[2023-06-30 17:00:13,271] [INFO] DFAST_QC pipeline started.
[2023-06-30 17:00:13,274] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 17:00:13,274] [INFO] DQC Reference Directory: /var/lib/cwl/stg81b1122c-f8dd-4fbe-9ccc-6747991cfb16/dqc_reference
[2023-06-30 17:00:14,533] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 17:00:14,534] [INFO] Task started: Prodigal
[2023-06-30 17:00:14,534] [INFO] Running command: gunzip -c /var/lib/cwl/stg00b9d8b0-a874-4186-9503-5b44f578b7e7/GCA_939799055.1_SRR2134650_bin.18_metaWRAP_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_939799055.1_SRR2134650_bin.18_metaWRAP_v1.1_MAG_genomic.fna/cds.fna -a GCA_939799055.1_SRR2134650_bin.18_metaWRAP_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 17:00:24,934] [INFO] Task succeeded: Prodigal
[2023-06-30 17:00:24,934] [INFO] Task started: HMMsearch
[2023-06-30 17:00:24,934] [INFO] Running command: hmmsearch --tblout GCA_939799055.1_SRR2134650_bin.18_metaWRAP_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81b1122c-f8dd-4fbe-9ccc-6747991cfb16/dqc_reference/reference_markers.hmm GCA_939799055.1_SRR2134650_bin.18_metaWRAP_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-30 17:00:25,184] [INFO] Task succeeded: HMMsearch
[2023-06-30 17:00:25,186] [INFO] Found 6/6 markers.
[2023-06-30 17:00:25,214] [INFO] Query marker FASTA was written to GCA_939799055.1_SRR2134650_bin.18_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-30 17:00:25,214] [INFO] Task started: Blastn
[2023-06-30 17:00:25,214] [INFO] Running command: blastn -query GCA_939799055.1_SRR2134650_bin.18_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg81b1122c-f8dd-4fbe-9ccc-6747991cfb16/dqc_reference/reference_markers.fasta -out GCA_939799055.1_SRR2134650_bin.18_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:00:25,814] [INFO] Task succeeded: Blastn
[2023-06-30 17:00:25,819] [INFO] Selected 22 target genomes.
[2023-06-30 17:00:25,820] [INFO] Target genome list was writen to GCA_939799055.1_SRR2134650_bin.18_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-30 17:00:25,823] [INFO] Task started: fastANI
[2023-06-30 17:00:25,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg00b9d8b0-a874-4186-9503-5b44f578b7e7/GCA_939799055.1_SRR2134650_bin.18_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_939799055.1_SRR2134650_bin.18_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_939799055.1_SRR2134650_bin.18_metaWRAP_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 17:00:38,142] [INFO] Task succeeded: fastANI
[2023-06-30 17:00:38,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81b1122c-f8dd-4fbe-9ccc-6747991cfb16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 17:00:38,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81b1122c-f8dd-4fbe-9ccc-6747991cfb16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 17:00:38,145] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 17:00:38,145] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 17:00:38,145] [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
--------------------------------------------------------------------------------
[2023-06-30 17:00:38,147] [INFO] DFAST Taxonomy check result was written to GCA_939799055.1_SRR2134650_bin.18_metaWRAP_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-30 17:00:38,148] [INFO] ===== Taxonomy check completed =====
[2023-06-30 17:00:38,148] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 17:00:38,148] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81b1122c-f8dd-4fbe-9ccc-6747991cfb16/dqc_reference/checkm_data
[2023-06-30 17:00:38,152] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 17:00:38,175] [INFO] Task started: CheckM
[2023-06-30 17:00:38,175] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_939799055.1_SRR2134650_bin.18_metaWRAP_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_939799055.1_SRR2134650_bin.18_metaWRAP_v1.1_MAG_genomic.fna/checkm_input GCA_939799055.1_SRR2134650_bin.18_metaWRAP_v1.1_MAG_genomic.fna/checkm_result
[2023-06-30 17:01:12,695] [INFO] Task succeeded: CheckM
[2023-06-30 17:01:12,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 17:01:12,727] [INFO] ===== Completeness check finished =====
[2023-06-30 17:01:12,727] [INFO] ===== Start GTDB Search =====
[2023-06-30 17:01:12,728] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_939799055.1_SRR2134650_bin.18_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-30 17:01:12,728] [INFO] Task started: Blastn
[2023-06-30 17:01:12,728] [INFO] Running command: blastn -query GCA_939799055.1_SRR2134650_bin.18_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg81b1122c-f8dd-4fbe-9ccc-6747991cfb16/dqc_reference/reference_markers_gtdb.fasta -out GCA_939799055.1_SRR2134650_bin.18_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:01:13,566] [INFO] Task succeeded: Blastn
[2023-06-30 17:01:13,580] [INFO] Selected 21 target genomes.
[2023-06-30 17:01:13,581] [INFO] Target genome list was writen to GCA_939799055.1_SRR2134650_bin.18_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 17:01:13,618] [INFO] Task started: fastANI
[2023-06-30 17:01:13,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg00b9d8b0-a874-4186-9503-5b44f578b7e7/GCA_939799055.1_SRR2134650_bin.18_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_939799055.1_SRR2134650_bin.18_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_939799055.1_SRR2134650_bin.18_metaWRAP_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 17:01:21,675] [INFO] Task succeeded: fastANI
[2023-06-30 17:01:21,693] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 17:01:21,693] [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_017695015.1	s__Cryptobacteroides faecigallinarum	98.3493	459	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017694785.1	s__Cryptobacteroides intestinigallinarum	79.3306	134	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017694845.1	s__Cryptobacteroides intestinavium	79.0078	240	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017695025.1	s__Cryptobacteroides excrementavium	77.4757	125	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017694755.1	s__Cryptobacteroides merdavium	77.4478	136	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017694995.1	s__Cryptobacteroides faecavium	77.3731	113	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015060405.1	s__Cryptobacteroides sp015060405	77.2516	65	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009774765.1	s__Cryptobacteroides sp009774765	77.1979	119	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.21	97.21	0.84	0.84	2	-
GCA_017694835.1	s__Cryptobacteroides gallistercoris	77.1727	120	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760425.1	s__Cryptobacteroides sp900760425	77.1678	103	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017694885.1	s__Cryptobacteroides faecipullorum	77.0334	92	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017452265.1	s__Cryptobacteroides sp017452265	76.7714	86	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017442315.1	s__Cryptobacteroides sp017442315	76.589	56	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.71	98.71	0.80	0.80	2	-
GCA_017502125.1	s__Cryptobacteroides sp017502125	76.3618	59	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017694655.1	s__Cryptobacteroides merdigallinarum	76.3283	88	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015060385.1	s__Cryptobacteroides sp015060385	76.3018	58	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 17:01:21,695] [INFO] GTDB search result was written to GCA_939799055.1_SRR2134650_bin.18_metaWRAP_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-30 17:01:21,696] [INFO] ===== GTDB Search completed =====
[2023-06-30 17:01:21,699] [INFO] DFAST_QC result json was written to GCA_939799055.1_SRR2134650_bin.18_metaWRAP_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-30 17:01:21,699] [INFO] DFAST_QC completed!
[2023-06-30 17:01:21,699] [INFO] Total running time: 0h1m8s