[2023-06-07 20:40:02,376] [INFO] DFAST_QC pipeline started.
[2023-06-07 20:40:02,379] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 20:40:02,379] [INFO] DQC Reference Directory: /var/lib/cwl/stg94030b0d-99da-4fdd-a51c-0289287b493c/dqc_reference
[2023-06-07 20:40:03,824] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 20:40:03,825] [INFO] Task started: Prodigal
[2023-06-07 20:40:03,825] [INFO] Running command: gunzip -c /var/lib/cwl/stg993f9b6a-c153-4d1c-af32-076e11d533bd/GCA_902793235.1_Rumen_uncultured_genome_RUG13845_genomic.fna.gz | prodigal -d GCA_902793235.1_Rumen_uncultured_genome_RUG13845_genomic.fna/cds.fna -a GCA_902793235.1_Rumen_uncultured_genome_RUG13845_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 20:40:15,468] [INFO] Task succeeded: Prodigal
[2023-06-07 20:40:15,469] [INFO] Task started: HMMsearch
[2023-06-07 20:40:15,469] [INFO] Running command: hmmsearch --tblout GCA_902793235.1_Rumen_uncultured_genome_RUG13845_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94030b0d-99da-4fdd-a51c-0289287b493c/dqc_reference/reference_markers.hmm GCA_902793235.1_Rumen_uncultured_genome_RUG13845_genomic.fna/protein.faa > /dev/null
[2023-06-07 20:40:15,731] [INFO] Task succeeded: HMMsearch
[2023-06-07 20:40:15,733] [INFO] Found 6/6 markers.
[2023-06-07 20:40:15,755] [INFO] Query marker FASTA was written to GCA_902793235.1_Rumen_uncultured_genome_RUG13845_genomic.fna/markers.fasta
[2023-06-07 20:40:15,756] [INFO] Task started: Blastn
[2023-06-07 20:40:15,756] [INFO] Running command: blastn -query GCA_902793235.1_Rumen_uncultured_genome_RUG13845_genomic.fna/markers.fasta -db /var/lib/cwl/stg94030b0d-99da-4fdd-a51c-0289287b493c/dqc_reference/reference_markers.fasta -out GCA_902793235.1_Rumen_uncultured_genome_RUG13845_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:40:16,350] [INFO] Task succeeded: Blastn
[2023-06-07 20:40:16,353] [INFO] Selected 28 target genomes.
[2023-06-07 20:40:16,354] [INFO] Target genome list was writen to GCA_902793235.1_Rumen_uncultured_genome_RUG13845_genomic.fna/target_genomes.txt
[2023-06-07 20:40:16,356] [INFO] Task started: fastANI
[2023-06-07 20:40:16,356] [INFO] Running command: fastANI --query /var/lib/cwl/stg993f9b6a-c153-4d1c-af32-076e11d533bd/GCA_902793235.1_Rumen_uncultured_genome_RUG13845_genomic.fna.gz --refList GCA_902793235.1_Rumen_uncultured_genome_RUG13845_genomic.fna/target_genomes.txt --output GCA_902793235.1_Rumen_uncultured_genome_RUG13845_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 20:40:31,710] [INFO] Task succeeded: fastANI
[2023-06-07 20:40:31,711] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94030b0d-99da-4fdd-a51c-0289287b493c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 20:40:31,711] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94030b0d-99da-4fdd-a51c-0289287b493c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 20:40:31,713] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 20:40:31,713] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 20:40:31,713] [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
--------------------------------------------------------------------------------
[2023-06-07 20:40:31,715] [INFO] DFAST Taxonomy check result was written to GCA_902793235.1_Rumen_uncultured_genome_RUG13845_genomic.fna/tc_result.tsv
[2023-06-07 20:40:31,715] [INFO] ===== Taxonomy check completed =====
[2023-06-07 20:40:31,716] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 20:40:31,716] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94030b0d-99da-4fdd-a51c-0289287b493c/dqc_reference/checkm_data
[2023-06-07 20:40:31,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 20:40:31,743] [INFO] Task started: CheckM
[2023-06-07 20:40:31,744] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902793235.1_Rumen_uncultured_genome_RUG13845_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902793235.1_Rumen_uncultured_genome_RUG13845_genomic.fna/checkm_input GCA_902793235.1_Rumen_uncultured_genome_RUG13845_genomic.fna/checkm_result
[2023-06-07 20:41:07,910] [INFO] Task succeeded: CheckM
[2023-06-07 20:41:07,911] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 6.25%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-07 20:41:07,933] [INFO] ===== Completeness check finished =====
[2023-06-07 20:41:07,933] [INFO] ===== Start GTDB Search =====
[2023-06-07 20:41:07,934] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902793235.1_Rumen_uncultured_genome_RUG13845_genomic.fna/markers.fasta)
[2023-06-07 20:41:07,934] [INFO] Task started: Blastn
[2023-06-07 20:41:07,934] [INFO] Running command: blastn -query GCA_902793235.1_Rumen_uncultured_genome_RUG13845_genomic.fna/markers.fasta -db /var/lib/cwl/stg94030b0d-99da-4fdd-a51c-0289287b493c/dqc_reference/reference_markers_gtdb.fasta -out GCA_902793235.1_Rumen_uncultured_genome_RUG13845_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:41:08,770] [INFO] Task succeeded: Blastn
[2023-06-07 20:41:08,775] [INFO] Selected 15 target genomes.
[2023-06-07 20:41:08,776] [INFO] Target genome list was writen to GCA_902793235.1_Rumen_uncultured_genome_RUG13845_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 20:41:08,778] [INFO] Task started: fastANI
[2023-06-07 20:41:08,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg993f9b6a-c153-4d1c-af32-076e11d533bd/GCA_902793235.1_Rumen_uncultured_genome_RUG13845_genomic.fna.gz --refList GCA_902793235.1_Rumen_uncultured_genome_RUG13845_genomic.fna/target_genomes_gtdb.txt --output GCA_902793235.1_Rumen_uncultured_genome_RUG13845_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 20:41:15,368] [INFO] Task succeeded: fastANI
[2023-06-07 20:41:15,385] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 20:41:15,385] [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_900320185.1	s__Cryptobacteroides sp900320185	98.8441	584	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.66	98.37	0.88	0.82	11	conclusive
GCA_017469745.1	s__Cryptobacteroides sp017469745	78.8545	235	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319685.1	s__Cryptobacteroides sp900319685	78.6142	188	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.18	97.13	0.85	0.68	20	-
GCA_902801885.1	s__Cryptobacteroides sp902801885	78.5844	190	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.96	97.31	0.90	0.87	8	-
GCA_902779765.1	s__Cryptobacteroides sp902779765	78.5597	225	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.01	96.70	0.92	0.90	3	-
GCA_905235085.1	s__Cryptobacteroides sp905235085	78.4936	200	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780935.1	s__Cryptobacteroides sp902780935	78.317	210	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.52	97.52	0.84	0.84	2	-
GCA_017429765.1	s__Cryptobacteroides sp017429765	78.2067	218	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785575.1	s__Cryptobacteroides sp902785575	78.2019	160	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.28	96.35	0.83	0.75	6	-
GCA_017958985.1	s__Cryptobacteroides sp017958985	78.1963	170	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544195.1	s__Cryptobacteroides sp900544195	77.9118	183	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.99	97.97	0.92	0.84	3	-
GCA_902797035.1	s__Cryptobacteroides sp902797035	77.7638	146	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017962025.1	s__Cryptobacteroides sp017962025	77.6843	134	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017557535.1	s__Cryptobacteroides sp017557535	77.6728	152	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018066065.1	s__Cryptobacteroides sp018066065	77.4965	148	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 20:41:15,387] [INFO] GTDB search result was written to GCA_902793235.1_Rumen_uncultured_genome_RUG13845_genomic.fna/result_gtdb.tsv
[2023-06-07 20:41:15,388] [INFO] ===== GTDB Search completed =====
[2023-06-07 20:41:15,391] [INFO] DFAST_QC result json was written to GCA_902793235.1_Rumen_uncultured_genome_RUG13845_genomic.fna/dqc_result.json
[2023-06-07 20:41:15,391] [INFO] DFAST_QC completed!
[2023-06-07 20:41:15,391] [INFO] Total running time: 0h1m13s