[2023-06-08 12:26:30,850] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:26:30,852] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:26:30,852] [INFO] DQC Reference Directory: /var/lib/cwl/stg630d484b-6e0f-4a3e-8078-bdea9d094989/dqc_reference
[2023-06-08 12:26:32,240] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:26:32,241] [INFO] Task started: Prodigal
[2023-06-08 12:26:32,242] [INFO] Running command: gunzip -c /var/lib/cwl/stg38cdc129-f58e-4aec-ab8c-247fd2cb11ec/GCA_902800045.1_Rumen_uncultured_genome_RUG14538_genomic.fna.gz | prodigal -d GCA_902800045.1_Rumen_uncultured_genome_RUG14538_genomic.fna/cds.fna -a GCA_902800045.1_Rumen_uncultured_genome_RUG14538_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:26:49,617] [INFO] Task succeeded: Prodigal
[2023-06-08 12:26:49,618] [INFO] Task started: HMMsearch
[2023-06-08 12:26:49,618] [INFO] Running command: hmmsearch --tblout GCA_902800045.1_Rumen_uncultured_genome_RUG14538_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg630d484b-6e0f-4a3e-8078-bdea9d094989/dqc_reference/reference_markers.hmm GCA_902800045.1_Rumen_uncultured_genome_RUG14538_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:26:49,906] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:26:49,907] [INFO] Found 6/6 markers.
[2023-06-08 12:26:49,939] [INFO] Query marker FASTA was written to GCA_902800045.1_Rumen_uncultured_genome_RUG14538_genomic.fna/markers.fasta
[2023-06-08 12:26:49,940] [INFO] Task started: Blastn
[2023-06-08 12:26:49,940] [INFO] Running command: blastn -query GCA_902800045.1_Rumen_uncultured_genome_RUG14538_genomic.fna/markers.fasta -db /var/lib/cwl/stg630d484b-6e0f-4a3e-8078-bdea9d094989/dqc_reference/reference_markers.fasta -out GCA_902800045.1_Rumen_uncultured_genome_RUG14538_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:26:50,586] [INFO] Task succeeded: Blastn
[2023-06-08 12:26:50,596] [INFO] Selected 25 target genomes.
[2023-06-08 12:26:50,597] [INFO] Target genome list was writen to GCA_902800045.1_Rumen_uncultured_genome_RUG14538_genomic.fna/target_genomes.txt
[2023-06-08 12:26:50,604] [INFO] Task started: fastANI
[2023-06-08 12:26:50,605] [INFO] Running command: fastANI --query /var/lib/cwl/stg38cdc129-f58e-4aec-ab8c-247fd2cb11ec/GCA_902800045.1_Rumen_uncultured_genome_RUG14538_genomic.fna.gz --refList GCA_902800045.1_Rumen_uncultured_genome_RUG14538_genomic.fna/target_genomes.txt --output GCA_902800045.1_Rumen_uncultured_genome_RUG14538_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:27:06,108] [INFO] Task succeeded: fastANI
[2023-06-08 12:27:06,109] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg630d484b-6e0f-4a3e-8078-bdea9d094989/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:27:06,109] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg630d484b-6e0f-4a3e-8078-bdea9d094989/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:27:06,111] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:27:06,111] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 12:27:06,111] [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 12:27:06,113] [INFO] DFAST Taxonomy check result was written to GCA_902800045.1_Rumen_uncultured_genome_RUG14538_genomic.fna/tc_result.tsv
[2023-06-08 12:27:06,113] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:27:06,114] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:27:06,114] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg630d484b-6e0f-4a3e-8078-bdea9d094989/dqc_reference/checkm_data
[2023-06-08 12:27:06,116] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:27:06,155] [INFO] Task started: CheckM
[2023-06-08 12:27:06,155] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902800045.1_Rumen_uncultured_genome_RUG14538_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902800045.1_Rumen_uncultured_genome_RUG14538_genomic.fna/checkm_input GCA_902800045.1_Rumen_uncultured_genome_RUG14538_genomic.fna/checkm_result
[2023-06-08 12:27:58,079] [INFO] Task succeeded: CheckM
[2023-06-08 12:27:58,080] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:27:58,104] [INFO] ===== Completeness check finished =====
[2023-06-08 12:27:58,104] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:27:58,105] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902800045.1_Rumen_uncultured_genome_RUG14538_genomic.fna/markers.fasta)
[2023-06-08 12:27:58,105] [INFO] Task started: Blastn
[2023-06-08 12:27:58,106] [INFO] Running command: blastn -query GCA_902800045.1_Rumen_uncultured_genome_RUG14538_genomic.fna/markers.fasta -db /var/lib/cwl/stg630d484b-6e0f-4a3e-8078-bdea9d094989/dqc_reference/reference_markers_gtdb.fasta -out GCA_902800045.1_Rumen_uncultured_genome_RUG14538_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:27:58,988] [INFO] Task succeeded: Blastn
[2023-06-08 12:27:58,992] [INFO] Selected 12 target genomes.
[2023-06-08 12:27:58,993] [INFO] Target genome list was writen to GCA_902800045.1_Rumen_uncultured_genome_RUG14538_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:27:59,000] [INFO] Task started: fastANI
[2023-06-08 12:27:59,001] [INFO] Running command: fastANI --query /var/lib/cwl/stg38cdc129-f58e-4aec-ab8c-247fd2cb11ec/GCA_902800045.1_Rumen_uncultured_genome_RUG14538_genomic.fna.gz --refList GCA_902800045.1_Rumen_uncultured_genome_RUG14538_genomic.fna/target_genomes_gtdb.txt --output GCA_902800045.1_Rumen_uncultured_genome_RUG14538_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:28:08,550] [INFO] Task succeeded: fastANI
[2023-06-08 12:28:08,565] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 12:28:08,565] [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_902800045.1	s__Bact-19 sp902800045	100.0	1057	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902790405.1	s__Bact-19 sp902790405	93.8262	703	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902776565.1	s__Bact-19 sp902776565	88.6018	713	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	96.47	95.98	0.86	0.82	3	-
GCA_902762455.1	s__Bact-19 sp902762455	87.9382	514	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	95.34	95.27	0.87	0.87	3	-
GCA_017617125.1	s__Bact-19 sp017617125	87.5875	762	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002310235.1	s__Bact-19 sp002310235	86.8277	718	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	97.60	97.60	0.89	0.89	2	-
GCA_017620015.1	s__Bact-19 sp017620015	86.6315	718	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902791865.1	s__Bact-19 sp902791865	85.9169	656	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	95.98	95.98	0.86	0.86	2	-
GCA_905233405.1	s__Bact-19 sp905233405	85.3756	456	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	95.16	95.16	0.76	0.76	2	-
GCA_905234755.1	s__Bact-19 sp905234755	83.8832	640	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017645925.1	s__Bact-19 sp017645925	83.1273	474	1059	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__ML635J-15;g__Bact-19	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 12:28:08,567] [INFO] GTDB search result was written to GCA_902800045.1_Rumen_uncultured_genome_RUG14538_genomic.fna/result_gtdb.tsv
[2023-06-08 12:28:08,568] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:28:08,571] [INFO] DFAST_QC result json was written to GCA_902800045.1_Rumen_uncultured_genome_RUG14538_genomic.fna/dqc_result.json
[2023-06-08 12:28:08,571] [INFO] DFAST_QC completed!
[2023-06-08 12:28:08,571] [INFO] Total running time: 0h1m38s