[2023-06-08 08:49:18,336] [INFO] DFAST_QC pipeline started.
[2023-06-08 08:49:18,338] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 08:49:18,339] [INFO] DQC Reference Directory: /var/lib/cwl/stge45c36bd-e555-4ee2-bcb4-18e8ab60965d/dqc_reference
[2023-06-08 08:49:19,477] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 08:49:19,478] [INFO] Task started: Prodigal
[2023-06-08 08:49:19,478] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ad513d0-396e-484a-94c1-91f6dd0e3f0e/GCA_947166005.1_SRR8387715_bin.101_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947166005.1_SRR8387715_bin.101_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_947166005.1_SRR8387715_bin.101_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 08:49:22,551] [INFO] Task succeeded: Prodigal
[2023-06-08 08:49:22,551] [INFO] Task started: HMMsearch
[2023-06-08 08:49:22,551] [INFO] Running command: hmmsearch --tblout GCA_947166005.1_SRR8387715_bin.101_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge45c36bd-e555-4ee2-bcb4-18e8ab60965d/dqc_reference/reference_markers.hmm GCA_947166005.1_SRR8387715_bin.101_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 08:49:22,711] [INFO] Task succeeded: HMMsearch
[2023-06-08 08:49:22,713] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg0ad513d0-396e-484a-94c1-91f6dd0e3f0e/GCA_947166005.1_SRR8387715_bin.101_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 08:49:22,731] [INFO] Query marker FASTA was written to GCA_947166005.1_SRR8387715_bin.101_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 08:49:22,731] [INFO] Task started: Blastn
[2023-06-08 08:49:22,731] [INFO] Running command: blastn -query GCA_947166005.1_SRR8387715_bin.101_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stge45c36bd-e555-4ee2-bcb4-18e8ab60965d/dqc_reference/reference_markers.fasta -out GCA_947166005.1_SRR8387715_bin.101_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:49:23,212] [INFO] Task succeeded: Blastn
[2023-06-08 08:49:23,215] [INFO] Selected 1 target genomes.
[2023-06-08 08:49:23,215] [INFO] Target genome list was writen to GCA_947166005.1_SRR8387715_bin.101_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 08:49:23,216] [INFO] Task started: fastANI
[2023-06-08 08:49:23,216] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ad513d0-396e-484a-94c1-91f6dd0e3f0e/GCA_947166005.1_SRR8387715_bin.101_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947166005.1_SRR8387715_bin.101_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947166005.1_SRR8387715_bin.101_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 08:49:23,659] [INFO] Task succeeded: fastANI
[2023-06-08 08:49:23,659] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge45c36bd-e555-4ee2-bcb4-18e8ab60965d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 08:49:23,660] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge45c36bd-e555-4ee2-bcb4-18e8ab60965d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 08:49:23,663] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 08:49:23,663] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 08:49:23,663] [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
Methanobrevibacter millerae	strain=DSM 16643	GCA_900103415.1	230361	230361	type	True	76.1116	64	499	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 08:49:23,665] [INFO] DFAST Taxonomy check result was written to GCA_947166005.1_SRR8387715_bin.101_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 08:49:23,666] [INFO] ===== Taxonomy check completed =====
[2023-06-08 08:49:23,666] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 08:49:23,666] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge45c36bd-e555-4ee2-bcb4-18e8ab60965d/dqc_reference/checkm_data
[2023-06-08 08:49:23,667] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 08:49:23,705] [INFO] Task started: CheckM
[2023-06-08 08:49:23,705] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947166005.1_SRR8387715_bin.101_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947166005.1_SRR8387715_bin.101_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_947166005.1_SRR8387715_bin.101_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 08:49:39,938] [INFO] Task succeeded: CheckM
[2023-06-08 08:49:39,939] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 08:49:39,954] [INFO] ===== Completeness check finished =====
[2023-06-08 08:49:39,954] [INFO] ===== Start GTDB Search =====
[2023-06-08 08:49:39,954] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947166005.1_SRR8387715_bin.101_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 08:49:39,955] [INFO] Task started: Blastn
[2023-06-08 08:49:39,955] [INFO] Running command: blastn -query GCA_947166005.1_SRR8387715_bin.101_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stge45c36bd-e555-4ee2-bcb4-18e8ab60965d/dqc_reference/reference_markers_gtdb.fasta -out GCA_947166005.1_SRR8387715_bin.101_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:49:40,408] [INFO] Task succeeded: Blastn
[2023-06-08 08:49:40,411] [INFO] Selected 5 target genomes.
[2023-06-08 08:49:40,411] [INFO] Target genome list was writen to GCA_947166005.1_SRR8387715_bin.101_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 08:49:40,413] [INFO] Task started: fastANI
[2023-06-08 08:49:40,413] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ad513d0-396e-484a-94c1-91f6dd0e3f0e/GCA_947166005.1_SRR8387715_bin.101_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947166005.1_SRR8387715_bin.101_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947166005.1_SRR8387715_bin.101_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 08:49:42,378] [INFO] Task succeeded: fastANI
[2023-06-08 08:49:42,384] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 08:49:42,384] [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_900314635.1	s__Methanobrevibacter sp900314635	95.6036	451	499	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	97.81	97.12	0.91	0.86	21	conclusive
GCA_902784195.1	s__Methanobrevibacter sp902784195	78.8593	159	499	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	98.44	98.21	0.91	0.88	7	-
GCA_016838945.1	s__Methanobrevibacter sp016838945	78.6202	127	499	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	99.68	99.68	0.88	0.88	2	-
GCA_004553595.1	s__Methanobrevibacter ruminantium_A	78.375	161	499	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	99.31	99.31	0.95	0.95	2	-
GCA_905235495.1	s__Methanobrevibacter sp905235495	78.3036	109	499	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 08:49:42,386] [INFO] GTDB search result was written to GCA_947166005.1_SRR8387715_bin.101_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 08:49:42,387] [INFO] ===== GTDB Search completed =====
[2023-06-08 08:49:42,389] [INFO] DFAST_QC result json was written to GCA_947166005.1_SRR8387715_bin.101_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 08:49:42,389] [INFO] DFAST_QC completed!
[2023-06-08 08:49:42,389] [INFO] Total running time: 0h0m24s