[2023-06-05 02:26:52,461] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:26:52,463] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:26:52,463] [INFO] DQC Reference Directory: /var/lib/cwl/stgd910b180-d4bd-4be4-ad92-2516154511dc/dqc_reference
[2023-06-05 02:26:53,750] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:26:53,751] [INFO] Task started: Prodigal
[2023-06-05 02:26:53,751] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ec949f0-7503-4ce3-a384-156b0828bf04/GCA_902771025.1_Rumen_uncultured_genome_RUG11630_genomic.fna.gz | prodigal -d GCA_902771025.1_Rumen_uncultured_genome_RUG11630_genomic.fna/cds.fna -a GCA_902771025.1_Rumen_uncultured_genome_RUG11630_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:27:02,913] [INFO] Task succeeded: Prodigal
[2023-06-05 02:27:02,914] [INFO] Task started: HMMsearch
[2023-06-05 02:27:02,914] [INFO] Running command: hmmsearch --tblout GCA_902771025.1_Rumen_uncultured_genome_RUG11630_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd910b180-d4bd-4be4-ad92-2516154511dc/dqc_reference/reference_markers.hmm GCA_902771025.1_Rumen_uncultured_genome_RUG11630_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:27:03,234] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:27:03,235] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2ec949f0-7503-4ce3-a384-156b0828bf04/GCA_902771025.1_Rumen_uncultured_genome_RUG11630_genomic.fna.gz]
[2023-06-05 02:27:03,266] [INFO] Query marker FASTA was written to GCA_902771025.1_Rumen_uncultured_genome_RUG11630_genomic.fna/markers.fasta
[2023-06-05 02:27:03,267] [INFO] Task started: Blastn
[2023-06-05 02:27:03,267] [INFO] Running command: blastn -query GCA_902771025.1_Rumen_uncultured_genome_RUG11630_genomic.fna/markers.fasta -db /var/lib/cwl/stgd910b180-d4bd-4be4-ad92-2516154511dc/dqc_reference/reference_markers.fasta -out GCA_902771025.1_Rumen_uncultured_genome_RUG11630_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:27:03,931] [INFO] Task succeeded: Blastn
[2023-06-05 02:27:03,936] [INFO] Selected 20 target genomes.
[2023-06-05 02:27:03,936] [INFO] Target genome list was writen to GCA_902771025.1_Rumen_uncultured_genome_RUG11630_genomic.fna/target_genomes.txt
[2023-06-05 02:27:03,939] [INFO] Task started: fastANI
[2023-06-05 02:27:03,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ec949f0-7503-4ce3-a384-156b0828bf04/GCA_902771025.1_Rumen_uncultured_genome_RUG11630_genomic.fna.gz --refList GCA_902771025.1_Rumen_uncultured_genome_RUG11630_genomic.fna/target_genomes.txt --output GCA_902771025.1_Rumen_uncultured_genome_RUG11630_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:27:17,227] [INFO] Task succeeded: fastANI
[2023-06-05 02:27:17,227] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd910b180-d4bd-4be4-ad92-2516154511dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:27:17,228] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd910b180-d4bd-4be4-ad92-2516154511dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:27:17,230] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:27:17,230] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 02:27:17,230] [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
--------------------------------------------------------------------------------
[2023-06-05 02:27:17,232] [INFO] DFAST Taxonomy check result was written to GCA_902771025.1_Rumen_uncultured_genome_RUG11630_genomic.fna/tc_result.tsv
[2023-06-05 02:27:17,233] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:27:17,233] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:27:17,234] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd910b180-d4bd-4be4-ad92-2516154511dc/dqc_reference/checkm_data
[2023-06-05 02:27:17,238] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:27:17,263] [INFO] Task started: CheckM
[2023-06-05 02:27:17,263] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902771025.1_Rumen_uncultured_genome_RUG11630_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902771025.1_Rumen_uncultured_genome_RUG11630_genomic.fna/checkm_input GCA_902771025.1_Rumen_uncultured_genome_RUG11630_genomic.fna/checkm_result
[2023-06-05 02:27:48,452] [INFO] Task succeeded: CheckM
[2023-06-05 02:27:48,454] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:27:48,474] [INFO] ===== Completeness check finished =====
[2023-06-05 02:27:48,475] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:27:48,475] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902771025.1_Rumen_uncultured_genome_RUG11630_genomic.fna/markers.fasta)
[2023-06-05 02:27:48,476] [INFO] Task started: Blastn
[2023-06-05 02:27:48,476] [INFO] Running command: blastn -query GCA_902771025.1_Rumen_uncultured_genome_RUG11630_genomic.fna/markers.fasta -db /var/lib/cwl/stgd910b180-d4bd-4be4-ad92-2516154511dc/dqc_reference/reference_markers_gtdb.fasta -out GCA_902771025.1_Rumen_uncultured_genome_RUG11630_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:27:49,388] [INFO] Task succeeded: Blastn
[2023-06-05 02:27:49,392] [INFO] Selected 12 target genomes.
[2023-06-05 02:27:49,392] [INFO] Target genome list was writen to GCA_902771025.1_Rumen_uncultured_genome_RUG11630_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:27:49,400] [INFO] Task started: fastANI
[2023-06-05 02:27:49,400] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ec949f0-7503-4ce3-a384-156b0828bf04/GCA_902771025.1_Rumen_uncultured_genome_RUG11630_genomic.fna.gz --refList GCA_902771025.1_Rumen_uncultured_genome_RUG11630_genomic.fna/target_genomes_gtdb.txt --output GCA_902771025.1_Rumen_uncultured_genome_RUG11630_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:27:54,341] [INFO] Task succeeded: fastANI
[2023-06-05 02:27:54,357] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 02:27:54,357] [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_902769525.1	s__Egerieousia sp902769525	97.7939	514	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Egerieousia	95.0	97.50	96.68	0.91	0.90	5	conclusive
GCA_902789435.1	s__Egerieousia sp002309115	88.7452	403	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Egerieousia	95.0	97.53	97.23	0.88	0.84	8	-
GCA_017962375.1	s__Egerieousia sp017962375	88.0968	475	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Egerieousia	95.0	97.98	97.98	0.88	0.88	2	-
GCA_017961175.1	s__Egerieousia sp017961175	83.8451	359	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Egerieousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316795.1	s__Egerieousia sp900316795	83.4139	411	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Egerieousia	95.0	98.53	97.81	0.94	0.89	6	-
GCA_016285455.1	s__Egerieousia sp016285455	83.0172	390	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Egerieousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017550655.1	s__Egerieousia sp017550655	82.2877	371	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Egerieousia	95.0	96.13	96.13	0.90	0.90	2	-
GCA_017548505.1	s__Egerieousia sp017548505	82.2327	345	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Egerieousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017428325.1	s__Egerieousia sp017428325	81.7913	368	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Egerieousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780455.1	s__Egerieousia sp902780455	81.7208	356	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Egerieousia	95.0	97.74	97.63	0.85	0.84	3	-
GCA_017959005.1	s__Egerieousia sp017959005	78.2281	155	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Egerieousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017554305.1	s__Egerieousia sp017554305	78.1011	139	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Egerieousia	95.0	97.32	97.32	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-06-05 02:27:54,359] [INFO] GTDB search result was written to GCA_902771025.1_Rumen_uncultured_genome_RUG11630_genomic.fna/result_gtdb.tsv
[2023-06-05 02:27:54,359] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:27:54,377] [INFO] DFAST_QC result json was written to GCA_902771025.1_Rumen_uncultured_genome_RUG11630_genomic.fna/dqc_result.json
[2023-06-05 02:27:54,377] [INFO] DFAST_QC completed!
[2023-06-05 02:27:54,378] [INFO] Total running time: 0h1m2s