[2023-06-08 11:16:14,500] [INFO] DFAST_QC pipeline started.
[2023-06-08 11:16:14,506] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 11:16:14,506] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d4e2b32-8a68-4578-a8a0-b9f99f22cc94/dqc_reference
[2023-06-08 11:16:15,740] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 11:16:15,741] [INFO] Task started: Prodigal
[2023-06-08 11:16:15,742] [INFO] Running command: gunzip -c /var/lib/cwl/stg43b335ae-346a-4494-a38a-f552e698c210/GCA_947072115.1_ERR5094856_bin.26_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947072115.1_ERR5094856_bin.26_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_947072115.1_ERR5094856_bin.26_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 11:16:17,581] [INFO] Task succeeded: Prodigal
[2023-06-08 11:16:17,582] [INFO] Task started: HMMsearch
[2023-06-08 11:16:17,582] [INFO] Running command: hmmsearch --tblout GCA_947072115.1_ERR5094856_bin.26_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d4e2b32-8a68-4578-a8a0-b9f99f22cc94/dqc_reference/reference_markers.hmm GCA_947072115.1_ERR5094856_bin.26_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 11:16:17,888] [INFO] Task succeeded: HMMsearch
[2023-06-08 11:16:17,889] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg43b335ae-346a-4494-a38a-f552e698c210/GCA_947072115.1_ERR5094856_bin.26_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 11:16:17,904] [INFO] Query marker FASTA was written to GCA_947072115.1_ERR5094856_bin.26_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 11:16:17,905] [INFO] Task started: Blastn
[2023-06-08 11:16:17,905] [INFO] Running command: blastn -query GCA_947072115.1_ERR5094856_bin.26_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d4e2b32-8a68-4578-a8a0-b9f99f22cc94/dqc_reference/reference_markers.fasta -out GCA_947072115.1_ERR5094856_bin.26_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:16:21,099] [INFO] Task succeeded: Blastn
[2023-06-08 11:16:21,103] [INFO] Selected 12 target genomes.
[2023-06-08 11:16:21,103] [INFO] Target genome list was writen to GCA_947072115.1_ERR5094856_bin.26_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 11:16:21,137] [INFO] Task started: fastANI
[2023-06-08 11:16:21,137] [INFO] Running command: fastANI --query /var/lib/cwl/stg43b335ae-346a-4494-a38a-f552e698c210/GCA_947072115.1_ERR5094856_bin.26_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947072115.1_ERR5094856_bin.26_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947072115.1_ERR5094856_bin.26_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 11:16:31,365] [INFO] Task succeeded: fastANI
[2023-06-08 11:16:31,365] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d4e2b32-8a68-4578-a8a0-b9f99f22cc94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 11:16:31,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d4e2b32-8a68-4578-a8a0-b9f99f22cc94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 11:16:31,367] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 11:16:31,367] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 11:16:31,367] [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
--------------------------------------------------------------------------------
[2023-06-08 11:16:31,369] [INFO] DFAST Taxonomy check result was written to GCA_947072115.1_ERR5094856_bin.26_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 11:16:31,370] [INFO] ===== Taxonomy check completed =====
[2023-06-08 11:16:31,370] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 11:16:31,370] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d4e2b32-8a68-4578-a8a0-b9f99f22cc94/dqc_reference/checkm_data
[2023-06-08 11:16:31,372] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 11:16:31,402] [INFO] Task started: CheckM
[2023-06-08 11:16:31,402] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947072115.1_ERR5094856_bin.26_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947072115.1_ERR5094856_bin.26_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_947072115.1_ERR5094856_bin.26_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 11:16:46,296] [INFO] Task succeeded: CheckM
[2023-06-08 11:16:46,297] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.47%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 11:16:46,316] [INFO] ===== Completeness check finished =====
[2023-06-08 11:16:46,316] [INFO] ===== Start GTDB Search =====
[2023-06-08 11:16:46,317] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947072115.1_ERR5094856_bin.26_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 11:16:46,317] [INFO] Task started: Blastn
[2023-06-08 11:16:46,317] [INFO] Running command: blastn -query GCA_947072115.1_ERR5094856_bin.26_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d4e2b32-8a68-4578-a8a0-b9f99f22cc94/dqc_reference/reference_markers_gtdb.fasta -out GCA_947072115.1_ERR5094856_bin.26_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:16:46,955] [INFO] Task succeeded: Blastn
[2023-06-08 11:16:46,960] [INFO] Selected 13 target genomes.
[2023-06-08 11:16:46,960] [INFO] Target genome list was writen to GCA_947072115.1_ERR5094856_bin.26_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 11:16:46,965] [INFO] Task started: fastANI
[2023-06-08 11:16:46,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg43b335ae-346a-4494-a38a-f552e698c210/GCA_947072115.1_ERR5094856_bin.26_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947072115.1_ERR5094856_bin.26_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947072115.1_ERR5094856_bin.26_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 11:16:51,685] [INFO] Task succeeded: fastANI
[2023-06-08 11:16:51,693] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 11:16:51,693] [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_004556165.1	s__PeH17 sp004556165	98.7591	209	224	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	98.62	98.21	0.87	0.80	6	conclusive
GCA_900542285.1	s__PeH17 sp900542285	79.4009	87	224	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	98.90	98.16	0.94	0.91	7	-
GCA_902794055.1	s__PeH17 sp902794055	78.0008	53	224	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 11:16:51,696] [INFO] GTDB search result was written to GCA_947072115.1_ERR5094856_bin.26_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 11:16:51,696] [INFO] ===== GTDB Search completed =====
[2023-06-08 11:16:51,699] [INFO] DFAST_QC result json was written to GCA_947072115.1_ERR5094856_bin.26_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 11:16:51,699] [INFO] DFAST_QC completed!
[2023-06-08 11:16:51,699] [INFO] Total running time: 0h0m37s