[2023-06-08 16:47:48,953] [INFO] DFAST_QC pipeline started.
[2023-06-08 16:47:48,955] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 16:47:48,956] [INFO] DQC Reference Directory: /var/lib/cwl/stg6416c58c-e692-4a22-83c9-c9265f4e30c8/dqc_reference
[2023-06-08 16:47:50,277] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 16:47:50,278] [INFO] Task started: Prodigal
[2023-06-08 16:47:50,279] [INFO] Running command: gunzip -c /var/lib/cwl/stgbcd05ba2-a6f9-4caf-bb67-1ff2568fa2a7/GCA_947573005.1_SRR15730553_bin.24_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947573005.1_SRR15730553_bin.24_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947573005.1_SRR15730553_bin.24_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 16:47:54,816] [INFO] Task succeeded: Prodigal
[2023-06-08 16:47:54,816] [INFO] Task started: HMMsearch
[2023-06-08 16:47:54,816] [INFO] Running command: hmmsearch --tblout GCA_947573005.1_SRR15730553_bin.24_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6416c58c-e692-4a22-83c9-c9265f4e30c8/dqc_reference/reference_markers.hmm GCA_947573005.1_SRR15730553_bin.24_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 16:47:55,050] [INFO] Task succeeded: HMMsearch
[2023-06-08 16:47:55,056] [INFO] Found 6/6 markers.
[2023-06-08 16:47:55,077] [INFO] Query marker FASTA was written to GCA_947573005.1_SRR15730553_bin.24_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 16:47:55,077] [INFO] Task started: Blastn
[2023-06-08 16:47:55,077] [INFO] Running command: blastn -query GCA_947573005.1_SRR15730553_bin.24_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6416c58c-e692-4a22-83c9-c9265f4e30c8/dqc_reference/reference_markers.fasta -out GCA_947573005.1_SRR15730553_bin.24_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 16:47:55,747] [INFO] Task succeeded: Blastn
[2023-06-08 16:47:55,751] [INFO] Selected 24 target genomes.
[2023-06-08 16:47:55,751] [INFO] Target genome list was writen to GCA_947573005.1_SRR15730553_bin.24_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 16:47:55,756] [INFO] Task started: fastANI
[2023-06-08 16:47:55,756] [INFO] Running command: fastANI --query /var/lib/cwl/stgbcd05ba2-a6f9-4caf-bb67-1ff2568fa2a7/GCA_947573005.1_SRR15730553_bin.24_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947573005.1_SRR15730553_bin.24_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947573005.1_SRR15730553_bin.24_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 16:48:11,237] [INFO] Task succeeded: fastANI
[2023-06-08 16:48:11,237] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6416c58c-e692-4a22-83c9-c9265f4e30c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 16:48:11,237] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6416c58c-e692-4a22-83c9-c9265f4e30c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 16:48:11,242] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 16:48:11,242] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 16:48:11,242] [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
Guopingia tenuis	strain=NSJ-63	GCA_014384805.1	2763656	2763656	type	True	77.2672	79	513	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 16:48:11,244] [INFO] DFAST Taxonomy check result was written to GCA_947573005.1_SRR15730553_bin.24_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 16:48:11,246] [INFO] ===== Taxonomy check completed =====
[2023-06-08 16:48:11,246] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 16:48:11,247] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6416c58c-e692-4a22-83c9-c9265f4e30c8/dqc_reference/checkm_data
[2023-06-08 16:48:11,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 16:48:11,270] [INFO] Task started: CheckM
[2023-06-08 16:48:11,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947573005.1_SRR15730553_bin.24_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947573005.1_SRR15730553_bin.24_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947573005.1_SRR15730553_bin.24_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 16:48:31,244] [INFO] Task succeeded: CheckM
[2023-06-08 16:48:31,246] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 16:48:31,267] [INFO] ===== Completeness check finished =====
[2023-06-08 16:48:31,267] [INFO] ===== Start GTDB Search =====
[2023-06-08 16:48:31,268] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947573005.1_SRR15730553_bin.24_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 16:48:31,268] [INFO] Task started: Blastn
[2023-06-08 16:48:31,268] [INFO] Running command: blastn -query GCA_947573005.1_SRR15730553_bin.24_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6416c58c-e692-4a22-83c9-c9265f4e30c8/dqc_reference/reference_markers_gtdb.fasta -out GCA_947573005.1_SRR15730553_bin.24_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 16:48:32,196] [INFO] Task succeeded: Blastn
[2023-06-08 16:48:32,200] [INFO] Selected 23 target genomes.
[2023-06-08 16:48:32,200] [INFO] Target genome list was writen to GCA_947573005.1_SRR15730553_bin.24_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 16:48:32,211] [INFO] Task started: fastANI
[2023-06-08 16:48:32,212] [INFO] Running command: fastANI --query /var/lib/cwl/stgbcd05ba2-a6f9-4caf-bb67-1ff2568fa2a7/GCA_947573005.1_SRR15730553_bin.24_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947573005.1_SRR15730553_bin.24_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947573005.1_SRR15730553_bin.24_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 16:48:40,930] [INFO] Task succeeded: fastANI
[2023-06-08 16:48:40,935] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 16:48:40,935] [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_910588425.1	s__QANA01 sp910588425	98.0662	490	513	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Christensenellaceae;g__QANA01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900554725.1	s__QANA01 sp900554725	78.9928	151	513	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Christensenellaceae;g__QANA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014384805.1	s__NSJ-63 sp014384805	77.2672	79	513	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Christensenellaceae;g__NSJ-63	95.0	98.08	98.04	0.97	0.96	3	-
--------------------------------------------------------------------------------
[2023-06-08 16:48:40,937] [INFO] GTDB search result was written to GCA_947573005.1_SRR15730553_bin.24_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 16:48:40,937] [INFO] ===== GTDB Search completed =====
[2023-06-08 16:48:40,940] [INFO] DFAST_QC result json was written to GCA_947573005.1_SRR15730553_bin.24_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 16:48:40,940] [INFO] DFAST_QC completed!
[2023-06-08 16:48:40,940] [INFO] Total running time: 0h0m52s