[2023-06-19 04:14:35,319] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:14:35,321] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:14:35,321] [INFO] DQC Reference Directory: /var/lib/cwl/stgc42cb566-6f4c-407d-8480-5af7a2bae2bc/dqc_reference
[2023-06-19 04:14:36,564] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:14:36,565] [INFO] Task started: Prodigal
[2023-06-19 04:14:36,565] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9c6572a-d56a-425a-b419-5f7bcdf18337/GCA_029068355.1_ASM2906835v1_genomic.fna.gz | prodigal -d GCA_029068355.1_ASM2906835v1_genomic.fna/cds.fna -a GCA_029068355.1_ASM2906835v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:14:38,537] [INFO] Task succeeded: Prodigal
[2023-06-19 04:14:38,537] [INFO] Task started: HMMsearch
[2023-06-19 04:14:38,538] [INFO] Running command: hmmsearch --tblout GCA_029068355.1_ASM2906835v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc42cb566-6f4c-407d-8480-5af7a2bae2bc/dqc_reference/reference_markers.hmm GCA_029068355.1_ASM2906835v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:14:38,690] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:14:38,691] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb9c6572a-d56a-425a-b419-5f7bcdf18337/GCA_029068355.1_ASM2906835v1_genomic.fna.gz]
[2023-06-19 04:14:38,705] [INFO] Query marker FASTA was written to GCA_029068355.1_ASM2906835v1_genomic.fna/markers.fasta
[2023-06-19 04:14:38,705] [INFO] Task started: Blastn
[2023-06-19 04:14:38,705] [INFO] Running command: blastn -query GCA_029068355.1_ASM2906835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc42cb566-6f4c-407d-8480-5af7a2bae2bc/dqc_reference/reference_markers.fasta -out GCA_029068355.1_ASM2906835v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:14:39,244] [INFO] Task succeeded: Blastn
[2023-06-19 04:14:39,247] [INFO] Selected 15 target genomes.
[2023-06-19 04:14:39,247] [INFO] Target genome list was writen to GCA_029068355.1_ASM2906835v1_genomic.fna/target_genomes.txt
[2023-06-19 04:14:39,249] [INFO] Task started: fastANI
[2023-06-19 04:14:39,249] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9c6572a-d56a-425a-b419-5f7bcdf18337/GCA_029068355.1_ASM2906835v1_genomic.fna.gz --refList GCA_029068355.1_ASM2906835v1_genomic.fna/target_genomes.txt --output GCA_029068355.1_ASM2906835v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 04:14:50,131] [INFO] Task succeeded: fastANI
[2023-06-19 04:14:50,132] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc42cb566-6f4c-407d-8480-5af7a2bae2bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 04:14:50,132] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc42cb566-6f4c-407d-8480-5af7a2bae2bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 04:14:50,134] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 04:14:50,134] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 04:14:50,134] [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
--------------------------------------------------------------------------------
[2023-06-19 04:14:50,136] [INFO] DFAST Taxonomy check result was written to GCA_029068355.1_ASM2906835v1_genomic.fna/tc_result.tsv
[2023-06-19 04:14:50,137] [INFO] ===== Taxonomy check completed =====
[2023-06-19 04:14:50,137] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 04:14:50,137] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc42cb566-6f4c-407d-8480-5af7a2bae2bc/dqc_reference/checkm_data
[2023-06-19 04:14:50,140] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 04:14:50,161] [INFO] Task started: CheckM
[2023-06-19 04:14:50,162] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_029068355.1_ASM2906835v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_029068355.1_ASM2906835v1_genomic.fna/checkm_input GCA_029068355.1_ASM2906835v1_genomic.fna/checkm_result
[2023-06-19 04:15:03,378] [INFO] Task succeeded: CheckM
[2023-06-19 04:15:03,379] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.52%
Contamintation: 0.84%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-19 04:15:03,395] [INFO] ===== Completeness check finished =====
[2023-06-19 04:15:03,395] [INFO] ===== Start GTDB Search =====
[2023-06-19 04:15:03,395] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_029068355.1_ASM2906835v1_genomic.fna/markers.fasta)
[2023-06-19 04:15:03,396] [INFO] Task started: Blastn
[2023-06-19 04:15:03,396] [INFO] Running command: blastn -query GCA_029068355.1_ASM2906835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc42cb566-6f4c-407d-8480-5af7a2bae2bc/dqc_reference/reference_markers_gtdb.fasta -out GCA_029068355.1_ASM2906835v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:15:04,185] [INFO] Task succeeded: Blastn
[2023-06-19 04:15:04,191] [INFO] Selected 11 target genomes.
[2023-06-19 04:15:04,191] [INFO] Target genome list was writen to GCA_029068355.1_ASM2906835v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 04:15:04,219] [INFO] Task started: fastANI
[2023-06-19 04:15:04,220] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9c6572a-d56a-425a-b419-5f7bcdf18337/GCA_029068355.1_ASM2906835v1_genomic.fna.gz --refList GCA_029068355.1_ASM2906835v1_genomic.fna/target_genomes_gtdb.txt --output GCA_029068355.1_ASM2906835v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 04:15:07,208] [INFO] Task succeeded: fastANI
[2023-06-19 04:15:07,218] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 04:15:07,219] [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_910579525.1	s__Coproplasma sp910579525	79.8539	117	198	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	78.8784	100	198	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	78.8751	88	198	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	78.7139	72	198	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_910587005.1	s__Coproplasma sp910587005	78.6997	85	198	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_910577055.1	s__Coproplasma sp910577055	78.6444	82	198	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_910588645.1	s__Coproplasma sp910588645	78.6232	66	198	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	78.6157	103	198	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_910579585.1	s__Coproplasma sp910579585	78.2754	81	198	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	78.1809	71	198	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_910586035.1	s__Coproplasma sp910586035	77.0589	54	198	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 04:15:07,220] [INFO] GTDB search result was written to GCA_029068355.1_ASM2906835v1_genomic.fna/result_gtdb.tsv
[2023-06-19 04:15:07,221] [INFO] ===== GTDB Search completed =====
[2023-06-19 04:15:07,223] [INFO] DFAST_QC result json was written to GCA_029068355.1_ASM2906835v1_genomic.fna/dqc_result.json
[2023-06-19 04:15:07,223] [INFO] DFAST_QC completed!
[2023-06-19 04:15:07,223] [INFO] Total running time: 0h0m32s