[2023-06-08 03:14:39,278] [INFO] DFAST_QC pipeline started.
[2023-06-08 03:14:39,287] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 03:14:39,287] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0880d6d-cd99-46fd-8bc1-1820a944e207/dqc_reference
[2023-06-08 03:14:40,594] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 03:14:40,595] [INFO] Task started: Prodigal
[2023-06-08 03:14:40,595] [INFO] Running command: gunzip -c /var/lib/cwl/stgfbd4bbc4-c064-4cc0-9b06-784e81d2cc9e/GCA_902757285.1_Rumen_uncultured_genome_RUG10242_genomic.fna.gz | prodigal -d GCA_902757285.1_Rumen_uncultured_genome_RUG10242_genomic.fna/cds.fna -a GCA_902757285.1_Rumen_uncultured_genome_RUG10242_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 03:14:55,194] [INFO] Task succeeded: Prodigal
[2023-06-08 03:14:55,195] [INFO] Task started: HMMsearch
[2023-06-08 03:14:55,195] [INFO] Running command: hmmsearch --tblout GCA_902757285.1_Rumen_uncultured_genome_RUG10242_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0880d6d-cd99-46fd-8bc1-1820a944e207/dqc_reference/reference_markers.hmm GCA_902757285.1_Rumen_uncultured_genome_RUG10242_genomic.fna/protein.faa > /dev/null
[2023-06-08 03:14:55,432] [INFO] Task succeeded: HMMsearch
[2023-06-08 03:14:55,433] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfbd4bbc4-c064-4cc0-9b06-784e81d2cc9e/GCA_902757285.1_Rumen_uncultured_genome_RUG10242_genomic.fna.gz]
[2023-06-08 03:14:55,463] [INFO] Query marker FASTA was written to GCA_902757285.1_Rumen_uncultured_genome_RUG10242_genomic.fna/markers.fasta
[2023-06-08 03:14:55,464] [INFO] Task started: Blastn
[2023-06-08 03:14:55,464] [INFO] Running command: blastn -query GCA_902757285.1_Rumen_uncultured_genome_RUG10242_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0880d6d-cd99-46fd-8bc1-1820a944e207/dqc_reference/reference_markers.fasta -out GCA_902757285.1_Rumen_uncultured_genome_RUG10242_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:14:56,103] [INFO] Task succeeded: Blastn
[2023-06-08 03:14:56,107] [INFO] Selected 17 target genomes.
[2023-06-08 03:14:56,107] [INFO] Target genome list was writen to GCA_902757285.1_Rumen_uncultured_genome_RUG10242_genomic.fna/target_genomes.txt
[2023-06-08 03:14:56,108] [INFO] Task started: fastANI
[2023-06-08 03:14:56,108] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbd4bbc4-c064-4cc0-9b06-784e81d2cc9e/GCA_902757285.1_Rumen_uncultured_genome_RUG10242_genomic.fna.gz --refList GCA_902757285.1_Rumen_uncultured_genome_RUG10242_genomic.fna/target_genomes.txt --output GCA_902757285.1_Rumen_uncultured_genome_RUG10242_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 03:15:04,344] [INFO] Task succeeded: fastANI
[2023-06-08 03:15:04,344] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0880d6d-cd99-46fd-8bc1-1820a944e207/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 03:15:04,345] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0880d6d-cd99-46fd-8bc1-1820a944e207/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 03:15:04,346] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 03:15:04,346] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 03:15:04,346] [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 03:15:04,348] [INFO] DFAST Taxonomy check result was written to GCA_902757285.1_Rumen_uncultured_genome_RUG10242_genomic.fna/tc_result.tsv
[2023-06-08 03:15:04,349] [INFO] ===== Taxonomy check completed =====
[2023-06-08 03:15:04,349] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 03:15:04,349] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0880d6d-cd99-46fd-8bc1-1820a944e207/dqc_reference/checkm_data
[2023-06-08 03:15:04,352] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 03:15:04,382] [INFO] Task started: CheckM
[2023-06-08 03:15:04,382] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902757285.1_Rumen_uncultured_genome_RUG10242_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902757285.1_Rumen_uncultured_genome_RUG10242_genomic.fna/checkm_input GCA_902757285.1_Rumen_uncultured_genome_RUG10242_genomic.fna/checkm_result
[2023-06-08 03:15:47,858] [INFO] Task succeeded: CheckM
[2023-06-08 03:15:47,860] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 03:15:47,881] [INFO] ===== Completeness check finished =====
[2023-06-08 03:15:47,881] [INFO] ===== Start GTDB Search =====
[2023-06-08 03:15:47,882] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902757285.1_Rumen_uncultured_genome_RUG10242_genomic.fna/markers.fasta)
[2023-06-08 03:15:47,882] [INFO] Task started: Blastn
[2023-06-08 03:15:47,882] [INFO] Running command: blastn -query GCA_902757285.1_Rumen_uncultured_genome_RUG10242_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0880d6d-cd99-46fd-8bc1-1820a944e207/dqc_reference/reference_markers_gtdb.fasta -out GCA_902757285.1_Rumen_uncultured_genome_RUG10242_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:15:48,931] [INFO] Task succeeded: Blastn
[2023-06-08 03:15:48,935] [INFO] Selected 10 target genomes.
[2023-06-08 03:15:48,936] [INFO] Target genome list was writen to GCA_902757285.1_Rumen_uncultured_genome_RUG10242_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 03:15:48,937] [INFO] Task started: fastANI
[2023-06-08 03:15:48,937] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbd4bbc4-c064-4cc0-9b06-784e81d2cc9e/GCA_902757285.1_Rumen_uncultured_genome_RUG10242_genomic.fna.gz --refList GCA_902757285.1_Rumen_uncultured_genome_RUG10242_genomic.fna/target_genomes_gtdb.txt --output GCA_902757285.1_Rumen_uncultured_genome_RUG10242_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 03:15:54,431] [INFO] Task succeeded: fastANI
[2023-06-08 03:15:54,446] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 03:15:54,446] [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_900318835.1	s__UBA1711 sp900318835	100.0	756	759	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_900316235.1	s__UBA1711 sp900316235	84.5816	517	759	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	97.94	97.43	0.88	0.79	8	-
GCA_002349055.1	s__UBA1711 sp002349055	84.3991	526	759	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	99.90	99.90	0.97	0.97	2	-
GCA_902771735.1	s__UBA1711 sp902771735	83.1559	462	759	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	97.93	97.68	0.89	0.88	5	-
GCA_902800395.1	s__UBA1711 sp902800395	82.6943	396	759	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902774395.1	s__UBA1711 sp902774395	82.6349	442	759	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775135.1	s__UBA1711 sp902775135	82.0031	401	759	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002372855.1	s__UBA1711 sp002372855	81.5985	331	759	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	97.33	96.12	0.84	0.73	7	-
GCA_017483575.1	s__UBA1711 sp017483575	81.5177	364	759	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902776365.1	s__UBA1711 sp902776365	81.4728	408	759	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	98.34	98.29	0.90	0.84	6	-
--------------------------------------------------------------------------------
[2023-06-08 03:15:54,448] [INFO] GTDB search result was written to GCA_902757285.1_Rumen_uncultured_genome_RUG10242_genomic.fna/result_gtdb.tsv
[2023-06-08 03:15:54,449] [INFO] ===== GTDB Search completed =====
[2023-06-08 03:15:54,452] [INFO] DFAST_QC result json was written to GCA_902757285.1_Rumen_uncultured_genome_RUG10242_genomic.fna/dqc_result.json
[2023-06-08 03:15:54,452] [INFO] DFAST_QC completed!
[2023-06-08 03:15:54,452] [INFO] Total running time: 0h1m15s