[2023-06-14 01:07:34,869] [INFO] DFAST_QC pipeline started.
[2023-06-14 01:07:34,872] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 01:07:34,872] [INFO] DQC Reference Directory: /var/lib/cwl/stg0153d6bc-10cf-4b97-acc1-8ce0d62eacd3/dqc_reference
[2023-06-14 01:07:37,940] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 01:07:37,942] [INFO] Task started: Prodigal
[2023-06-14 01:07:37,942] [INFO] Running command: gunzip -c /var/lib/cwl/stgd098476f-616d-44a7-8b15-b80da5d5413e/GCA_947302285.1_SRR10912534_bin.69_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947302285.1_SRR10912534_bin.69_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_947302285.1_SRR10912534_bin.69_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 01:07:51,180] [INFO] Task succeeded: Prodigal
[2023-06-14 01:07:51,181] [INFO] Task started: HMMsearch
[2023-06-14 01:07:51,181] [INFO] Running command: hmmsearch --tblout GCA_947302285.1_SRR10912534_bin.69_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0153d6bc-10cf-4b97-acc1-8ce0d62eacd3/dqc_reference/reference_markers.hmm GCA_947302285.1_SRR10912534_bin.69_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-14 01:07:51,398] [INFO] Task succeeded: HMMsearch
[2023-06-14 01:07:51,399] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgd098476f-616d-44a7-8b15-b80da5d5413e/GCA_947302285.1_SRR10912534_bin.69_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-14 01:07:51,425] [INFO] Query marker FASTA was written to GCA_947302285.1_SRR10912534_bin.69_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-14 01:07:51,426] [INFO] Task started: Blastn
[2023-06-14 01:07:51,426] [INFO] Running command: blastn -query GCA_947302285.1_SRR10912534_bin.69_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0153d6bc-10cf-4b97-acc1-8ce0d62eacd3/dqc_reference/reference_markers.fasta -out GCA_947302285.1_SRR10912534_bin.69_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:07:52,012] [INFO] Task succeeded: Blastn
[2023-06-14 01:07:52,015] [INFO] Selected 15 target genomes.
[2023-06-14 01:07:52,016] [INFO] Target genome list was writen to GCA_947302285.1_SRR10912534_bin.69_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-14 01:07:52,022] [INFO] Task started: fastANI
[2023-06-14 01:07:52,022] [INFO] Running command: fastANI --query /var/lib/cwl/stgd098476f-616d-44a7-8b15-b80da5d5413e/GCA_947302285.1_SRR10912534_bin.69_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947302285.1_SRR10912534_bin.69_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947302285.1_SRR10912534_bin.69_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 01:07:59,413] [INFO] Task succeeded: fastANI
[2023-06-14 01:07:59,414] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0153d6bc-10cf-4b97-acc1-8ce0d62eacd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 01:07:59,414] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0153d6bc-10cf-4b97-acc1-8ce0d62eacd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 01:07:59,416] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 01:07:59,416] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-14 01:07:59,416] [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
--------------------------------------------------------------------------------
[2023-06-14 01:07:59,418] [INFO] DFAST Taxonomy check result was written to GCA_947302285.1_SRR10912534_bin.69_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-14 01:07:59,418] [INFO] ===== Taxonomy check completed =====
[2023-06-14 01:07:59,418] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 01:07:59,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0153d6bc-10cf-4b97-acc1-8ce0d62eacd3/dqc_reference/checkm_data
[2023-06-14 01:07:59,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 01:07:59,452] [INFO] Task started: CheckM
[2023-06-14 01:07:59,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947302285.1_SRR10912534_bin.69_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947302285.1_SRR10912534_bin.69_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_947302285.1_SRR10912534_bin.69_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-14 01:08:41,300] [INFO] Task succeeded: CheckM
[2023-06-14 01:08:41,302] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 36.98%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 01:08:41,323] [INFO] ===== Completeness check finished =====
[2023-06-14 01:08:41,323] [INFO] ===== Start GTDB Search =====
[2023-06-14 01:08:41,324] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947302285.1_SRR10912534_bin.69_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-14 01:08:41,324] [INFO] Task started: Blastn
[2023-06-14 01:08:41,324] [INFO] Running command: blastn -query GCA_947302285.1_SRR10912534_bin.69_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0153d6bc-10cf-4b97-acc1-8ce0d62eacd3/dqc_reference/reference_markers_gtdb.fasta -out GCA_947302285.1_SRR10912534_bin.69_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:08:42,135] [INFO] Task succeeded: Blastn
[2023-06-14 01:08:42,140] [INFO] Selected 14 target genomes.
[2023-06-14 01:08:42,140] [INFO] Target genome list was writen to GCA_947302285.1_SRR10912534_bin.69_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 01:08:42,151] [INFO] Task started: fastANI
[2023-06-14 01:08:42,151] [INFO] Running command: fastANI --query /var/lib/cwl/stgd098476f-616d-44a7-8b15-b80da5d5413e/GCA_947302285.1_SRR10912534_bin.69_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947302285.1_SRR10912534_bin.69_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947302285.1_SRR10912534_bin.69_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 01:08:52,063] [INFO] Task succeeded: fastANI
[2023-06-14 01:08:52,078] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-14 01:08:52,079] [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_900315745.1	s__Prevotella sp900315745	97.8926	449	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.44	97.86	0.88	0.79	6	conclusive
GCA_902786665.1	s__Prevotella sp902786665	78.903	201	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.72	98.72	0.89	0.89	2	-
GCA_902767775.1	s__Prevotella sp902767775	78.0459	170	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.97	97.97	0.86	0.86	2	-
GCA_902795605.1	s__Prevotella sp902795605	78.0155	147	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902792855.1	s__Prevotella sp902792855	77.9602	165	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.67	98.62	0.88	0.82	4	-
GCA_017524385.1	s__Prevotella sp017524385	77.9487	183	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017617615.1	s__Prevotella sp017617615	77.8116	96	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017619375.1	s__Prevotella sp017619375	77.6934	166	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017961115.1	s__Prevotella sp017961115	77.3674	135	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902766505.1	s__Prevotella sp902766505	76.9152	107	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.34	98.34	0.73	0.73	2	-
--------------------------------------------------------------------------------
[2023-06-14 01:08:52,081] [INFO] GTDB search result was written to GCA_947302285.1_SRR10912534_bin.69_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-14 01:08:52,081] [INFO] ===== GTDB Search completed =====
[2023-06-14 01:08:52,084] [INFO] DFAST_QC result json was written to GCA_947302285.1_SRR10912534_bin.69_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-14 01:08:52,084] [INFO] DFAST_QC completed!
[2023-06-14 01:08:52,084] [INFO] Total running time: 0h1m17s