[2023-06-08 12:44:45,838] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:44:45,842] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:44:45,842] [INFO] DQC Reference Directory: /var/lib/cwl/stg7565f69b-bd75-4098-9011-d3fcb80eb035/dqc_reference
[2023-06-08 12:44:48,032] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:44:48,033] [INFO] Task started: Prodigal
[2023-06-08 12:44:48,033] [INFO] Running command: gunzip -c /var/lib/cwl/stg691377dd-f4ca-4e10-b7b4-9adb6eace9ae/GCA_902795735.1_Rumen_uncultured_genome_RUG14092_genomic.fna.gz | prodigal -d GCA_902795735.1_Rumen_uncultured_genome_RUG14092_genomic.fna/cds.fna -a GCA_902795735.1_Rumen_uncultured_genome_RUG14092_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:44:59,910] [INFO] Task succeeded: Prodigal
[2023-06-08 12:44:59,911] [INFO] Task started: HMMsearch
[2023-06-08 12:44:59,911] [INFO] Running command: hmmsearch --tblout GCA_902795735.1_Rumen_uncultured_genome_RUG14092_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7565f69b-bd75-4098-9011-d3fcb80eb035/dqc_reference/reference_markers.hmm GCA_902795735.1_Rumen_uncultured_genome_RUG14092_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:45:00,140] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:45:00,142] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg691377dd-f4ca-4e10-b7b4-9adb6eace9ae/GCA_902795735.1_Rumen_uncultured_genome_RUG14092_genomic.fna.gz]
[2023-06-08 12:45:00,168] [INFO] Query marker FASTA was written to GCA_902795735.1_Rumen_uncultured_genome_RUG14092_genomic.fna/markers.fasta
[2023-06-08 12:45:00,168] [INFO] Task started: Blastn
[2023-06-08 12:45:00,168] [INFO] Running command: blastn -query GCA_902795735.1_Rumen_uncultured_genome_RUG14092_genomic.fna/markers.fasta -db /var/lib/cwl/stg7565f69b-bd75-4098-9011-d3fcb80eb035/dqc_reference/reference_markers.fasta -out GCA_902795735.1_Rumen_uncultured_genome_RUG14092_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:45:00,741] [INFO] Task succeeded: Blastn
[2023-06-08 12:45:00,746] [INFO] Selected 23 target genomes.
[2023-06-08 12:45:00,746] [INFO] Target genome list was writen to GCA_902795735.1_Rumen_uncultured_genome_RUG14092_genomic.fna/target_genomes.txt
[2023-06-08 12:45:00,750] [INFO] Task started: fastANI
[2023-06-08 12:45:00,751] [INFO] Running command: fastANI --query /var/lib/cwl/stg691377dd-f4ca-4e10-b7b4-9adb6eace9ae/GCA_902795735.1_Rumen_uncultured_genome_RUG14092_genomic.fna.gz --refList GCA_902795735.1_Rumen_uncultured_genome_RUG14092_genomic.fna/target_genomes.txt --output GCA_902795735.1_Rumen_uncultured_genome_RUG14092_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:45:14,918] [INFO] Task succeeded: fastANI
[2023-06-08 12:45:14,919] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7565f69b-bd75-4098-9011-d3fcb80eb035/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:45:14,920] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7565f69b-bd75-4098-9011-d3fcb80eb035/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:45:14,922] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:45:14,922] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 12:45:14,922] [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
--------------------------------------------------------------------------------
[2023-06-08 12:45:14,925] [INFO] DFAST Taxonomy check result was written to GCA_902795735.1_Rumen_uncultured_genome_RUG14092_genomic.fna/tc_result.tsv
[2023-06-08 12:45:14,925] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:45:14,926] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:45:14,926] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7565f69b-bd75-4098-9011-d3fcb80eb035/dqc_reference/checkm_data
[2023-06-08 12:45:14,930] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:45:14,957] [INFO] Task started: CheckM
[2023-06-08 12:45:14,957] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902795735.1_Rumen_uncultured_genome_RUG14092_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902795735.1_Rumen_uncultured_genome_RUG14092_genomic.fna/checkm_input GCA_902795735.1_Rumen_uncultured_genome_RUG14092_genomic.fna/checkm_result
[2023-06-08 12:45:52,894] [INFO] Task succeeded: CheckM
[2023-06-08 12:45:52,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.40%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:45:52,922] [INFO] ===== Completeness check finished =====
[2023-06-08 12:45:52,922] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:45:52,923] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902795735.1_Rumen_uncultured_genome_RUG14092_genomic.fna/markers.fasta)
[2023-06-08 12:45:52,923] [INFO] Task started: Blastn
[2023-06-08 12:45:52,923] [INFO] Running command: blastn -query GCA_902795735.1_Rumen_uncultured_genome_RUG14092_genomic.fna/markers.fasta -db /var/lib/cwl/stg7565f69b-bd75-4098-9011-d3fcb80eb035/dqc_reference/reference_markers_gtdb.fasta -out GCA_902795735.1_Rumen_uncultured_genome_RUG14092_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:45:53,746] [INFO] Task succeeded: Blastn
[2023-06-08 12:45:53,751] [INFO] Selected 17 target genomes.
[2023-06-08 12:45:53,751] [INFO] Target genome list was writen to GCA_902795735.1_Rumen_uncultured_genome_RUG14092_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:45:53,756] [INFO] Task started: fastANI
[2023-06-08 12:45:53,756] [INFO] Running command: fastANI --query /var/lib/cwl/stg691377dd-f4ca-4e10-b7b4-9adb6eace9ae/GCA_902795735.1_Rumen_uncultured_genome_RUG14092_genomic.fna.gz --refList GCA_902795735.1_Rumen_uncultured_genome_RUG14092_genomic.fna/target_genomes_gtdb.txt --output GCA_902795735.1_Rumen_uncultured_genome_RUG14092_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:46:00,751] [INFO] Task succeeded: fastANI
[2023-06-08 12:46:00,767] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 12:46:00,768] [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_902795735.1	s__Cryptobacteroides sp902795735	100.0	668	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.61	98.61	0.80	0.80	2	conclusive
GCA_017469745.1	s__Cryptobacteroides sp017469745	79.201	321	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902801885.1	s__Cryptobacteroides sp902801885	79.1621	316	677	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	78.5986	281	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.01	96.70	0.92	0.90	3	-
GCA_902780935.1	s__Cryptobacteroides sp902780935	78.3637	240	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.52	97.52	0.84	0.84	2	-
GCA_902785825.1	s__Cryptobacteroides sp902785825	78.1699	225	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	96.93	95.98	0.90	0.88	3	-
GCA_017429765.1	s__Cryptobacteroides sp017429765	78.0219	234	677	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	77.9492	243	677	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	77.8722	199	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.28	96.35	0.83	0.75	6	-
GCA_017548985.1	s__Cryptobacteroides sp017548985	77.5934	215	677	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	77.5636	155	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.18	97.13	0.85	0.68	20	-
GCA_017478125.1	s__Cryptobacteroides sp017478125	77.2854	158	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000431015.1	s__Cryptobacteroides sp000431015	77.1973	149	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.39	98.13	0.87	0.74	9	-
GCA_016290835.1	s__Cryptobacteroides sp016290835	76.1587	51	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900167895.1	s__Cryptobacteroides sp900167895	75.8326	52	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.18	97.90	0.94	0.93	3	-
--------------------------------------------------------------------------------
[2023-06-08 12:46:00,770] [INFO] GTDB search result was written to GCA_902795735.1_Rumen_uncultured_genome_RUG14092_genomic.fna/result_gtdb.tsv
[2023-06-08 12:46:00,770] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:46:00,773] [INFO] DFAST_QC result json was written to GCA_902795735.1_Rumen_uncultured_genome_RUG14092_genomic.fna/dqc_result.json
[2023-06-08 12:46:00,773] [INFO] DFAST_QC completed!
[2023-06-08 12:46:00,773] [INFO] Total running time: 0h1m15s