[2023-06-08 09:42:40,082] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:42:40,087] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:42:40,087] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c73fbf3-8ccb-461b-9d82-180bf88e9f23/dqc_reference
[2023-06-08 09:42:42,344] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:42:42,345] [INFO] Task started: Prodigal
[2023-06-08 09:42:42,345] [INFO] Running command: gunzip -c /var/lib/cwl/stg22651eb7-0820-46c5-ac99-7d2cbe535399/GCA_902778145.1_Rumen_uncultured_genome_RUG12346_genomic.fna.gz | prodigal -d GCA_902778145.1_Rumen_uncultured_genome_RUG12346_genomic.fna/cds.fna -a GCA_902778145.1_Rumen_uncultured_genome_RUG12346_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:42:47,706] [INFO] Task succeeded: Prodigal
[2023-06-08 09:42:47,706] [INFO] Task started: HMMsearch
[2023-06-08 09:42:47,707] [INFO] Running command: hmmsearch --tblout GCA_902778145.1_Rumen_uncultured_genome_RUG12346_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c73fbf3-8ccb-461b-9d82-180bf88e9f23/dqc_reference/reference_markers.hmm GCA_902778145.1_Rumen_uncultured_genome_RUG12346_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:42:47,983] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:42:47,985] [INFO] Found 6/6 markers.
[2023-06-08 09:42:48,010] [INFO] Query marker FASTA was written to GCA_902778145.1_Rumen_uncultured_genome_RUG12346_genomic.fna/markers.fasta
[2023-06-08 09:42:48,010] [INFO] Task started: Blastn
[2023-06-08 09:42:48,011] [INFO] Running command: blastn -query GCA_902778145.1_Rumen_uncultured_genome_RUG12346_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c73fbf3-8ccb-461b-9d82-180bf88e9f23/dqc_reference/reference_markers.fasta -out GCA_902778145.1_Rumen_uncultured_genome_RUG12346_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:42:48,592] [INFO] Task succeeded: Blastn
[2023-06-08 09:42:48,598] [INFO] Selected 20 target genomes.
[2023-06-08 09:42:48,599] [INFO] Target genome list was writen to GCA_902778145.1_Rumen_uncultured_genome_RUG12346_genomic.fna/target_genomes.txt
[2023-06-08 09:42:48,606] [INFO] Task started: fastANI
[2023-06-08 09:42:48,606] [INFO] Running command: fastANI --query /var/lib/cwl/stg22651eb7-0820-46c5-ac99-7d2cbe535399/GCA_902778145.1_Rumen_uncultured_genome_RUG12346_genomic.fna.gz --refList GCA_902778145.1_Rumen_uncultured_genome_RUG12346_genomic.fna/target_genomes.txt --output GCA_902778145.1_Rumen_uncultured_genome_RUG12346_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:43:03,874] [INFO] Task succeeded: fastANI
[2023-06-08 09:43:03,874] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c73fbf3-8ccb-461b-9d82-180bf88e9f23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:43:03,875] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c73fbf3-8ccb-461b-9d82-180bf88e9f23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:43:03,877] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:43:03,877] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 09:43:03,877] [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
--------------------------------------------------------------------------------
[2023-06-08 09:43:03,879] [INFO] DFAST Taxonomy check result was written to GCA_902778145.1_Rumen_uncultured_genome_RUG12346_genomic.fna/tc_result.tsv
[2023-06-08 09:43:03,880] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:43:03,880] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:43:03,881] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c73fbf3-8ccb-461b-9d82-180bf88e9f23/dqc_reference/checkm_data
[2023-06-08 09:43:03,884] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:43:03,916] [INFO] Task started: CheckM
[2023-06-08 09:43:03,917] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902778145.1_Rumen_uncultured_genome_RUG12346_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902778145.1_Rumen_uncultured_genome_RUG12346_genomic.fna/checkm_input GCA_902778145.1_Rumen_uncultured_genome_RUG12346_genomic.fna/checkm_result
[2023-06-08 09:43:26,316] [INFO] Task succeeded: CheckM
[2023-06-08 09:43:26,324] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:43:26,348] [INFO] ===== Completeness check finished =====
[2023-06-08 09:43:26,348] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:43:26,349] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902778145.1_Rumen_uncultured_genome_RUG12346_genomic.fna/markers.fasta)
[2023-06-08 09:43:26,349] [INFO] Task started: Blastn
[2023-06-08 09:43:26,349] [INFO] Running command: blastn -query GCA_902778145.1_Rumen_uncultured_genome_RUG12346_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c73fbf3-8ccb-461b-9d82-180bf88e9f23/dqc_reference/reference_markers_gtdb.fasta -out GCA_902778145.1_Rumen_uncultured_genome_RUG12346_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:43:27,292] [INFO] Task succeeded: Blastn
[2023-06-08 09:43:27,339] [INFO] Selected 11 target genomes.
[2023-06-08 09:43:27,339] [INFO] Target genome list was writen to GCA_902778145.1_Rumen_uncultured_genome_RUG12346_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:43:27,345] [INFO] Task started: fastANI
[2023-06-08 09:43:27,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg22651eb7-0820-46c5-ac99-7d2cbe535399/GCA_902778145.1_Rumen_uncultured_genome_RUG12346_genomic.fna.gz --refList GCA_902778145.1_Rumen_uncultured_genome_RUG12346_genomic.fna/target_genomes_gtdb.txt --output GCA_902778145.1_Rumen_uncultured_genome_RUG12346_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:43:33,912] [INFO] Task succeeded: fastANI
[2023-06-08 09:43:33,925] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 09:43:33,925] [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_902778145.1	s__UBA1248 sp902778145	100.0	757	762	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UBA1248	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902762505.1	s__UBA1248 sp902762505	84.9625	456	762	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UBA1248	95.0	97.76	97.76	0.87	0.87	2	-
GCA_017619885.1	s__UBA1248 sp017619885	80.6237	366	762	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UBA1248	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017958705.1	s__UBA1248 sp017958705	80.4963	320	762	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UBA1248	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902784545.1	s__UBA1248 sp902784545	79.4855	298	762	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UBA1248	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002308615.1	s__UBA1248 sp002308615	78.7218	245	762	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UBA1248	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797235.1	s__UBA1248 sp902797235	78.6469	265	762	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UBA1248	95.0	98.46	98.46	0.90	0.90	2	-
GCA_902782785.1	s__UBA1248 sp902782785	78.3916	214	762	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UBA1248	95.0	97.78	97.78	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-06-08 09:43:33,927] [INFO] GTDB search result was written to GCA_902778145.1_Rumen_uncultured_genome_RUG12346_genomic.fna/result_gtdb.tsv
[2023-06-08 09:43:33,928] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:43:33,931] [INFO] DFAST_QC result json was written to GCA_902778145.1_Rumen_uncultured_genome_RUG12346_genomic.fna/dqc_result.json
[2023-06-08 09:43:33,931] [INFO] DFAST_QC completed!
[2023-06-08 09:43:33,931] [INFO] Total running time: 0h0m54s