[2023-06-04 21:46:05,364] [INFO] DFAST_QC pipeline started.
[2023-06-04 21:46:05,366] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 21:46:05,366] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f8b970f-52b9-4d7f-93b7-87112c7a00b0/dqc_reference
[2023-06-04 21:46:06,621] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 21:46:06,622] [INFO] Task started: Prodigal
[2023-06-04 21:46:06,622] [INFO] Running command: gunzip -c /var/lib/cwl/stg33b356f5-cf09-4524-8da0-fa2affd22182/GCA_902767625.1_Rumen_uncultured_genome_RUG11278_genomic.fna.gz | prodigal -d GCA_902767625.1_Rumen_uncultured_genome_RUG11278_genomic.fna/cds.fna -a GCA_902767625.1_Rumen_uncultured_genome_RUG11278_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 21:46:20,938] [INFO] Task succeeded: Prodigal
[2023-06-04 21:46:20,939] [INFO] Task started: HMMsearch
[2023-06-04 21:46:20,939] [INFO] Running command: hmmsearch --tblout GCA_902767625.1_Rumen_uncultured_genome_RUG11278_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f8b970f-52b9-4d7f-93b7-87112c7a00b0/dqc_reference/reference_markers.hmm GCA_902767625.1_Rumen_uncultured_genome_RUG11278_genomic.fna/protein.faa > /dev/null
[2023-06-04 21:46:21,173] [INFO] Task succeeded: HMMsearch
[2023-06-04 21:46:21,174] [INFO] Found 6/6 markers.
[2023-06-04 21:46:21,204] [INFO] Query marker FASTA was written to GCA_902767625.1_Rumen_uncultured_genome_RUG11278_genomic.fna/markers.fasta
[2023-06-04 21:46:21,205] [INFO] Task started: Blastn
[2023-06-04 21:46:21,205] [INFO] Running command: blastn -query GCA_902767625.1_Rumen_uncultured_genome_RUG11278_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f8b970f-52b9-4d7f-93b7-87112c7a00b0/dqc_reference/reference_markers.fasta -out GCA_902767625.1_Rumen_uncultured_genome_RUG11278_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:46:21,867] [INFO] Task succeeded: Blastn
[2023-06-04 21:46:21,871] [INFO] Selected 33 target genomes.
[2023-06-04 21:46:21,872] [INFO] Target genome list was writen to GCA_902767625.1_Rumen_uncultured_genome_RUG11278_genomic.fna/target_genomes.txt
[2023-06-04 21:46:21,876] [INFO] Task started: fastANI
[2023-06-04 21:46:21,876] [INFO] Running command: fastANI --query /var/lib/cwl/stg33b356f5-cf09-4524-8da0-fa2affd22182/GCA_902767625.1_Rumen_uncultured_genome_RUG11278_genomic.fna.gz --refList GCA_902767625.1_Rumen_uncultured_genome_RUG11278_genomic.fna/target_genomes.txt --output GCA_902767625.1_Rumen_uncultured_genome_RUG11278_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 21:46:41,623] [INFO] Task succeeded: fastANI
[2023-06-04 21:46:41,623] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f8b970f-52b9-4d7f-93b7-87112c7a00b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 21:46:41,624] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f8b970f-52b9-4d7f-93b7-87112c7a00b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 21:46:41,626] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 21:46:41,626] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 21:46:41,627] [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
--------------------------------------------------------------------------------
[2023-06-04 21:46:41,629] [INFO] DFAST Taxonomy check result was written to GCA_902767625.1_Rumen_uncultured_genome_RUG11278_genomic.fna/tc_result.tsv
[2023-06-04 21:46:41,629] [INFO] ===== Taxonomy check completed =====
[2023-06-04 21:46:41,630] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 21:46:41,630] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f8b970f-52b9-4d7f-93b7-87112c7a00b0/dqc_reference/checkm_data
[2023-06-04 21:46:41,634] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 21:46:41,665] [INFO] Task started: CheckM
[2023-06-04 21:46:41,665] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902767625.1_Rumen_uncultured_genome_RUG11278_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902767625.1_Rumen_uncultured_genome_RUG11278_genomic.fna/checkm_input GCA_902767625.1_Rumen_uncultured_genome_RUG11278_genomic.fna/checkm_result
[2023-06-04 21:47:24,612] [INFO] Task succeeded: CheckM
[2023-06-04 21:47:24,614] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 18.23%
Strain heterogeneity: 27.27%
--------------------------------------------------------------------------------
[2023-06-04 21:47:24,642] [INFO] ===== Completeness check finished =====
[2023-06-04 21:47:24,642] [INFO] ===== Start GTDB Search =====
[2023-06-04 21:47:24,643] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902767625.1_Rumen_uncultured_genome_RUG11278_genomic.fna/markers.fasta)
[2023-06-04 21:47:24,643] [INFO] Task started: Blastn
[2023-06-04 21:47:24,643] [INFO] Running command: blastn -query GCA_902767625.1_Rumen_uncultured_genome_RUG11278_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f8b970f-52b9-4d7f-93b7-87112c7a00b0/dqc_reference/reference_markers_gtdb.fasta -out GCA_902767625.1_Rumen_uncultured_genome_RUG11278_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:47:25,691] [INFO] Task succeeded: Blastn
[2023-06-04 21:47:25,696] [INFO] Selected 15 target genomes.
[2023-06-04 21:47:25,696] [INFO] Target genome list was writen to GCA_902767625.1_Rumen_uncultured_genome_RUG11278_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 21:47:25,732] [INFO] Task started: fastANI
[2023-06-04 21:47:25,732] [INFO] Running command: fastANI --query /var/lib/cwl/stg33b356f5-cf09-4524-8da0-fa2affd22182/GCA_902767625.1_Rumen_uncultured_genome_RUG11278_genomic.fna.gz --refList GCA_902767625.1_Rumen_uncultured_genome_RUG11278_genomic.fna/target_genomes_gtdb.txt --output GCA_902767625.1_Rumen_uncultured_genome_RUG11278_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 21:47:31,869] [INFO] Task succeeded: fastANI
[2023-06-04 21:47:31,888] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 21:47:31,888] [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_902792815.1	s__Cryptobacteroides sp902792815	97.3975	537	712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.52	96.82	0.86	0.75	13	conclusive
GCA_017651465.1	s__Cryptobacteroides sp017651465	88.1106	486	712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017561765.1	s__Cryptobacteroides sp017561765	80.6738	270	712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902782225.1	s__Cryptobacteroides sp902782225	80.4864	300	712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.55	97.13	0.87	0.83	3	-
GCA_902780175.1	s__Cryptobacteroides sp902780175	80.2343	211	712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	95.78	95.78	0.73	0.73	2	-
GCA_902766255.1	s__Cryptobacteroides sp902766255	80.1754	285	712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017634595.1	s__Cryptobacteroides sp017634595	79.8946	301	712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318565.1	s__Cryptobacteroides sp900318565	79.7941	246	712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.62	96.86	0.83	0.73	9	-
GCA_017554335.1	s__Cryptobacteroides sp017554335	79.1116	241	712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016288775.1	s__Cryptobacteroides sp016288775	79.0946	255	712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017617715.1	s__Cryptobacteroides sp017617715	79.0305	234	712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002309995.1	s__Cryptobacteroides sp002309995	78.6834	199	712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018065265.1	s__Cryptobacteroides sp018065265	77.1036	56	712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004555145.1	s__Cryptobacteroides sp004555145	76.6058	61	712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 21:47:31,890] [INFO] GTDB search result was written to GCA_902767625.1_Rumen_uncultured_genome_RUG11278_genomic.fna/result_gtdb.tsv
[2023-06-04 21:47:31,891] [INFO] ===== GTDB Search completed =====
[2023-06-04 21:47:31,894] [INFO] DFAST_QC result json was written to GCA_902767625.1_Rumen_uncultured_genome_RUG11278_genomic.fna/dqc_result.json
[2023-06-04 21:47:31,894] [INFO] DFAST_QC completed!
[2023-06-04 21:47:31,894] [INFO] Total running time: 0h1m27s