[2023-06-28 05:43:29,767] [INFO] DFAST_QC pipeline started.
[2023-06-28 05:43:29,770] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 05:43:29,771] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f5cfe02-f4d8-47e1-b167-42777a9aa3f6/dqc_reference
[2023-06-28 05:43:32,072] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 05:43:32,073] [INFO] Task started: Prodigal
[2023-06-28 05:43:32,073] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6eeb41e-8160-46f5-920b-2fe7f816dc81/GCA_913048435.1_ERR599163_bin.88_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913048435.1_ERR599163_bin.88_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913048435.1_ERR599163_bin.88_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 05:43:36,090] [INFO] Task succeeded: Prodigal
[2023-06-28 05:43:36,091] [INFO] Task started: HMMsearch
[2023-06-28 05:43:36,091] [INFO] Running command: hmmsearch --tblout GCA_913048435.1_ERR599163_bin.88_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f5cfe02-f4d8-47e1-b167-42777a9aa3f6/dqc_reference/reference_markers.hmm GCA_913048435.1_ERR599163_bin.88_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 05:43:36,302] [INFO] Task succeeded: HMMsearch
[2023-06-28 05:43:36,303] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd6eeb41e-8160-46f5-920b-2fe7f816dc81/GCA_913048435.1_ERR599163_bin.88_MetaBAT_v2.12.1_MAG_genomic.fna.gz]
[2023-06-28 05:43:36,356] [INFO] Query marker FASTA was written to GCA_913048435.1_ERR599163_bin.88_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 05:43:36,356] [INFO] Task started: Blastn
[2023-06-28 05:43:36,356] [INFO] Running command: blastn -query GCA_913048435.1_ERR599163_bin.88_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f5cfe02-f4d8-47e1-b167-42777a9aa3f6/dqc_reference/reference_markers.fasta -out GCA_913048435.1_ERR599163_bin.88_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:43:36,936] [INFO] Task succeeded: Blastn
[2023-06-28 05:43:36,951] [INFO] Selected 26 target genomes.
[2023-06-28 05:43:36,952] [INFO] Target genome list was writen to GCA_913048435.1_ERR599163_bin.88_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 05:43:36,957] [INFO] Task started: fastANI
[2023-06-28 05:43:36,958] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6eeb41e-8160-46f5-920b-2fe7f816dc81/GCA_913048435.1_ERR599163_bin.88_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913048435.1_ERR599163_bin.88_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913048435.1_ERR599163_bin.88_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 05:43:50,336] [INFO] Task succeeded: fastANI
[2023-06-28 05:43:50,336] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f5cfe02-f4d8-47e1-b167-42777a9aa3f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 05:43:50,337] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f5cfe02-f4d8-47e1-b167-42777a9aa3f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 05:43:50,339] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 05:43:50,339] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 05:43:50,339] [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
--------------------------------------------------------------------------------
[2023-06-28 05:43:50,344] [INFO] DFAST Taxonomy check result was written to GCA_913048435.1_ERR599163_bin.88_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 05:43:50,345] [INFO] ===== Taxonomy check completed =====
[2023-06-28 05:43:50,346] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 05:43:50,346] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f5cfe02-f4d8-47e1-b167-42777a9aa3f6/dqc_reference/checkm_data
[2023-06-28 05:43:50,351] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 05:43:50,368] [INFO] Task started: CheckM
[2023-06-28 05:43:50,368] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913048435.1_ERR599163_bin.88_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913048435.1_ERR599163_bin.88_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913048435.1_ERR599163_bin.88_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 05:44:09,545] [INFO] Task succeeded: CheckM
[2023-06-28 05:44:09,546] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 05:44:09,570] [INFO] ===== Completeness check finished =====
[2023-06-28 05:44:09,570] [INFO] ===== Start GTDB Search =====
[2023-06-28 05:44:09,571] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913048435.1_ERR599163_bin.88_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 05:44:09,571] [INFO] Task started: Blastn
[2023-06-28 05:44:09,571] [INFO] Running command: blastn -query GCA_913048435.1_ERR599163_bin.88_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f5cfe02-f4d8-47e1-b167-42777a9aa3f6/dqc_reference/reference_markers_gtdb.fasta -out GCA_913048435.1_ERR599163_bin.88_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:44:10,315] [INFO] Task succeeded: Blastn
[2023-06-28 05:44:10,320] [INFO] Selected 23 target genomes.
[2023-06-28 05:44:10,320] [INFO] Target genome list was writen to GCA_913048435.1_ERR599163_bin.88_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 05:44:10,333] [INFO] Task started: fastANI
[2023-06-28 05:44:10,333] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6eeb41e-8160-46f5-920b-2fe7f816dc81/GCA_913048435.1_ERR599163_bin.88_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913048435.1_ERR599163_bin.88_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913048435.1_ERR599163_bin.88_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 05:44:17,242] [INFO] Task succeeded: fastANI
[2023-06-28 05:44:17,261] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 05:44:17,262] [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_003454845.1	s__UBA8444 sp003454845	87.9662	141	397	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7312;g__UBA8444	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779995.1	s__UBA8444 sp016779995	87.6464	297	397	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7312;g__UBA8444	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714805.1	s__UBA8444 sp002714805	84.8542	295	397	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7312;g__UBA8444	95.0	95.59	95.59	0.86	0.86	2	-
GCA_016779935.1	s__GCA-2862585 sp016779935	77.1164	108	397	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7312;g__GCA-2862585	95.0	99.89	99.89	0.93	0.93	2	-
GCA_002862585.1	s__GCA-2862585 sp002862585	77.0369	64	397	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7312;g__GCA-2862585	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 05:44:17,265] [INFO] GTDB search result was written to GCA_913048435.1_ERR599163_bin.88_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 05:44:17,266] [INFO] ===== GTDB Search completed =====
[2023-06-28 05:44:17,269] [INFO] DFAST_QC result json was written to GCA_913048435.1_ERR599163_bin.88_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 05:44:17,269] [INFO] DFAST_QC completed!
[2023-06-28 05:44:17,269] [INFO] Total running time: 0h0m48s