[2023-06-05 23:13:56,927] [INFO] DFAST_QC pipeline started.
[2023-06-05 23:13:56,929] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 23:13:56,929] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c533a05-99c0-46da-85ba-dcce6dd076ea/dqc_reference
[2023-06-05 23:13:58,075] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 23:13:58,076] [INFO] Task started: Prodigal
[2023-06-05 23:13:58,076] [INFO] Running command: gunzip -c /var/lib/cwl/stg5e15896b-2ca8-4984-90c1-fdf1c20fb18e/GCA_902767005.1_Rumen_uncultured_genome_RUG11224_genomic.fna.gz | prodigal -d GCA_902767005.1_Rumen_uncultured_genome_RUG11224_genomic.fna/cds.fna -a GCA_902767005.1_Rumen_uncultured_genome_RUG11224_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 23:13:59,442] [INFO] Task succeeded: Prodigal
[2023-06-05 23:13:59,443] [INFO] Task started: HMMsearch
[2023-06-05 23:13:59,443] [INFO] Running command: hmmsearch --tblout GCA_902767005.1_Rumen_uncultured_genome_RUG11224_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c533a05-99c0-46da-85ba-dcce6dd076ea/dqc_reference/reference_markers.hmm GCA_902767005.1_Rumen_uncultured_genome_RUG11224_genomic.fna/protein.faa > /dev/null
[2023-06-05 23:13:59,590] [INFO] Task succeeded: HMMsearch
[2023-06-05 23:13:59,591] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5e15896b-2ca8-4984-90c1-fdf1c20fb18e/GCA_902767005.1_Rumen_uncultured_genome_RUG11224_genomic.fna.gz]
[2023-06-05 23:13:59,608] [INFO] Query marker FASTA was written to GCA_902767005.1_Rumen_uncultured_genome_RUG11224_genomic.fna/markers.fasta
[2023-06-05 23:13:59,608] [INFO] Task started: Blastn
[2023-06-05 23:13:59,608] [INFO] Running command: blastn -query GCA_902767005.1_Rumen_uncultured_genome_RUG11224_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c533a05-99c0-46da-85ba-dcce6dd076ea/dqc_reference/reference_markers.fasta -out GCA_902767005.1_Rumen_uncultured_genome_RUG11224_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 23:14:00,054] [INFO] Task succeeded: Blastn
[2023-06-05 23:14:00,057] [INFO] Selected 15 target genomes.
[2023-06-05 23:14:00,057] [INFO] Target genome list was writen to GCA_902767005.1_Rumen_uncultured_genome_RUG11224_genomic.fna/target_genomes.txt
[2023-06-05 23:14:00,065] [INFO] Task started: fastANI
[2023-06-05 23:14:00,065] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e15896b-2ca8-4984-90c1-fdf1c20fb18e/GCA_902767005.1_Rumen_uncultured_genome_RUG11224_genomic.fna.gz --refList GCA_902767005.1_Rumen_uncultured_genome_RUG11224_genomic.fna/target_genomes.txt --output GCA_902767005.1_Rumen_uncultured_genome_RUG11224_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 23:14:04,702] [INFO] Task succeeded: fastANI
[2023-06-05 23:14:04,703] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c533a05-99c0-46da-85ba-dcce6dd076ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 23:14:04,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c533a05-99c0-46da-85ba-dcce6dd076ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 23:14:04,704] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 23:14:04,704] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 23:14:04,704] [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 23:14:04,706] [INFO] DFAST Taxonomy check result was written to GCA_902767005.1_Rumen_uncultured_genome_RUG11224_genomic.fna/tc_result.tsv
[2023-06-05 23:14:04,706] [INFO] ===== Taxonomy check completed =====
[2023-06-05 23:14:04,707] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 23:14:04,707] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c533a05-99c0-46da-85ba-dcce6dd076ea/dqc_reference/checkm_data
[2023-06-05 23:14:04,710] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 23:14:04,725] [INFO] Task started: CheckM
[2023-06-05 23:14:04,725] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902767005.1_Rumen_uncultured_genome_RUG11224_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902767005.1_Rumen_uncultured_genome_RUG11224_genomic.fna/checkm_input GCA_902767005.1_Rumen_uncultured_genome_RUG11224_genomic.fna/checkm_result
[2023-06-05 23:14:15,754] [INFO] Task succeeded: CheckM
[2023-06-05 23:14:15,755] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.61%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 23:14:15,771] [INFO] ===== Completeness check finished =====
[2023-06-05 23:14:15,772] [INFO] ===== Start GTDB Search =====
[2023-06-05 23:14:15,772] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902767005.1_Rumen_uncultured_genome_RUG11224_genomic.fna/markers.fasta)
[2023-06-05 23:14:15,772] [INFO] Task started: Blastn
[2023-06-05 23:14:15,772] [INFO] Running command: blastn -query GCA_902767005.1_Rumen_uncultured_genome_RUG11224_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c533a05-99c0-46da-85ba-dcce6dd076ea/dqc_reference/reference_markers_gtdb.fasta -out GCA_902767005.1_Rumen_uncultured_genome_RUG11224_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 23:14:16,238] [INFO] Task succeeded: Blastn
[2023-06-05 23:14:16,241] [INFO] Selected 17 target genomes.
[2023-06-05 23:14:16,241] [INFO] Target genome list was writen to GCA_902767005.1_Rumen_uncultured_genome_RUG11224_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 23:14:16,247] [INFO] Task started: fastANI
[2023-06-05 23:14:16,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e15896b-2ca8-4984-90c1-fdf1c20fb18e/GCA_902767005.1_Rumen_uncultured_genome_RUG11224_genomic.fna.gz --refList GCA_902767005.1_Rumen_uncultured_genome_RUG11224_genomic.fna/target_genomes_gtdb.txt --output GCA_902767005.1_Rumen_uncultured_genome_RUG11224_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 23:14:20,176] [INFO] Task succeeded: fastANI
[2023-06-05 23:14:20,185] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 23:14:20,185] [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_902767005.1	s__RUG11224 sp902767005	100.0	278	285	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG11224	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002369415.1	s__UBA3789 sp002369415	78.7236	115	285	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017541885.1	s__UBA3789 sp017541885	78.6423	110	285	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783435.1	s__UBA3789 sp902783435	78.5276	105	285	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017432665.1	s__UBA3789 sp017432665	78.3989	97	285	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017511605.1	s__UBA3789 sp017511605	78.2373	70	285	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017550205.1	s__UBA3789 sp017550205	78.1549	66	285	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017510225.1	s__Faecimonas sp017510225	78.0082	75	285	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902798815.1	s__UBA3789 sp902798815	77.9626	85	285	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017519965.1	s__RUG14891 sp017519965	77.877	107	285	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG14891	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017525015.1	s__Coprovivens sp017525015	77.871	50	285	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Coprovivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902768065.1	s__UBA3789 sp902768065	77.3311	88	285	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902796215.1	s__UBA3789 sp902796215	77.0683	67	285	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 23:14:20,187] [INFO] GTDB search result was written to GCA_902767005.1_Rumen_uncultured_genome_RUG11224_genomic.fna/result_gtdb.tsv
[2023-06-05 23:14:20,187] [INFO] ===== GTDB Search completed =====
[2023-06-05 23:14:20,190] [INFO] DFAST_QC result json was written to GCA_902767005.1_Rumen_uncultured_genome_RUG11224_genomic.fna/dqc_result.json
[2023-06-05 23:14:20,190] [INFO] DFAST_QC completed!
[2023-06-05 23:14:20,190] [INFO] Total running time: 0h0m23s