[2023-06-04 18:26:16,666] [INFO] DFAST_QC pipeline started.
[2023-06-04 18:26:16,672] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 18:26:16,673] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4a76106-8ac1-463f-b4fc-85d28874a297/dqc_reference
[2023-06-04 18:26:19,527] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 18:26:19,528] [INFO] Task started: Prodigal
[2023-06-04 18:26:19,528] [INFO] Running command: gunzip -c /var/lib/cwl/stg2def14f8-a773-4d30-93c9-b116b9798e74/GCA_902790035.1_Rumen_uncultured_genome_RUG13528_genomic.fna.gz | prodigal -d GCA_902790035.1_Rumen_uncultured_genome_RUG13528_genomic.fna/cds.fna -a GCA_902790035.1_Rumen_uncultured_genome_RUG13528_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 18:26:32,442] [INFO] Task succeeded: Prodigal
[2023-06-04 18:26:32,443] [INFO] Task started: HMMsearch
[2023-06-04 18:26:32,443] [INFO] Running command: hmmsearch --tblout GCA_902790035.1_Rumen_uncultured_genome_RUG13528_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4a76106-8ac1-463f-b4fc-85d28874a297/dqc_reference/reference_markers.hmm GCA_902790035.1_Rumen_uncultured_genome_RUG13528_genomic.fna/protein.faa > /dev/null
[2023-06-04 18:26:32,706] [INFO] Task succeeded: HMMsearch
[2023-06-04 18:26:32,707] [INFO] Found 6/6 markers.
[2023-06-04 18:26:32,731] [INFO] Query marker FASTA was written to GCA_902790035.1_Rumen_uncultured_genome_RUG13528_genomic.fna/markers.fasta
[2023-06-04 18:26:32,732] [INFO] Task started: Blastn
[2023-06-04 18:26:32,732] [INFO] Running command: blastn -query GCA_902790035.1_Rumen_uncultured_genome_RUG13528_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4a76106-8ac1-463f-b4fc-85d28874a297/dqc_reference/reference_markers.fasta -out GCA_902790035.1_Rumen_uncultured_genome_RUG13528_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:26:33,332] [INFO] Task succeeded: Blastn
[2023-06-04 18:26:33,336] [INFO] Selected 28 target genomes.
[2023-06-04 18:26:33,337] [INFO] Target genome list was writen to GCA_902790035.1_Rumen_uncultured_genome_RUG13528_genomic.fna/target_genomes.txt
[2023-06-04 18:26:33,499] [INFO] Task started: fastANI
[2023-06-04 18:26:33,499] [INFO] Running command: fastANI --query /var/lib/cwl/stg2def14f8-a773-4d30-93c9-b116b9798e74/GCA_902790035.1_Rumen_uncultured_genome_RUG13528_genomic.fna.gz --refList GCA_902790035.1_Rumen_uncultured_genome_RUG13528_genomic.fna/target_genomes.txt --output GCA_902790035.1_Rumen_uncultured_genome_RUG13528_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 18:26:49,795] [INFO] Task succeeded: fastANI
[2023-06-04 18:26:49,796] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4a76106-8ac1-463f-b4fc-85d28874a297/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 18:26:49,796] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4a76106-8ac1-463f-b4fc-85d28874a297/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 18:26:49,798] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 18:26:49,798] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 18:26:49,798] [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 18:26:49,800] [INFO] DFAST Taxonomy check result was written to GCA_902790035.1_Rumen_uncultured_genome_RUG13528_genomic.fna/tc_result.tsv
[2023-06-04 18:26:49,801] [INFO] ===== Taxonomy check completed =====
[2023-06-04 18:26:49,801] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 18:26:49,801] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4a76106-8ac1-463f-b4fc-85d28874a297/dqc_reference/checkm_data
[2023-06-04 18:26:49,805] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 18:26:49,833] [INFO] Task started: CheckM
[2023-06-04 18:26:49,833] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902790035.1_Rumen_uncultured_genome_RUG13528_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902790035.1_Rumen_uncultured_genome_RUG13528_genomic.fna/checkm_input GCA_902790035.1_Rumen_uncultured_genome_RUG13528_genomic.fna/checkm_result
[2023-06-04 18:27:30,552] [INFO] Task succeeded: CheckM
[2023-06-04 18:27:30,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 18:27:30,578] [INFO] ===== Completeness check finished =====
[2023-06-04 18:27:30,578] [INFO] ===== Start GTDB Search =====
[2023-06-04 18:27:30,579] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902790035.1_Rumen_uncultured_genome_RUG13528_genomic.fna/markers.fasta)
[2023-06-04 18:27:30,579] [INFO] Task started: Blastn
[2023-06-04 18:27:30,579] [INFO] Running command: blastn -query GCA_902790035.1_Rumen_uncultured_genome_RUG13528_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4a76106-8ac1-463f-b4fc-85d28874a297/dqc_reference/reference_markers_gtdb.fasta -out GCA_902790035.1_Rumen_uncultured_genome_RUG13528_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:27:31,407] [INFO] Task succeeded: Blastn
[2023-06-04 18:27:31,412] [INFO] Selected 16 target genomes.
[2023-06-04 18:27:31,412] [INFO] Target genome list was writen to GCA_902790035.1_Rumen_uncultured_genome_RUG13528_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 18:27:31,423] [INFO] Task started: fastANI
[2023-06-04 18:27:31,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg2def14f8-a773-4d30-93c9-b116b9798e74/GCA_902790035.1_Rumen_uncultured_genome_RUG13528_genomic.fna.gz --refList GCA_902790035.1_Rumen_uncultured_genome_RUG13528_genomic.fna/target_genomes_gtdb.txt --output GCA_902790035.1_Rumen_uncultured_genome_RUG13528_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 18:27:39,000] [INFO] Task succeeded: fastANI
[2023-06-04 18:27:39,014] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 18:27:39,014] [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_902801885.1	s__Cryptobacteroides sp902801885	98.5226	727	800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.96	97.31	0.90	0.87	8	conclusive
GCA_017469745.1	s__Cryptobacteroides sp017469745	87.0089	628	800	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	80.6038	421	800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.01	96.70	0.92	0.90	3	-
GCA_017962025.1	s__Cryptobacteroides sp017962025	80.5739	420	800	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	80.0601	329	800	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	79.998	320	800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	96.93	95.98	0.90	0.88	3	-
GCA_017627955.1	s__Cryptobacteroides sp017627955	79.7142	321	800	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	79.5139	319	800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.28	96.35	0.83	0.75	6	-
GCA_017429765.1	s__Cryptobacteroides sp017429765	79.482	340	800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902795735.1	s__Cryptobacteroides sp902795735	79.1143	335	800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.61	98.61	0.80	0.80	2	-
GCA_017548985.1	s__Cryptobacteroides sp017548985	79.1002	283	800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900313275.1	s__Cryptobacteroides sp900313275	78.6914	243	800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.24	97.20	0.92	0.82	4	-
GCA_902797035.1	s__Cryptobacteroides sp902797035	78.4664	269	800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902801205.1	s__Cryptobacteroides sp902801205	77.9458	177	800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.36	98.05	0.90	0.89	3	-
GCA_900313205.1	s__Cryptobacteroides sp900313205	77.4395	54	800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.55	96.28	0.83	0.71	4	-
GCA_900318015.1	s__Cryptobacteroides sp900318015	76.4922	119	800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.28	97.03	0.89	0.81	4	-
--------------------------------------------------------------------------------
[2023-06-04 18:27:39,016] [INFO] GTDB search result was written to GCA_902790035.1_Rumen_uncultured_genome_RUG13528_genomic.fna/result_gtdb.tsv
[2023-06-04 18:27:39,017] [INFO] ===== GTDB Search completed =====
[2023-06-04 18:27:39,020] [INFO] DFAST_QC result json was written to GCA_902790035.1_Rumen_uncultured_genome_RUG13528_genomic.fna/dqc_result.json
[2023-06-04 18:27:39,021] [INFO] DFAST_QC completed!
[2023-06-04 18:27:39,021] [INFO] Total running time: 0h1m22s