[2023-06-05 18:04:11,367] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:04:11,374] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:04:11,374] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6f491f4-b0f0-4144-bf60-29d7f4138adc/dqc_reference
[2023-06-05 18:04:12,538] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:04:12,539] [INFO] Task started: Prodigal
[2023-06-05 18:04:12,539] [INFO] Running command: gunzip -c /var/lib/cwl/stgb86fa29d-bfde-47fc-a834-3b8134c5801e/GCA_934249145.1_ERR7738235_bin.141_genomic.fna.gz | prodigal -d GCA_934249145.1_ERR7738235_bin.141_genomic.fna/cds.fna -a GCA_934249145.1_ERR7738235_bin.141_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:04:16,738] [INFO] Task succeeded: Prodigal
[2023-06-05 18:04:16,739] [INFO] Task started: HMMsearch
[2023-06-05 18:04:16,739] [INFO] Running command: hmmsearch --tblout GCA_934249145.1_ERR7738235_bin.141_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6f491f4-b0f0-4144-bf60-29d7f4138adc/dqc_reference/reference_markers.hmm GCA_934249145.1_ERR7738235_bin.141_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:04:17,195] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:04:17,199] [INFO] Found 6/6 markers.
[2023-06-05 18:04:17,256] [INFO] Query marker FASTA was written to GCA_934249145.1_ERR7738235_bin.141_genomic.fna/markers.fasta
[2023-06-05 18:04:17,257] [INFO] Task started: Blastn
[2023-06-05 18:04:17,257] [INFO] Running command: blastn -query GCA_934249145.1_ERR7738235_bin.141_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6f491f4-b0f0-4144-bf60-29d7f4138adc/dqc_reference/reference_markers.fasta -out GCA_934249145.1_ERR7738235_bin.141_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:04:18,059] [INFO] Task succeeded: Blastn
[2023-06-05 18:04:18,062] [INFO] Selected 20 target genomes.
[2023-06-05 18:04:18,062] [INFO] Target genome list was writen to GCA_934249145.1_ERR7738235_bin.141_genomic.fna/target_genomes.txt
[2023-06-05 18:04:18,088] [INFO] Task started: fastANI
[2023-06-05 18:04:18,088] [INFO] Running command: fastANI --query /var/lib/cwl/stgb86fa29d-bfde-47fc-a834-3b8134c5801e/GCA_934249145.1_ERR7738235_bin.141_genomic.fna.gz --refList GCA_934249145.1_ERR7738235_bin.141_genomic.fna/target_genomes.txt --output GCA_934249145.1_ERR7738235_bin.141_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:04:30,754] [INFO] Task succeeded: fastANI
[2023-06-05 18:04:30,754] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6f491f4-b0f0-4144-bf60-29d7f4138adc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:04:30,755] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6f491f4-b0f0-4144-bf60-29d7f4138adc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:04:30,756] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:04:30,757] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:04:30,757] [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 18:04:30,759] [INFO] DFAST Taxonomy check result was written to GCA_934249145.1_ERR7738235_bin.141_genomic.fna/tc_result.tsv
[2023-06-05 18:04:30,759] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:04:30,759] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:04:30,759] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6f491f4-b0f0-4144-bf60-29d7f4138adc/dqc_reference/checkm_data
[2023-06-05 18:04:30,762] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:04:30,788] [INFO] Task started: CheckM
[2023-06-05 18:04:30,788] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934249145.1_ERR7738235_bin.141_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934249145.1_ERR7738235_bin.141_genomic.fna/checkm_input GCA_934249145.1_ERR7738235_bin.141_genomic.fna/checkm_result
[2023-06-05 18:04:50,225] [INFO] Task succeeded: CheckM
[2023-06-05 18:04:50,226] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:04:50,240] [INFO] ===== Completeness check finished =====
[2023-06-05 18:04:50,241] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:04:50,242] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934249145.1_ERR7738235_bin.141_genomic.fna/markers.fasta)
[2023-06-05 18:04:50,242] [INFO] Task started: Blastn
[2023-06-05 18:04:50,242] [INFO] Running command: blastn -query GCA_934249145.1_ERR7738235_bin.141_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6f491f4-b0f0-4144-bf60-29d7f4138adc/dqc_reference/reference_markers_gtdb.fasta -out GCA_934249145.1_ERR7738235_bin.141_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:04:50,999] [INFO] Task succeeded: Blastn
[2023-06-05 18:04:51,017] [INFO] Selected 19 target genomes.
[2023-06-05 18:04:51,017] [INFO] Target genome list was writen to GCA_934249145.1_ERR7738235_bin.141_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:04:51,038] [INFO] Task started: fastANI
[2023-06-05 18:04:51,038] [INFO] Running command: fastANI --query /var/lib/cwl/stgb86fa29d-bfde-47fc-a834-3b8134c5801e/GCA_934249145.1_ERR7738235_bin.141_genomic.fna.gz --refList GCA_934249145.1_ERR7738235_bin.141_genomic.fna/target_genomes_gtdb.txt --output GCA_934249145.1_ERR7738235_bin.141_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:04:57,969] [INFO] Task succeeded: fastANI
[2023-06-05 18:04:57,981] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:04:57,981] [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_900767815.1	s__UBA10281 sp900767815	96.5178	525	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281	95.0	96.63	96.03	0.81	0.74	3	conclusive
GCA_900764105.1	s__UBA10281 sp900764105	82.4937	261	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281	95.0	97.70	97.70	0.79	0.79	2	-
GCA_900548285.1	s__UBA10281 sp900548285	80.998	272	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281	95.0	99.08	98.17	0.92	0.86	3	-
GCA_900554485.1	s__UBA10281 sp900554485	78.9758	86	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281	95.0	98.83	98.82	0.88	0.85	3	-
GCA_900767885.1	s__UBA10281 sp900767885	78.8928	120	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902766475.1	s__UBA10281 sp902766475	77.7216	69	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281	95.0	97.57	97.49	0.86	0.78	3	-
GCA_902797945.1	s__UBA10281 sp902797945	77.1916	72	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797515.1	s__UBA10281 sp902797515	77.0475	56	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002405915.1	s__UBA4636 sp002405915	76.9034	55	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA4636	95.0	98.32	98.32	0.88	0.88	2	-
GCA_017504655.1	s__UBA10281 sp017504655	76.7516	59	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017479185.1	s__UBA10281 sp017479185	76.6912	65	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235815.1	s__UBA10281 sp905235815	76.5295	56	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003523255.1	s__UBA1259 sp003523255	76.4602	53	702	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA1259	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:04:57,983] [INFO] GTDB search result was written to GCA_934249145.1_ERR7738235_bin.141_genomic.fna/result_gtdb.tsv
[2023-06-05 18:04:57,983] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:04:58,001] [INFO] DFAST_QC result json was written to GCA_934249145.1_ERR7738235_bin.141_genomic.fna/dqc_result.json
[2023-06-05 18:04:58,001] [INFO] DFAST_QC completed!
[2023-06-05 18:04:58,002] [INFO] Total running time: 0h0m47s