[2023-06-05 07:16:23,890] [INFO] DFAST_QC pipeline started.
[2023-06-05 07:16:23,893] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 07:16:23,893] [INFO] DQC Reference Directory: /var/lib/cwl/stg31ef0a62-0419-4129-8c3a-8f4954800770/dqc_reference
[2023-06-05 07:16:27,032] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 07:16:27,033] [INFO] Task started: Prodigal
[2023-06-05 07:16:27,034] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d8625da-d5b8-4c4f-871a-a0f495f181db/GCA_902771885.1_Rumen_uncultured_genome_RUG11715_genomic.fna.gz | prodigal -d GCA_902771885.1_Rumen_uncultured_genome_RUG11715_genomic.fna/cds.fna -a GCA_902771885.1_Rumen_uncultured_genome_RUG11715_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 07:16:39,194] [INFO] Task succeeded: Prodigal
[2023-06-05 07:16:39,195] [INFO] Task started: HMMsearch
[2023-06-05 07:16:39,195] [INFO] Running command: hmmsearch --tblout GCA_902771885.1_Rumen_uncultured_genome_RUG11715_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31ef0a62-0419-4129-8c3a-8f4954800770/dqc_reference/reference_markers.hmm GCA_902771885.1_Rumen_uncultured_genome_RUG11715_genomic.fna/protein.faa > /dev/null
[2023-06-05 07:16:39,456] [INFO] Task succeeded: HMMsearch
[2023-06-05 07:16:39,458] [INFO] Found 6/6 markers.
[2023-06-05 07:16:39,486] [INFO] Query marker FASTA was written to GCA_902771885.1_Rumen_uncultured_genome_RUG11715_genomic.fna/markers.fasta
[2023-06-05 07:16:39,486] [INFO] Task started: Blastn
[2023-06-05 07:16:39,487] [INFO] Running command: blastn -query GCA_902771885.1_Rumen_uncultured_genome_RUG11715_genomic.fna/markers.fasta -db /var/lib/cwl/stg31ef0a62-0419-4129-8c3a-8f4954800770/dqc_reference/reference_markers.fasta -out GCA_902771885.1_Rumen_uncultured_genome_RUG11715_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:16:40,124] [INFO] Task succeeded: Blastn
[2023-06-05 07:16:40,129] [INFO] Selected 28 target genomes.
[2023-06-05 07:16:40,129] [INFO] Target genome list was writen to GCA_902771885.1_Rumen_uncultured_genome_RUG11715_genomic.fna/target_genomes.txt
[2023-06-05 07:16:40,135] [INFO] Task started: fastANI
[2023-06-05 07:16:40,136] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d8625da-d5b8-4c4f-871a-a0f495f181db/GCA_902771885.1_Rumen_uncultured_genome_RUG11715_genomic.fna.gz --refList GCA_902771885.1_Rumen_uncultured_genome_RUG11715_genomic.fna/target_genomes.txt --output GCA_902771885.1_Rumen_uncultured_genome_RUG11715_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 07:16:59,328] [INFO] Task succeeded: fastANI
[2023-06-05 07:16:59,328] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31ef0a62-0419-4129-8c3a-8f4954800770/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 07:16:59,329] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31ef0a62-0419-4129-8c3a-8f4954800770/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 07:16:59,331] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 07:16:59,332] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 07:16:59,332] [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
--------------------------------------------------------------------------------
[2023-06-05 07:16:59,334] [INFO] DFAST Taxonomy check result was written to GCA_902771885.1_Rumen_uncultured_genome_RUG11715_genomic.fna/tc_result.tsv
[2023-06-05 07:16:59,335] [INFO] ===== Taxonomy check completed =====
[2023-06-05 07:16:59,335] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 07:16:59,336] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31ef0a62-0419-4129-8c3a-8f4954800770/dqc_reference/checkm_data
[2023-06-05 07:16:59,340] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 07:16:59,370] [INFO] Task started: CheckM
[2023-06-05 07:16:59,371] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902771885.1_Rumen_uncultured_genome_RUG11715_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902771885.1_Rumen_uncultured_genome_RUG11715_genomic.fna/checkm_input GCA_902771885.1_Rumen_uncultured_genome_RUG11715_genomic.fna/checkm_result
[2023-06-05 07:17:35,929] [INFO] Task succeeded: CheckM
[2023-06-05 07:17:35,932] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 07:17:35,953] [INFO] ===== Completeness check finished =====
[2023-06-05 07:17:35,953] [INFO] ===== Start GTDB Search =====
[2023-06-05 07:17:35,954] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902771885.1_Rumen_uncultured_genome_RUG11715_genomic.fna/markers.fasta)
[2023-06-05 07:17:35,954] [INFO] Task started: Blastn
[2023-06-05 07:17:35,954] [INFO] Running command: blastn -query GCA_902771885.1_Rumen_uncultured_genome_RUG11715_genomic.fna/markers.fasta -db /var/lib/cwl/stg31ef0a62-0419-4129-8c3a-8f4954800770/dqc_reference/reference_markers_gtdb.fasta -out GCA_902771885.1_Rumen_uncultured_genome_RUG11715_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:17:36,832] [INFO] Task succeeded: Blastn
[2023-06-05 07:17:36,837] [INFO] Selected 11 target genomes.
[2023-06-05 07:17:36,837] [INFO] Target genome list was writen to GCA_902771885.1_Rumen_uncultured_genome_RUG11715_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 07:17:36,845] [INFO] Task started: fastANI
[2023-06-05 07:17:36,845] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d8625da-d5b8-4c4f-871a-a0f495f181db/GCA_902771885.1_Rumen_uncultured_genome_RUG11715_genomic.fna.gz --refList GCA_902771885.1_Rumen_uncultured_genome_RUG11715_genomic.fna/target_genomes_gtdb.txt --output GCA_902771885.1_Rumen_uncultured_genome_RUG11715_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 07:17:41,454] [INFO] Task succeeded: fastANI
[2023-06-05 07:17:41,471] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 07:17:41,471] [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_905235535.1	s__Cryptobacteroides sp905235535	91.5514	361	524	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	85.4674	374	524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900321655.1	s__Cryptobacteroides sp900321655	85.3375	354	524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.46	96.30	0.88	0.86	12	-
GCA_017617475.1	s__Cryptobacteroides sp017617475	84.5806	347	524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002373715.1	s__Cryptobacteroides sp002373715	83.8021	328	524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.02	98.02	0.86	0.86	2	-
GCA_900316245.1	s__Cryptobacteroides sp900316245	83.723	353	524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.83	97.67	0.94	0.87	3	-
GCA_017480345.1	s__Cryptobacteroides sp017480345	82.9062	287	524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.06	98.06	0.83	0.83	2	-
GCA_016285215.1	s__Cryptobacteroides sp016285215	82.7856	307	524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902794615.1	s__Cryptobacteroides sp902794615	82.5898	272	524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.63	96.28	0.79	0.72	4	-
GCA_900318445.1	s__Cryptobacteroides sp900318445	81.2984	253	524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	96.95	95.41	0.86	0.76	6	-
GCA_002392525.1	s__Cryptobacteroides sp002392525	80.7242	189	524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 07:17:41,473] [INFO] GTDB search result was written to GCA_902771885.1_Rumen_uncultured_genome_RUG11715_genomic.fna/result_gtdb.tsv
[2023-06-05 07:17:41,474] [INFO] ===== GTDB Search completed =====
[2023-06-05 07:17:41,477] [INFO] DFAST_QC result json was written to GCA_902771885.1_Rumen_uncultured_genome_RUG11715_genomic.fna/dqc_result.json
[2023-06-05 07:17:41,477] [INFO] DFAST_QC completed!
[2023-06-05 07:17:41,477] [INFO] Total running time: 0h1m18s