[2023-06-28 12:33:47,813] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:33:47,815] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:33:47,815] [INFO] DQC Reference Directory: /var/lib/cwl/stgf41c57b4-edac-4e27-8a5b-ffec9e013018/dqc_reference
[2023-06-28 12:33:49,198] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:33:49,199] [INFO] Task started: Prodigal
[2023-06-28 12:33:49,199] [INFO] Running command: gunzip -c /var/lib/cwl/stgbce81698-fc61-4e61-8530-927e64e75fc7/GCA_944385005.1_BRZ_GS_bin57_genomic.fna.gz | prodigal -d GCA_944385005.1_BRZ_GS_bin57_genomic.fna/cds.fna -a GCA_944385005.1_BRZ_GS_bin57_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:33:54,312] [INFO] Task succeeded: Prodigal
[2023-06-28 12:33:54,313] [INFO] Task started: HMMsearch
[2023-06-28 12:33:54,313] [INFO] Running command: hmmsearch --tblout GCA_944385005.1_BRZ_GS_bin57_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf41c57b4-edac-4e27-8a5b-ffec9e013018/dqc_reference/reference_markers.hmm GCA_944385005.1_BRZ_GS_bin57_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:33:54,581] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:33:54,583] [INFO] Found 6/6 markers.
[2023-06-28 12:33:54,612] [INFO] Query marker FASTA was written to GCA_944385005.1_BRZ_GS_bin57_genomic.fna/markers.fasta
[2023-06-28 12:33:54,613] [INFO] Task started: Blastn
[2023-06-28 12:33:54,613] [INFO] Running command: blastn -query GCA_944385005.1_BRZ_GS_bin57_genomic.fna/markers.fasta -db /var/lib/cwl/stgf41c57b4-edac-4e27-8a5b-ffec9e013018/dqc_reference/reference_markers.fasta -out GCA_944385005.1_BRZ_GS_bin57_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:33:55,442] [INFO] Task succeeded: Blastn
[2023-06-28 12:33:55,446] [INFO] Selected 22 target genomes.
[2023-06-28 12:33:55,447] [INFO] Target genome list was writen to GCA_944385005.1_BRZ_GS_bin57_genomic.fna/target_genomes.txt
[2023-06-28 12:33:55,453] [INFO] Task started: fastANI
[2023-06-28 12:33:55,454] [INFO] Running command: fastANI --query /var/lib/cwl/stgbce81698-fc61-4e61-8530-927e64e75fc7/GCA_944385005.1_BRZ_GS_bin57_genomic.fna.gz --refList GCA_944385005.1_BRZ_GS_bin57_genomic.fna/target_genomes.txt --output GCA_944385005.1_BRZ_GS_bin57_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:34:07,573] [INFO] Task succeeded: fastANI
[2023-06-28 12:34:07,573] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf41c57b4-edac-4e27-8a5b-ffec9e013018/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:34:07,574] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf41c57b4-edac-4e27-8a5b-ffec9e013018/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:34:07,576] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:34:07,576] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:34:07,576] [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 12:34:07,578] [INFO] DFAST Taxonomy check result was written to GCA_944385005.1_BRZ_GS_bin57_genomic.fna/tc_result.tsv
[2023-06-28 12:34:07,579] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:34:07,579] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:34:07,579] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf41c57b4-edac-4e27-8a5b-ffec9e013018/dqc_reference/checkm_data
[2023-06-28 12:34:07,582] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:34:07,615] [INFO] Task started: CheckM
[2023-06-28 12:34:07,616] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944385005.1_BRZ_GS_bin57_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944385005.1_BRZ_GS_bin57_genomic.fna/checkm_input GCA_944385005.1_BRZ_GS_bin57_genomic.fna/checkm_result
[2023-06-28 12:34:30,756] [INFO] Task succeeded: CheckM
[2023-06-28 12:34:30,758] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:34:30,783] [INFO] ===== Completeness check finished =====
[2023-06-28 12:34:30,784] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:34:30,784] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944385005.1_BRZ_GS_bin57_genomic.fna/markers.fasta)
[2023-06-28 12:34:30,784] [INFO] Task started: Blastn
[2023-06-28 12:34:30,785] [INFO] Running command: blastn -query GCA_944385005.1_BRZ_GS_bin57_genomic.fna/markers.fasta -db /var/lib/cwl/stgf41c57b4-edac-4e27-8a5b-ffec9e013018/dqc_reference/reference_markers_gtdb.fasta -out GCA_944385005.1_BRZ_GS_bin57_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:34:31,833] [INFO] Task succeeded: Blastn
[2023-06-28 12:34:31,838] [INFO] Selected 19 target genomes.
[2023-06-28 12:34:31,838] [INFO] Target genome list was writen to GCA_944385005.1_BRZ_GS_bin57_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:34:31,849] [INFO] Task started: fastANI
[2023-06-28 12:34:31,850] [INFO] Running command: fastANI --query /var/lib/cwl/stgbce81698-fc61-4e61-8530-927e64e75fc7/GCA_944385005.1_BRZ_GS_bin57_genomic.fna.gz --refList GCA_944385005.1_BRZ_GS_bin57_genomic.fna/target_genomes_gtdb.txt --output GCA_944385005.1_BRZ_GS_bin57_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:34:38,636] [INFO] Task succeeded: fastANI
[2023-06-28 12:34:38,647] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:34:38,647] [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_000431535.1	s__Eubacterium_R faecale	98.6072	603	656	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	98.79	98.10	0.92	0.82	9	conclusive
GCA_900546785.1	s__Eubacterium_R faecipullorum	80.9481	426	656	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	99.03	98.11	0.88	0.82	3	-
GCA_900539425.1	s__Eubacterium_R sp900539425	79.9379	347	656	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	97.89	97.76	0.89	0.86	5	-
GCA_900547915.1	s__Eubacterium_R sp900547915	79.4669	229	656	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539845.1	s__Eubacterium_R faecavium	79.3115	347	656	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	99.18	98.52	0.94	0.90	5	-
GCA_000433975.1	s__Eubacterium_R sp000433975	77.7403	189	656	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	99.06	97.98	0.95	0.88	9	-
GCA_900555015.1	s__Eubacterium_R sp900555015	77.409	65	656	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234995.1	s__Eubacterium_R sp905234995	77.3398	107	656	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584985.1	s__Eubacterium_R sp910584985	77.3268	124	656	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910583925.1	s__Eubacterium_R sp011958665	77.2174	91	656	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	98.28	98.18	0.92	0.92	3	-
GCA_000436335.1	s__CAG-217 sp000436335	76.2374	55	656	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-217	95.0	97.66	96.86	0.92	0.85	21	-
--------------------------------------------------------------------------------
[2023-06-28 12:34:38,649] [INFO] GTDB search result was written to GCA_944385005.1_BRZ_GS_bin57_genomic.fna/result_gtdb.tsv
[2023-06-28 12:34:38,650] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:34:38,652] [INFO] DFAST_QC result json was written to GCA_944385005.1_BRZ_GS_bin57_genomic.fna/dqc_result.json
[2023-06-28 12:34:38,653] [INFO] DFAST_QC completed!
[2023-06-28 12:34:38,653] [INFO] Total running time: 0h0m51s