[2023-06-28 16:14:13,879] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:14:13,885] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:14:13,886] [INFO] DQC Reference Directory: /var/lib/cwl/stg23973203-bb4f-44f4-86cf-d644aac7dff3/dqc_reference
[2023-06-28 16:14:15,057] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:14:15,057] [INFO] Task started: Prodigal
[2023-06-28 16:14:15,058] [INFO] Running command: gunzip -c /var/lib/cwl/stg03dcd527-885c-4c00-a5cc-1aaa06503fc6/GCA_944383705.1_BRZ_QS_bin85_genomic.fna.gz | prodigal -d GCA_944383705.1_BRZ_QS_bin85_genomic.fna/cds.fna -a GCA_944383705.1_BRZ_QS_bin85_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:14:20,055] [INFO] Task succeeded: Prodigal
[2023-06-28 16:14:20,055] [INFO] Task started: HMMsearch
[2023-06-28 16:14:20,055] [INFO] Running command: hmmsearch --tblout GCA_944383705.1_BRZ_QS_bin85_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23973203-bb4f-44f4-86cf-d644aac7dff3/dqc_reference/reference_markers.hmm GCA_944383705.1_BRZ_QS_bin85_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:14:20,236] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:14:20,237] [INFO] Found 6/6 markers.
[2023-06-28 16:14:20,257] [INFO] Query marker FASTA was written to GCA_944383705.1_BRZ_QS_bin85_genomic.fna/markers.fasta
[2023-06-28 16:14:20,258] [INFO] Task started: Blastn
[2023-06-28 16:14:20,258] [INFO] Running command: blastn -query GCA_944383705.1_BRZ_QS_bin85_genomic.fna/markers.fasta -db /var/lib/cwl/stg23973203-bb4f-44f4-86cf-d644aac7dff3/dqc_reference/reference_markers.fasta -out GCA_944383705.1_BRZ_QS_bin85_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:14:20,864] [INFO] Task succeeded: Blastn
[2023-06-28 16:14:20,869] [INFO] Selected 26 target genomes.
[2023-06-28 16:14:20,869] [INFO] Target genome list was writen to GCA_944383705.1_BRZ_QS_bin85_genomic.fna/target_genomes.txt
[2023-06-28 16:14:20,871] [INFO] Task started: fastANI
[2023-06-28 16:14:20,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg03dcd527-885c-4c00-a5cc-1aaa06503fc6/GCA_944383705.1_BRZ_QS_bin85_genomic.fna.gz --refList GCA_944383705.1_BRZ_QS_bin85_genomic.fna/target_genomes.txt --output GCA_944383705.1_BRZ_QS_bin85_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:14:36,738] [INFO] Task succeeded: fastANI
[2023-06-28 16:14:36,739] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23973203-bb4f-44f4-86cf-d644aac7dff3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:14:36,739] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23973203-bb4f-44f4-86cf-d644aac7dff3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:14:36,740] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:14:36,741] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 16:14:36,741] [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
--------------------------------------------------------------------------------
[2023-06-28 16:14:36,742] [INFO] DFAST Taxonomy check result was written to GCA_944383705.1_BRZ_QS_bin85_genomic.fna/tc_result.tsv
[2023-06-28 16:14:36,743] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:14:36,743] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:14:36,743] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23973203-bb4f-44f4-86cf-d644aac7dff3/dqc_reference/checkm_data
[2023-06-28 16:14:36,745] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:14:36,769] [INFO] Task started: CheckM
[2023-06-28 16:14:36,769] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944383705.1_BRZ_QS_bin85_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944383705.1_BRZ_QS_bin85_genomic.fna/checkm_input GCA_944383705.1_BRZ_QS_bin85_genomic.fna/checkm_result
[2023-06-28 16:14:56,479] [INFO] Task succeeded: CheckM
[2023-06-28 16:14:56,481] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:14:56,502] [INFO] ===== Completeness check finished =====
[2023-06-28 16:14:56,503] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:14:56,504] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944383705.1_BRZ_QS_bin85_genomic.fna/markers.fasta)
[2023-06-28 16:14:56,504] [INFO] Task started: Blastn
[2023-06-28 16:14:56,504] [INFO] Running command: blastn -query GCA_944383705.1_BRZ_QS_bin85_genomic.fna/markers.fasta -db /var/lib/cwl/stg23973203-bb4f-44f4-86cf-d644aac7dff3/dqc_reference/reference_markers_gtdb.fasta -out GCA_944383705.1_BRZ_QS_bin85_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:14:57,640] [INFO] Task succeeded: Blastn
[2023-06-28 16:14:57,643] [INFO] Selected 23 target genomes.
[2023-06-28 16:14:57,643] [INFO] Target genome list was writen to GCA_944383705.1_BRZ_QS_bin85_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:14:57,657] [INFO] Task started: fastANI
[2023-06-28 16:14:57,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg03dcd527-885c-4c00-a5cc-1aaa06503fc6/GCA_944383705.1_BRZ_QS_bin85_genomic.fna.gz --refList GCA_944383705.1_BRZ_QS_bin85_genomic.fna/target_genomes_gtdb.txt --output GCA_944383705.1_BRZ_QS_bin85_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:15:05,789] [INFO] Task succeeded: fastANI
[2023-06-28 16:15:05,800] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 16:15:05,800] [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_900768535.1	s__UMGS1865 sp900768535	78.0211	165	638	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1865	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555785.1	s__UMGS1865 sp900555785	77.7139	107	638	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1865	95.0	97.99	97.50	0.81	0.71	3	-
GCA_002438075.1	s__UMGS1865 sp002438075	77.524	133	638	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1865	95.0	99.71	99.71	0.83	0.83	2	-
GCA_900547725.1	s__UMGS1865 sp900547725	77.3467	109	638	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1865	95.0	97.94	97.81	0.84	0.81	3	-
GCA_017507905.1	s__UMGS1865 sp017507905	76.9797	110	638	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1865	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902795355.1	s__UMGS1865 sp902795355	76.8675	109	638	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1865	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017379815.1	s__UMGS1865 sp017379815	76.8165	80	638	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1865	95.0	98.29	98.29	0.78	0.78	2	-
GCA_900769475.1	s__UMGS1865 sp900769475	76.7885	99	638	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1865	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017453205.1	s__UMGS1865 sp017453205	76.6667	55	638	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1865	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905187695.1	s__Firm-07 sp905187695	76.6615	50	638	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__Firm-07	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017415805.1	s__Firm-07 sp017415805	76.5972	70	638	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__Firm-07	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015064525.1	s__UMGS1865 sp015064525	76.5969	92	638	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1865	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017452665.1	s__UMGS1865 sp017452665	76.4461	64	638	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1865	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548735.1	s__Firm-07 sp900548735	76.0472	64	638	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__Firm-07	95.0	97.86	97.81	0.89	0.83	3	-
GCA_015063585.1	s__UMGS1865 sp015063585	76.0186	55	638	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1865	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017463405.1	s__UMGS1865 sp017463405	75.8847	68	638	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1865	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015064005.1	s__Firm-07 sp015064005	75.8784	72	638	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__Firm-07	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:15:05,802] [INFO] GTDB search result was written to GCA_944383705.1_BRZ_QS_bin85_genomic.fna/result_gtdb.tsv
[2023-06-28 16:15:05,802] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:15:05,805] [INFO] DFAST_QC result json was written to GCA_944383705.1_BRZ_QS_bin85_genomic.fna/dqc_result.json
[2023-06-28 16:15:05,805] [INFO] DFAST_QC completed!
[2023-06-28 16:15:05,805] [INFO] Total running time: 0h0m52s