[2023-06-08 07:24:28,424] [INFO] DFAST_QC pipeline started.
[2023-06-08 07:24:28,430] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 07:24:28,431] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc3a890c-13cb-4021-8c1e-619bac6b7953/dqc_reference
[2023-06-08 07:24:30,093] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 07:24:30,093] [INFO] Task started: Prodigal
[2023-06-08 07:24:30,094] [INFO] Running command: gunzip -c /var/lib/cwl/stg9679d2e5-5d93-439a-8b8d-bfb7110241e0/GCA_902766985.1_Rumen_uncultured_genome_RUG11209_genomic.fna.gz | prodigal -d GCA_902766985.1_Rumen_uncultured_genome_RUG11209_genomic.fna/cds.fna -a GCA_902766985.1_Rumen_uncultured_genome_RUG11209_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 07:24:39,417] [INFO] Task succeeded: Prodigal
[2023-06-08 07:24:39,417] [INFO] Task started: HMMsearch
[2023-06-08 07:24:39,417] [INFO] Running command: hmmsearch --tblout GCA_902766985.1_Rumen_uncultured_genome_RUG11209_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc3a890c-13cb-4021-8c1e-619bac6b7953/dqc_reference/reference_markers.hmm GCA_902766985.1_Rumen_uncultured_genome_RUG11209_genomic.fna/protein.faa > /dev/null
[2023-06-08 07:24:39,673] [INFO] Task succeeded: HMMsearch
[2023-06-08 07:24:39,674] [INFO] Found 6/6 markers.
[2023-06-08 07:24:39,708] [INFO] Query marker FASTA was written to GCA_902766985.1_Rumen_uncultured_genome_RUG11209_genomic.fna/markers.fasta
[2023-06-08 07:24:39,708] [INFO] Task started: Blastn
[2023-06-08 07:24:39,708] [INFO] Running command: blastn -query GCA_902766985.1_Rumen_uncultured_genome_RUG11209_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc3a890c-13cb-4021-8c1e-619bac6b7953/dqc_reference/reference_markers.fasta -out GCA_902766985.1_Rumen_uncultured_genome_RUG11209_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:24:41,974] [INFO] Task succeeded: Blastn
[2023-06-08 07:24:41,982] [INFO] Selected 28 target genomes.
[2023-06-08 07:24:41,982] [INFO] Target genome list was writen to GCA_902766985.1_Rumen_uncultured_genome_RUG11209_genomic.fna/target_genomes.txt
[2023-06-08 07:24:42,049] [INFO] Task started: fastANI
[2023-06-08 07:24:42,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg9679d2e5-5d93-439a-8b8d-bfb7110241e0/GCA_902766985.1_Rumen_uncultured_genome_RUG11209_genomic.fna.gz --refList GCA_902766985.1_Rumen_uncultured_genome_RUG11209_genomic.fna/target_genomes.txt --output GCA_902766985.1_Rumen_uncultured_genome_RUG11209_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 07:24:58,236] [INFO] Task succeeded: fastANI
[2023-06-08 07:24:58,237] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc3a890c-13cb-4021-8c1e-619bac6b7953/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 07:24:58,237] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc3a890c-13cb-4021-8c1e-619bac6b7953/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 07:24:58,240] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 07:24:58,240] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 07:24:58,240] [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 07:24:58,243] [INFO] DFAST Taxonomy check result was written to GCA_902766985.1_Rumen_uncultured_genome_RUG11209_genomic.fna/tc_result.tsv
[2023-06-08 07:24:58,244] [INFO] ===== Taxonomy check completed =====
[2023-06-08 07:24:58,244] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 07:24:58,244] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc3a890c-13cb-4021-8c1e-619bac6b7953/dqc_reference/checkm_data
[2023-06-08 07:24:58,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 07:24:58,292] [INFO] Task started: CheckM
[2023-06-08 07:24:58,293] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902766985.1_Rumen_uncultured_genome_RUG11209_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902766985.1_Rumen_uncultured_genome_RUG11209_genomic.fna/checkm_input GCA_902766985.1_Rumen_uncultured_genome_RUG11209_genomic.fna/checkm_result
[2023-06-08 07:25:31,061] [INFO] Task succeeded: CheckM
[2023-06-08 07:25:31,063] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 18.52%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-08 07:25:31,165] [INFO] ===== Completeness check finished =====
[2023-06-08 07:25:31,165] [INFO] ===== Start GTDB Search =====
[2023-06-08 07:25:31,165] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902766985.1_Rumen_uncultured_genome_RUG11209_genomic.fna/markers.fasta)
[2023-06-08 07:25:31,166] [INFO] Task started: Blastn
[2023-06-08 07:25:31,166] [INFO] Running command: blastn -query GCA_902766985.1_Rumen_uncultured_genome_RUG11209_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc3a890c-13cb-4021-8c1e-619bac6b7953/dqc_reference/reference_markers_gtdb.fasta -out GCA_902766985.1_Rumen_uncultured_genome_RUG11209_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:25:32,039] [INFO] Task succeeded: Blastn
[2023-06-08 07:25:32,044] [INFO] Selected 21 target genomes.
[2023-06-08 07:25:32,045] [INFO] Target genome list was writen to GCA_902766985.1_Rumen_uncultured_genome_RUG11209_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 07:25:32,095] [INFO] Task started: fastANI
[2023-06-08 07:25:32,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg9679d2e5-5d93-439a-8b8d-bfb7110241e0/GCA_902766985.1_Rumen_uncultured_genome_RUG11209_genomic.fna.gz --refList GCA_902766985.1_Rumen_uncultured_genome_RUG11209_genomic.fna/target_genomes_gtdb.txt --output GCA_902766985.1_Rumen_uncultured_genome_RUG11209_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 07:25:39,201] [INFO] Task succeeded: fastANI
[2023-06-08 07:25:39,216] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 07:25:39,216] [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_902766985.1	s__Cryptobacteroides sp902766985	100.0	404	419	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.09	97.97	0.82	0.68	3	conclusive
GCA_017427885.1	s__Cryptobacteroides sp017427885	80.4802	251	419	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017469745.1	s__Cryptobacteroides sp017469745	78.4524	65	419	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017429765.1	s__Cryptobacteroides sp017429765	77.5356	68	419	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	77.5261	64	419	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.01	96.70	0.92	0.90	3	-
GCA_900320185.1	s__Cryptobacteroides sp900320185	77.1297	65	419	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.66	98.37	0.88	0.82	11	-
GCA_902785825.1	s__Cryptobacteroides sp902785825	77.1284	58	419	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	96.93	95.98	0.90	0.88	3	-
GCA_900319855.1	s__Cryptobacteroides sp900319855	77.0319	58	419	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.60	97.81	0.89	0.84	6	-
GCA_017554335.1	s__Cryptobacteroides sp017554335	76.8563	51	419	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	76.8479	78	419	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.52	97.52	0.84	0.84	2	-
GCA_900317925.1	s__Cryptobacteroides sp900317925	76.7684	58	419	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.64	96.11	0.85	0.74	52	-
GCA_900320545.1	s__Cryptobacteroides sp900320545	76.7242	63	419	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.60	97.27	0.87	0.79	3	-
GCA_902803715.1	s__Cryptobacteroides sp902803715	76.6558	56	419	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.42	97.90	0.88	0.86	3	-
GCA_017428725.1	s__Cryptobacteroides sp017428725	76.5589	58	419	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.64	97.64	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-06-08 07:25:39,218] [INFO] GTDB search result was written to GCA_902766985.1_Rumen_uncultured_genome_RUG11209_genomic.fna/result_gtdb.tsv
[2023-06-08 07:25:39,218] [INFO] ===== GTDB Search completed =====
[2023-06-08 07:25:39,222] [INFO] DFAST_QC result json was written to GCA_902766985.1_Rumen_uncultured_genome_RUG11209_genomic.fna/dqc_result.json
[2023-06-08 07:25:39,222] [INFO] DFAST_QC completed!
[2023-06-08 07:25:39,222] [INFO] Total running time: 0h1m11s