[2023-06-08 08:34:51,030] [INFO] DFAST_QC pipeline started.
[2023-06-08 08:34:51,034] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 08:34:51,034] [INFO] DQC Reference Directory: /var/lib/cwl/stg87412898-6f91-495e-8c73-1725589fbe8b/dqc_reference
[2023-06-08 08:34:52,347] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 08:34:52,348] [INFO] Task started: Prodigal
[2023-06-08 08:34:52,349] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd7691e3-843e-4a74-8ab5-10a9d26955a7/GCA_902795165.1_Rumen_uncultured_genome_RUG14044_genomic.fna.gz | prodigal -d GCA_902795165.1_Rumen_uncultured_genome_RUG14044_genomic.fna/cds.fna -a GCA_902795165.1_Rumen_uncultured_genome_RUG14044_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 08:35:06,821] [INFO] Task succeeded: Prodigal
[2023-06-08 08:35:06,822] [INFO] Task started: HMMsearch
[2023-06-08 08:35:06,822] [INFO] Running command: hmmsearch --tblout GCA_902795165.1_Rumen_uncultured_genome_RUG14044_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87412898-6f91-495e-8c73-1725589fbe8b/dqc_reference/reference_markers.hmm GCA_902795165.1_Rumen_uncultured_genome_RUG14044_genomic.fna/protein.faa > /dev/null
[2023-06-08 08:35:07,116] [INFO] Task succeeded: HMMsearch
[2023-06-08 08:35:07,117] [INFO] Found 6/6 markers.
[2023-06-08 08:35:07,144] [INFO] Query marker FASTA was written to GCA_902795165.1_Rumen_uncultured_genome_RUG14044_genomic.fna/markers.fasta
[2023-06-08 08:35:07,144] [INFO] Task started: Blastn
[2023-06-08 08:35:07,144] [INFO] Running command: blastn -query GCA_902795165.1_Rumen_uncultured_genome_RUG14044_genomic.fna/markers.fasta -db /var/lib/cwl/stg87412898-6f91-495e-8c73-1725589fbe8b/dqc_reference/reference_markers.fasta -out GCA_902795165.1_Rumen_uncultured_genome_RUG14044_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:35:07,770] [INFO] Task succeeded: Blastn
[2023-06-08 08:35:07,774] [INFO] Selected 24 target genomes.
[2023-06-08 08:35:07,774] [INFO] Target genome list was writen to GCA_902795165.1_Rumen_uncultured_genome_RUG14044_genomic.fna/target_genomes.txt
[2023-06-08 08:35:07,775] [INFO] Task started: fastANI
[2023-06-08 08:35:07,775] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd7691e3-843e-4a74-8ab5-10a9d26955a7/GCA_902795165.1_Rumen_uncultured_genome_RUG14044_genomic.fna.gz --refList GCA_902795165.1_Rumen_uncultured_genome_RUG14044_genomic.fna/target_genomes.txt --output GCA_902795165.1_Rumen_uncultured_genome_RUG14044_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 08:35:23,207] [INFO] Task succeeded: fastANI
[2023-06-08 08:35:23,207] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87412898-6f91-495e-8c73-1725589fbe8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 08:35:23,208] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87412898-6f91-495e-8c73-1725589fbe8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 08:35:23,209] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 08:35:23,209] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 08:35:23,209] [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 08:35:23,211] [INFO] DFAST Taxonomy check result was written to GCA_902795165.1_Rumen_uncultured_genome_RUG14044_genomic.fna/tc_result.tsv
[2023-06-08 08:35:23,211] [INFO] ===== Taxonomy check completed =====
[2023-06-08 08:35:23,211] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 08:35:23,212] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87412898-6f91-495e-8c73-1725589fbe8b/dqc_reference/checkm_data
[2023-06-08 08:35:23,214] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 08:35:23,241] [INFO] Task started: CheckM
[2023-06-08 08:35:23,241] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902795165.1_Rumen_uncultured_genome_RUG14044_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902795165.1_Rumen_uncultured_genome_RUG14044_genomic.fna/checkm_input GCA_902795165.1_Rumen_uncultured_genome_RUG14044_genomic.fna/checkm_result
[2023-06-08 08:36:06,668] [INFO] Task succeeded: CheckM
[2023-06-08 08:36:06,669] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 08:36:06,690] [INFO] ===== Completeness check finished =====
[2023-06-08 08:36:06,691] [INFO] ===== Start GTDB Search =====
[2023-06-08 08:36:06,691] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902795165.1_Rumen_uncultured_genome_RUG14044_genomic.fna/markers.fasta)
[2023-06-08 08:36:06,692] [INFO] Task started: Blastn
[2023-06-08 08:36:06,692] [INFO] Running command: blastn -query GCA_902795165.1_Rumen_uncultured_genome_RUG14044_genomic.fna/markers.fasta -db /var/lib/cwl/stg87412898-6f91-495e-8c73-1725589fbe8b/dqc_reference/reference_markers_gtdb.fasta -out GCA_902795165.1_Rumen_uncultured_genome_RUG14044_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:36:07,545] [INFO] Task succeeded: Blastn
[2023-06-08 08:36:07,549] [INFO] Selected 19 target genomes.
[2023-06-08 08:36:07,549] [INFO] Target genome list was writen to GCA_902795165.1_Rumen_uncultured_genome_RUG14044_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 08:36:07,551] [INFO] Task started: fastANI
[2023-06-08 08:36:07,551] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd7691e3-843e-4a74-8ab5-10a9d26955a7/GCA_902795165.1_Rumen_uncultured_genome_RUG14044_genomic.fna.gz --refList GCA_902795165.1_Rumen_uncultured_genome_RUG14044_genomic.fna/target_genomes_gtdb.txt --output GCA_902795165.1_Rumen_uncultured_genome_RUG14044_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 08:36:15,388] [INFO] Task succeeded: fastANI
[2023-06-08 08:36:15,413] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 08:36:15,414] [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_002393945.1	s__Cryptobacteroides sp002393945	96.9699	658	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.01	96.97	0.87	0.81	4	conclusive
GCA_017458265.1	s__Cryptobacteroides sp017458265	89.8647	508	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.67	97.67	0.81	0.81	2	-
GCA_017428945.1	s__Cryptobacteroides sp017428945	80.4436	340	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002395605.1	s__Cryptobacteroides sp002395605	80.0167	249	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.45	97.45	0.83	0.83	2	-
GCA_017477335.1	s__Cryptobacteroides sp017477335	79.7126	131	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017447815.1	s__Cryptobacteroides sp017447815	79.1983	240	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017480345.1	s__Cryptobacteroides sp017480345	79.0982	231	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.06	98.06	0.83	0.83	2	-
GCA_905233655.1	s__Cryptobacteroides sp905233655	79.0566	193	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017423025.1	s__Cryptobacteroides sp017423025	78.8766	224	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017550525.1	s__Cryptobacteroides sp017550525	78.6915	231	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016288055.1	s__Cryptobacteroides sp016288055	78.6801	201	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017617475.1	s__Cryptobacteroides sp017617475	78.6201	209	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902794005.1	s__Cryptobacteroides sp902794005	78.6084	220	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.50	98.20	0.83	0.80	3	-
GCA_900320795.1	s__Cryptobacteroides sp900320795	78.5611	223	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	100.00	100.00	0.99	0.99	2	-
GCA_017934185.1	s__Cryptobacteroides sp017934185	78.5555	216	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017509685.1	s__Cryptobacteroides sp017509685	78.5382	228	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017478685.1	s__Cryptobacteroides sp017478685	78.4974	167	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002392525.1	s__Cryptobacteroides sp002392525	78.4422	165	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017412645.1	s__Cryptobacteroides sp017412645	77.4751	79	817	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 08:36:15,416] [INFO] GTDB search result was written to GCA_902795165.1_Rumen_uncultured_genome_RUG14044_genomic.fna/result_gtdb.tsv
[2023-06-08 08:36:15,417] [INFO] ===== GTDB Search completed =====
[2023-06-08 08:36:15,420] [INFO] DFAST_QC result json was written to GCA_902795165.1_Rumen_uncultured_genome_RUG14044_genomic.fna/dqc_result.json
[2023-06-08 08:36:15,421] [INFO] DFAST_QC completed!
[2023-06-08 08:36:15,421] [INFO] Total running time: 0h1m24s