[2023-06-04 18:26:46,784] [INFO] DFAST_QC pipeline started.
[2023-06-04 18:26:46,787] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 18:26:46,787] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e9f2c1e-cdbc-47f2-b78b-aa5012ba24ed/dqc_reference
[2023-06-04 18:26:48,018] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 18:26:48,019] [INFO] Task started: Prodigal
[2023-06-04 18:26:48,019] [INFO] Running command: gunzip -c /var/lib/cwl/stgf43722b5-e4ad-4f8c-bc52-4c27f3b7da80/GCA_902792585.1_Rumen_uncultured_genome_RUG13791_genomic.fna.gz | prodigal -d GCA_902792585.1_Rumen_uncultured_genome_RUG13791_genomic.fna/cds.fna -a GCA_902792585.1_Rumen_uncultured_genome_RUG13791_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 18:27:00,004] [INFO] Task succeeded: Prodigal
[2023-06-04 18:27:00,005] [INFO] Task started: HMMsearch
[2023-06-04 18:27:00,005] [INFO] Running command: hmmsearch --tblout GCA_902792585.1_Rumen_uncultured_genome_RUG13791_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e9f2c1e-cdbc-47f2-b78b-aa5012ba24ed/dqc_reference/reference_markers.hmm GCA_902792585.1_Rumen_uncultured_genome_RUG13791_genomic.fna/protein.faa > /dev/null
[2023-06-04 18:27:00,201] [INFO] Task succeeded: HMMsearch
[2023-06-04 18:27:00,202] [INFO] Found 6/6 markers.
[2023-06-04 18:27:00,226] [INFO] Query marker FASTA was written to GCA_902792585.1_Rumen_uncultured_genome_RUG13791_genomic.fna/markers.fasta
[2023-06-04 18:27:00,227] [INFO] Task started: Blastn
[2023-06-04 18:27:00,227] [INFO] Running command: blastn -query GCA_902792585.1_Rumen_uncultured_genome_RUG13791_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e9f2c1e-cdbc-47f2-b78b-aa5012ba24ed/dqc_reference/reference_markers.fasta -out GCA_902792585.1_Rumen_uncultured_genome_RUG13791_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:27:00,794] [INFO] Task succeeded: Blastn
[2023-06-04 18:27:00,798] [INFO] Selected 28 target genomes.
[2023-06-04 18:27:00,799] [INFO] Target genome list was writen to GCA_902792585.1_Rumen_uncultured_genome_RUG13791_genomic.fna/target_genomes.txt
[2023-06-04 18:27:00,846] [INFO] Task started: fastANI
[2023-06-04 18:27:00,846] [INFO] Running command: fastANI --query /var/lib/cwl/stgf43722b5-e4ad-4f8c-bc52-4c27f3b7da80/GCA_902792585.1_Rumen_uncultured_genome_RUG13791_genomic.fna.gz --refList GCA_902792585.1_Rumen_uncultured_genome_RUG13791_genomic.fna/target_genomes.txt --output GCA_902792585.1_Rumen_uncultured_genome_RUG13791_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 18:27:14,572] [INFO] Task succeeded: fastANI
[2023-06-04 18:27:14,573] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e9f2c1e-cdbc-47f2-b78b-aa5012ba24ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 18:27:14,573] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e9f2c1e-cdbc-47f2-b78b-aa5012ba24ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 18:27:14,575] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 18:27:14,576] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 18:27:14,576] [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 18:27:14,577] [INFO] DFAST Taxonomy check result was written to GCA_902792585.1_Rumen_uncultured_genome_RUG13791_genomic.fna/tc_result.tsv
[2023-06-04 18:27:14,578] [INFO] ===== Taxonomy check completed =====
[2023-06-04 18:27:14,578] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 18:27:14,578] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e9f2c1e-cdbc-47f2-b78b-aa5012ba24ed/dqc_reference/checkm_data
[2023-06-04 18:27:14,581] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 18:27:14,611] [INFO] Task started: CheckM
[2023-06-04 18:27:14,611] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902792585.1_Rumen_uncultured_genome_RUG13791_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902792585.1_Rumen_uncultured_genome_RUG13791_genomic.fna/checkm_input GCA_902792585.1_Rumen_uncultured_genome_RUG13791_genomic.fna/checkm_result
[2023-06-04 18:27:50,405] [INFO] Task succeeded: CheckM
[2023-06-04 18:27:50,406] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-04 18:27:50,425] [INFO] ===== Completeness check finished =====
[2023-06-04 18:27:50,425] [INFO] ===== Start GTDB Search =====
[2023-06-04 18:27:50,425] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902792585.1_Rumen_uncultured_genome_RUG13791_genomic.fna/markers.fasta)
[2023-06-04 18:27:50,426] [INFO] Task started: Blastn
[2023-06-04 18:27:50,426] [INFO] Running command: blastn -query GCA_902792585.1_Rumen_uncultured_genome_RUG13791_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e9f2c1e-cdbc-47f2-b78b-aa5012ba24ed/dqc_reference/reference_markers_gtdb.fasta -out GCA_902792585.1_Rumen_uncultured_genome_RUG13791_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:27:51,262] [INFO] Task succeeded: Blastn
[2023-06-04 18:27:51,266] [INFO] Selected 16 target genomes.
[2023-06-04 18:27:51,266] [INFO] Target genome list was writen to GCA_902792585.1_Rumen_uncultured_genome_RUG13791_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 18:27:51,335] [INFO] Task started: fastANI
[2023-06-04 18:27:51,335] [INFO] Running command: fastANI --query /var/lib/cwl/stgf43722b5-e4ad-4f8c-bc52-4c27f3b7da80/GCA_902792585.1_Rumen_uncultured_genome_RUG13791_genomic.fna.gz --refList GCA_902792585.1_Rumen_uncultured_genome_RUG13791_genomic.fna/target_genomes_gtdb.txt --output GCA_902792585.1_Rumen_uncultured_genome_RUG13791_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 18:27:58,447] [INFO] Task succeeded: fastANI
[2023-06-04 18:27:58,461] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 18:27:58,461] [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	98.8319	545	658	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_902801885.1	s__Cryptobacteroides sp902801885	78.8371	191	658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.96	97.31	0.90	0.87	8	-
GCA_900319685.1	s__Cryptobacteroides sp900319685	78.7774	180	658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.18	97.13	0.85	0.68	20	-
GCA_017469745.1	s__Cryptobacteroides sp017469745	78.7615	223	658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779765.1	s__Cryptobacteroides sp902779765	78.5992	210	658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.01	96.70	0.92	0.90	3	-
GCA_017429765.1	s__Cryptobacteroides sp017429765	78.5259	191	658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235085.1	s__Cryptobacteroides sp905235085	78.4399	189	658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017958985.1	s__Cryptobacteroides sp017958985	78.4215	172	658	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	78.3865	197	658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.52	97.52	0.84	0.84	2	-
GCA_017962025.1	s__Cryptobacteroides sp017962025	78.1897	121	658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000433355.1	s__Cryptobacteroides sp000433355	78.1537	162	658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.66	97.93	0.86	0.80	6	-
GCA_002438845.1	s__Cryptobacteroides sp002438845	78.0563	148	658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.65	99.58	0.89	0.89	3	-
GCA_900320365.1	s__Cryptobacteroides sp900320365	78.0094	116	658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.02	96.04	0.92	0.86	3	-
GCA_902785575.1	s__Cryptobacteroides sp902785575	77.8189	153	658	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.28	96.35	0.83	0.75	6	-
GCA_017557535.1	s__Cryptobacteroides sp017557535	77.7461	144	658	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	77.5329	139	658	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 18:27:58,467] [INFO] GTDB search result was written to GCA_902792585.1_Rumen_uncultured_genome_RUG13791_genomic.fna/result_gtdb.tsv
[2023-06-04 18:27:58,467] [INFO] ===== GTDB Search completed =====
[2023-06-04 18:27:58,470] [INFO] DFAST_QC result json was written to GCA_902792585.1_Rumen_uncultured_genome_RUG13791_genomic.fna/dqc_result.json
[2023-06-04 18:27:58,470] [INFO] DFAST_QC completed!
[2023-06-04 18:27:58,470] [INFO] Total running time: 0h1m12s