[2023-06-07 21:53:21,267] [INFO] DFAST_QC pipeline started.
[2023-06-07 21:53:21,273] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 21:53:21,273] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f9986be-fd44-4c67-b3ab-2a05191b1ccf/dqc_reference
[2023-06-07 21:53:22,569] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 21:53:22,570] [INFO] Task started: Prodigal
[2023-06-07 21:53:22,570] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd0bd533-0ae6-4077-8b44-8f8da2ef73f2/GCA_902774475.1_Rumen_uncultured_genome_RUG11973_genomic.fna.gz | prodigal -d GCA_902774475.1_Rumen_uncultured_genome_RUG11973_genomic.fna/cds.fna -a GCA_902774475.1_Rumen_uncultured_genome_RUG11973_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 21:53:31,893] [INFO] Task succeeded: Prodigal
[2023-06-07 21:53:31,894] [INFO] Task started: HMMsearch
[2023-06-07 21:53:31,894] [INFO] Running command: hmmsearch --tblout GCA_902774475.1_Rumen_uncultured_genome_RUG11973_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f9986be-fd44-4c67-b3ab-2a05191b1ccf/dqc_reference/reference_markers.hmm GCA_902774475.1_Rumen_uncultured_genome_RUG11973_genomic.fna/protein.faa > /dev/null
[2023-06-07 21:53:32,133] [INFO] Task succeeded: HMMsearch
[2023-06-07 21:53:32,135] [INFO] Found 6/6 markers.
[2023-06-07 21:53:32,164] [INFO] Query marker FASTA was written to GCA_902774475.1_Rumen_uncultured_genome_RUG11973_genomic.fna/markers.fasta
[2023-06-07 21:53:32,164] [INFO] Task started: Blastn
[2023-06-07 21:53:32,164] [INFO] Running command: blastn -query GCA_902774475.1_Rumen_uncultured_genome_RUG11973_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f9986be-fd44-4c67-b3ab-2a05191b1ccf/dqc_reference/reference_markers.fasta -out GCA_902774475.1_Rumen_uncultured_genome_RUG11973_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:53:32,853] [INFO] Task succeeded: Blastn
[2023-06-07 21:53:32,857] [INFO] Selected 30 target genomes.
[2023-06-07 21:53:32,858] [INFO] Target genome list was writen to GCA_902774475.1_Rumen_uncultured_genome_RUG11973_genomic.fna/target_genomes.txt
[2023-06-07 21:53:32,862] [INFO] Task started: fastANI
[2023-06-07 21:53:32,862] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd0bd533-0ae6-4077-8b44-8f8da2ef73f2/GCA_902774475.1_Rumen_uncultured_genome_RUG11973_genomic.fna.gz --refList GCA_902774475.1_Rumen_uncultured_genome_RUG11973_genomic.fna/target_genomes.txt --output GCA_902774475.1_Rumen_uncultured_genome_RUG11973_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 21:53:52,701] [INFO] Task succeeded: fastANI
[2023-06-07 21:53:52,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f9986be-fd44-4c67-b3ab-2a05191b1ccf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 21:53:52,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f9986be-fd44-4c67-b3ab-2a05191b1ccf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 21:53:52,705] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 21:53:52,705] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 21:53:52,705] [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 21:53:52,708] [INFO] DFAST Taxonomy check result was written to GCA_902774475.1_Rumen_uncultured_genome_RUG11973_genomic.fna/tc_result.tsv
[2023-06-07 21:53:52,708] [INFO] ===== Taxonomy check completed =====
[2023-06-07 21:53:52,708] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 21:53:52,709] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f9986be-fd44-4c67-b3ab-2a05191b1ccf/dqc_reference/checkm_data
[2023-06-07 21:53:52,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 21:53:52,735] [INFO] Task started: CheckM
[2023-06-07 21:53:52,735] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902774475.1_Rumen_uncultured_genome_RUG11973_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902774475.1_Rumen_uncultured_genome_RUG11973_genomic.fna/checkm_input GCA_902774475.1_Rumen_uncultured_genome_RUG11973_genomic.fna/checkm_result
[2023-06-07 21:54:23,158] [INFO] Task succeeded: CheckM
[2023-06-07 21:54:23,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.71%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 21:54:23,190] [INFO] ===== Completeness check finished =====
[2023-06-07 21:54:23,190] [INFO] ===== Start GTDB Search =====
[2023-06-07 21:54:23,191] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902774475.1_Rumen_uncultured_genome_RUG11973_genomic.fna/markers.fasta)
[2023-06-07 21:54:23,191] [INFO] Task started: Blastn
[2023-06-07 21:54:23,191] [INFO] Running command: blastn -query GCA_902774475.1_Rumen_uncultured_genome_RUG11973_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f9986be-fd44-4c67-b3ab-2a05191b1ccf/dqc_reference/reference_markers_gtdb.fasta -out GCA_902774475.1_Rumen_uncultured_genome_RUG11973_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:54:24,231] [INFO] Task succeeded: Blastn
[2023-06-07 21:54:24,236] [INFO] Selected 22 target genomes.
[2023-06-07 21:54:24,236] [INFO] Target genome list was writen to GCA_902774475.1_Rumen_uncultured_genome_RUG11973_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 21:54:24,245] [INFO] Task started: fastANI
[2023-06-07 21:54:24,245] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd0bd533-0ae6-4077-8b44-8f8da2ef73f2/GCA_902774475.1_Rumen_uncultured_genome_RUG11973_genomic.fna.gz --refList GCA_902774475.1_Rumen_uncultured_genome_RUG11973_genomic.fna/target_genomes_gtdb.txt --output GCA_902774475.1_Rumen_uncultured_genome_RUG11973_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 21:54:34,139] [INFO] Task succeeded: fastANI
[2023-06-07 21:54:34,160] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 21:54:34,160] [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_902768665.1	s__Cryptobacteroides sp902768665	98.8481	522	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.70	96.60	0.87	0.83	3	conclusive
GCA_900316525.1	s__Cryptobacteroides sp900316525	80.1598	238	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.78	96.71	0.88	0.84	4	-
GCA_900316955.1	s__Cryptobacteroides sp900316955	79.9251	240	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017429205.1	s__Cryptobacteroides sp017429205	79.8537	203	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016287075.1	s__Cryptobacteroides sp016287075	79.8169	227	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017464245.1	s__Cryptobacteroides sp017464245	79.7845	203	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318015.1	s__Cryptobacteroides sp900318015	79.458	211	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.28	97.03	0.89	0.81	4	-
GCA_902781705.1	s__Cryptobacteroides sp902781705	79.4565	236	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	96.56	96.56	0.81	0.81	2	-
GCA_017395045.1	s__Cryptobacteroides sp017395045	79.4407	217	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002361625.1	s__Cryptobacteroides sp002361625	79.2185	215	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.42	96.65	0.85	0.82	6	-
GCA_017439305.1	s__Cryptobacteroides sp017439305	79.1629	193	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017476575.1	s__Cryptobacteroides sp017476575	79.1369	200	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017438265.1	s__Cryptobacteroides sp017438265	78.9932	170	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	96.23	96.11	0.87	0.85	4	-
GCA_900167895.1	s__Cryptobacteroides sp900167895	78.6982	177	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.18	97.90	0.94	0.93	3	-
GCA_017438975.1	s__Cryptobacteroides sp017438975	78.6486	175	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233275.1	s__Cryptobacteroides sp905233275	78.6092	190	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016281015.1	s__Cryptobacteroides sp016281015	78.4265	165	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002396335.1	s__Cryptobacteroides sp002396335	78.4016	126	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.10	98.10	0.91	0.91	2	-
GCA_017400135.1	s__Cryptobacteroides sp017400135	78.1399	135	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319185.1	s__Cryptobacteroides sp900319185	78.0771	113	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.95	98.63	0.93	0.89	6	-
GCA_001602885.1	s__Cryptobacteroides sp001602885	78.0307	90	573	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017557325.1	s__Cryptobacteroides sp017557325	77.5463	95	573	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 21:54:34,162] [INFO] GTDB search result was written to GCA_902774475.1_Rumen_uncultured_genome_RUG11973_genomic.fna/result_gtdb.tsv
[2023-06-07 21:54:34,163] [INFO] ===== GTDB Search completed =====
[2023-06-07 21:54:34,166] [INFO] DFAST_QC result json was written to GCA_902774475.1_Rumen_uncultured_genome_RUG11973_genomic.fna/dqc_result.json
[2023-06-07 21:54:34,166] [INFO] DFAST_QC completed!
[2023-06-07 21:54:34,166] [INFO] Total running time: 0h1m13s