Selected 22 target genomes.
[2023-06-08 12:31:45,470] [INFO] Target genome list was writen to GCA_947074365.1_SRR13169520_bin.1_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 12:31:45,477] [INFO] Task started: fastANI
[2023-06-08 12:31:45,477] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bcf09e9-6dfe-44cb-b698-e36d284d8a06/GCA_947074365.1_SRR13169520_bin.1_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947074365.1_SRR13169520_bin.1_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947074365.1_SRR13169520_bin.1_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:31:59,062] [INFO] Task succeeded: fastANI
[2023-06-08 12:31:59,063] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8e1af0f-313e-44be-abec-bd2b1501b7a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:31:59,064] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8e1af0f-313e-44be-abec-bd2b1501b7a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:31:59,065] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:31:59,066] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 12:31:59,066] [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
--------------------------------------------------------------------------------
[2023-06-08 12:31:59,068] [INFO] DFAST Taxonomy check result was written to GCA_947074365.1_SRR13169520_bin.1_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 12:31:59,069] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:31:59,069] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:31:59,069] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8e1af0f-313e-44be-abec-bd2b1501b7a7/dqc_reference/checkm_data
[2023-06-08 12:31:59,073] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:31:59,098] [INFO] Task started: CheckM
[2023-06-08 12:31:59,098] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947074365.1_SRR13169520_bin.1_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947074365.1_SRR13169520_bin.1_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947074365.1_SRR13169520_bin.1_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 12:32:18,741] [INFO] Task succeeded: CheckM
[2023-06-08 12:32:18,742] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:32:18,761] [INFO] ===== Completeness check finished =====
[2023-06-08 12:32:18,762] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:32:18,762] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947074365.1_SRR13169520_bin.1_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 12:32:18,763] [INFO] Task started: Blastn
[2023-06-08 12:32:18,763] [INFO] Running command: blastn -query GCA_947074365.1_SRR13169520_bin.1_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8e1af0f-313e-44be-abec-bd2b1501b7a7/dqc_reference/reference_markers_gtdb.fasta -out GCA_947074365.1_SRR13169520_bin.1_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:32:19,542] [INFO] Task succeeded: Blastn
[2023-06-08 12:32:19,547] [INFO] Selected 20 target genomes.
[2023-06-08 12:32:19,547] [INFO] Target genome list was writen to GCA_947074365.1_SRR13169520_bin.1_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:32:19,554] [INFO] Task started: fastANI
[2023-06-08 12:32:19,554] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bcf09e9-6dfe-44cb-b698-e36d284d8a06/GCA_947074365.1_SRR13169520_bin.1_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947074365.1_SRR13169520_bin.1_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947074365.1_SRR13169520_bin.1_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:32:25,730] [INFO] Task succeeded: fastANI
[2023-06-08 12:32:25,749] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 12:32:25,749] [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_910586065.1	s__Coproplasma sp910586065	99.5018	540	612	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910587005.1	s__Coproplasma sp910587005	80.9047	240	612	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587825.1	s__Coproplasma sp910587825	80.3607	152	612	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578655.1	s__Coproplasma sp910578655	79.116	96	612	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585785.1	s__Coproplasma sp910585785	79.0374	187	612	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587015.1	s__Coproplasma sp910587015	79.0127	168	612	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013316055.1	s__Coproplasma sp013316055	79.0048	145	612	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	97.79	97.79	0.95	0.95	2	-
GCA_910577055.1	s__Coproplasma sp910577055	78.4921	156	612	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578145.1	s__Coproplasma sp910578145	78.4669	154	612	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014805025.1	s__Coproplasma sp014805025	78.2848	136	612	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577555.1	s__Coproplasma sp910577555	78.1667	160	612	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577375.1	s__Coproplasma sp910577375	78.1486	188	612	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910583855.1	s__Coproplasma sp910583855	78.064	147	612	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578765.1	s__Coproplasma sp910578765	78.0208	136	612	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577875.1	s__Coproplasma sp910577875	77.312	102	612	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579705.1	s__Coproplasma sp910579705	77.2921	115	612	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 12:32:25,751] [INFO] GTDB search result was written to GCA_947074365.1_SRR13169520_bin.1_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 12:32:25,751] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:32:25,754] [INFO] DFAST_QC result json was written to GCA_947074365.1_SRR13169520_bin.1_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 12:32:25,754] [INFO] DFAST_QC completed!
[2023-06-08 12:32:25,754] [INFO] Total running time: 0h0m47s