[2023-06-29 17:08:01,124] [INFO] DFAST_QC pipeline started.
[2023-06-29 17:08:01,155] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 17:08:01,155] [INFO] DQC Reference Directory: /var/lib/cwl/stg69f1eb75-ccb6-4bea-9794-02f423472063/dqc_reference
[2023-06-29 17:08:03,544] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 17:08:03,545] [INFO] Task started: Prodigal
[2023-06-29 17:08:03,545] [INFO] Running command: gunzip -c /var/lib/cwl/stg100676bf-ea35-4ca1-9c61-222f4c21665d/GCA_932183045.1_0308_Ms_metabat.013_genomic.fna.gz | prodigal -d GCA_932183045.1_0308_Ms_metabat.013_genomic.fna/cds.fna -a GCA_932183045.1_0308_Ms_metabat.013_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 17:08:08,480] [INFO] Task succeeded: Prodigal
[2023-06-29 17:08:08,480] [INFO] Task started: HMMsearch
[2023-06-29 17:08:08,480] [INFO] Running command: hmmsearch --tblout GCA_932183045.1_0308_Ms_metabat.013_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69f1eb75-ccb6-4bea-9794-02f423472063/dqc_reference/reference_markers.hmm GCA_932183045.1_0308_Ms_metabat.013_genomic.fna/protein.faa > /dev/null
[2023-06-29 17:08:08,711] [INFO] Task succeeded: HMMsearch
[2023-06-29 17:08:08,712] [INFO] Found 6/6 markers.
[2023-06-29 17:08:08,738] [INFO] Query marker FASTA was written to GCA_932183045.1_0308_Ms_metabat.013_genomic.fna/markers.fasta
[2023-06-29 17:08:08,739] [INFO] Task started: Blastn
[2023-06-29 17:08:08,739] [INFO] Running command: blastn -query GCA_932183045.1_0308_Ms_metabat.013_genomic.fna/markers.fasta -db /var/lib/cwl/stg69f1eb75-ccb6-4bea-9794-02f423472063/dqc_reference/reference_markers.fasta -out GCA_932183045.1_0308_Ms_metabat.013_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 17:08:10,171] [INFO] Task succeeded: Blastn
[2023-06-29 17:08:10,174] [INFO] Selected 25 target genomes.
[2023-06-29 17:08:10,175] [INFO] Target genome list was writen to GCA_932183045.1_0308_Ms_metabat.013_genomic.fna/target_genomes.txt
[2023-06-29 17:08:10,238] [INFO] Task started: fastANI
[2023-06-29 17:08:10,238] [INFO] Running command: fastANI --query /var/lib/cwl/stg100676bf-ea35-4ca1-9c61-222f4c21665d/GCA_932183045.1_0308_Ms_metabat.013_genomic.fna.gz --refList GCA_932183045.1_0308_Ms_metabat.013_genomic.fna/target_genomes.txt --output GCA_932183045.1_0308_Ms_metabat.013_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 17:08:24,703] [INFO] Task succeeded: fastANI
[2023-06-29 17:08:24,704] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69f1eb75-ccb6-4bea-9794-02f423472063/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 17:08:24,704] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69f1eb75-ccb6-4bea-9794-02f423472063/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 17:08:24,706] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 17:08:24,707] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 17:08:24,707] [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
--------------------------------------------------------------------------------
[2023-06-29 17:08:24,709] [INFO] DFAST Taxonomy check result was written to GCA_932183045.1_0308_Ms_metabat.013_genomic.fna/tc_result.tsv
[2023-06-29 17:08:24,710] [INFO] ===== Taxonomy check completed =====
[2023-06-29 17:08:24,710] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 17:08:24,710] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69f1eb75-ccb6-4bea-9794-02f423472063/dqc_reference/checkm_data
[2023-06-29 17:08:24,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 17:08:24,738] [INFO] Task started: CheckM
[2023-06-29 17:08:24,738] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_932183045.1_0308_Ms_metabat.013_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_932183045.1_0308_Ms_metabat.013_genomic.fna/checkm_input GCA_932183045.1_0308_Ms_metabat.013_genomic.fna/checkm_result
[2023-06-29 17:08:46,314] [INFO] Task succeeded: CheckM
[2023-06-29 17:08:46,315] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 17:08:46,334] [INFO] ===== Completeness check finished =====
[2023-06-29 17:08:46,334] [INFO] ===== Start GTDB Search =====
[2023-06-29 17:08:46,335] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_932183045.1_0308_Ms_metabat.013_genomic.fna/markers.fasta)
[2023-06-29 17:08:46,335] [INFO] Task started: Blastn
[2023-06-29 17:08:46,335] [INFO] Running command: blastn -query GCA_932183045.1_0308_Ms_metabat.013_genomic.fna/markers.fasta -db /var/lib/cwl/stg69f1eb75-ccb6-4bea-9794-02f423472063/dqc_reference/reference_markers_gtdb.fasta -out GCA_932183045.1_0308_Ms_metabat.013_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 17:08:47,125] [INFO] Task succeeded: Blastn
[2023-06-29 17:08:47,133] [INFO] Selected 13 target genomes.
[2023-06-29 17:08:47,134] [INFO] Target genome list was writen to GCA_932183045.1_0308_Ms_metabat.013_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 17:08:47,143] [INFO] Task started: fastANI
[2023-06-29 17:08:47,144] [INFO] Running command: fastANI --query /var/lib/cwl/stg100676bf-ea35-4ca1-9c61-222f4c21665d/GCA_932183045.1_0308_Ms_metabat.013_genomic.fna.gz --refList GCA_932183045.1_0308_Ms_metabat.013_genomic.fna/target_genomes_gtdb.txt --output GCA_932183045.1_0308_Ms_metabat.013_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 17:08:51,565] [INFO] Task succeeded: fastANI
[2023-06-29 17:08:51,581] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 17:08:51,582] [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_910578065.1	s__Gallimonas sp910578065	98.488	535	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910588465.1	s__Gallimonas sp910588465	79.8411	179	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586365.1	s__Gallimonas sp910586365	79.1021	180	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586825.1	s__Gallimonas sp910586825	78.8024	164	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586675.1	s__Gallimonas sp910586675	78.6976	207	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586245.1	s__Gallimonas sp910586245	78.3208	187	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589015.1	s__Gallimonas sp910589015	78.1525	153	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017621735.1	s__Gallimonas sp017621735	77.8806	153	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904373325.1	s__Gallimonas merdigallinarum	77.5291	125	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	98.69	97.92	0.89	0.88	4	-
GCA_900547645.1	s__Gallimonas faecium	77.4277	105	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	98.43	98.37	0.87	0.83	4	-
GCA_017471945.1	s__Scatosoma sp017471945	76.1843	50	632	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 17:08:51,584] [INFO] GTDB search result was written to GCA_932183045.1_0308_Ms_metabat.013_genomic.fna/result_gtdb.tsv
[2023-06-29 17:08:51,585] [INFO] ===== GTDB Search completed =====
[2023-06-29 17:08:51,588] [INFO] DFAST_QC result json was written to GCA_932183045.1_0308_Ms_metabat.013_genomic.fna/dqc_result.json
[2023-06-29 17:08:51,589] [INFO] DFAST_QC completed!
[2023-06-29 17:08:51,589] [INFO] Total running time: 0h0m50s