[2023-06-29 20:13:54,820] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:13:54,825] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:13:54,825] [INFO] DQC Reference Directory: /var/lib/cwl/stg63fa2e6d-c319-486c-8d34-dfcb9970afb4/dqc_reference
[2023-06-29 20:13:56,260] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:13:56,262] [INFO] Task started: Prodigal
[2023-06-29 20:13:56,262] [INFO] Running command: gunzip -c /var/lib/cwl/stge4ef7649-5171-44fa-93aa-93a797338a32/GCA_021824435.1_ASM2182443v1_genomic.fna.gz | prodigal -d GCA_021824435.1_ASM2182443v1_genomic.fna/cds.fna -a GCA_021824435.1_ASM2182443v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:13:58,867] [INFO] Task succeeded: Prodigal
[2023-06-29 20:13:58,867] [INFO] Task started: HMMsearch
[2023-06-29 20:13:58,867] [INFO] Running command: hmmsearch --tblout GCA_021824435.1_ASM2182443v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63fa2e6d-c319-486c-8d34-dfcb9970afb4/dqc_reference/reference_markers.hmm GCA_021824435.1_ASM2182443v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:13:59,089] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:13:59,090] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge4ef7649-5171-44fa-93aa-93a797338a32/GCA_021824435.1_ASM2182443v1_genomic.fna.gz]
[2023-06-29 20:13:59,110] [INFO] Query marker FASTA was written to GCA_021824435.1_ASM2182443v1_genomic.fna/markers.fasta
[2023-06-29 20:13:59,110] [INFO] Task started: Blastn
[2023-06-29 20:13:59,111] [INFO] Running command: blastn -query GCA_021824435.1_ASM2182443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63fa2e6d-c319-486c-8d34-dfcb9970afb4/dqc_reference/reference_markers.fasta -out GCA_021824435.1_ASM2182443v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:13:59,645] [INFO] Task succeeded: Blastn
[2023-06-29 20:13:59,652] [INFO] Selected 15 target genomes.
[2023-06-29 20:13:59,652] [INFO] Target genome list was writen to GCA_021824435.1_ASM2182443v1_genomic.fna/target_genomes.txt
[2023-06-29 20:13:59,654] [INFO] Task started: fastANI
[2023-06-29 20:13:59,654] [INFO] Running command: fastANI --query /var/lib/cwl/stge4ef7649-5171-44fa-93aa-93a797338a32/GCA_021824435.1_ASM2182443v1_genomic.fna.gz --refList GCA_021824435.1_ASM2182443v1_genomic.fna/target_genomes.txt --output GCA_021824435.1_ASM2182443v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:14:06,744] [INFO] Task succeeded: fastANI
[2023-06-29 20:14:06,745] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63fa2e6d-c319-486c-8d34-dfcb9970afb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:14:06,745] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63fa2e6d-c319-486c-8d34-dfcb9970afb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:14:06,746] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:14:06,746] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 20:14:06,747] [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
--------------------------------------------------------------------------------
[2023-06-29 20:14:06,748] [INFO] DFAST Taxonomy check result was written to GCA_021824435.1_ASM2182443v1_genomic.fna/tc_result.tsv
[2023-06-29 20:14:06,749] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:14:06,749] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:14:06,749] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63fa2e6d-c319-486c-8d34-dfcb9970afb4/dqc_reference/checkm_data
[2023-06-29 20:14:06,752] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:14:06,778] [INFO] Task started: CheckM
[2023-06-29 20:14:06,778] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021824435.1_ASM2182443v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021824435.1_ASM2182443v1_genomic.fna/checkm_input GCA_021824435.1_ASM2182443v1_genomic.fna/checkm_result
[2023-06-29 20:14:23,682] [INFO] Task succeeded: CheckM
[2023-06-29 20:14:23,686] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:14:23,706] [INFO] ===== Completeness check finished =====
[2023-06-29 20:14:23,706] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:14:23,707] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021824435.1_ASM2182443v1_genomic.fna/markers.fasta)
[2023-06-29 20:14:23,707] [INFO] Task started: Blastn
[2023-06-29 20:14:23,707] [INFO] Running command: blastn -query GCA_021824435.1_ASM2182443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63fa2e6d-c319-486c-8d34-dfcb9970afb4/dqc_reference/reference_markers_gtdb.fasta -out GCA_021824435.1_ASM2182443v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:14:24,369] [INFO] Task succeeded: Blastn
[2023-06-29 20:14:24,373] [INFO] Selected 12 target genomes.
[2023-06-29 20:14:24,373] [INFO] Target genome list was writen to GCA_021824435.1_ASM2182443v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:14:24,375] [INFO] Task started: fastANI
[2023-06-29 20:14:24,375] [INFO] Running command: fastANI --query /var/lib/cwl/stge4ef7649-5171-44fa-93aa-93a797338a32/GCA_021824435.1_ASM2182443v1_genomic.fna.gz --refList GCA_021824435.1_ASM2182443v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021824435.1_ASM2182443v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:14:31,068] [INFO] Task succeeded: fastANI
[2023-06-29 20:14:31,088] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 20:14:31,088] [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_001803165.1	s__XYB12-FULL-38-5 sp001803165	76.9009	93	391	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__XYB12-FULL-38-5	95.0	98.45	95.26	0.97	0.91	11	-
GCA_009773205.1	s__XYB12-FULL-38-5 sp009773205	76.7992	105	391	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__XYB12-FULL-38-5	95.0	99.94	99.94	0.94	0.94	2	-
GCA_011367925.1	s__DSXH01 sp011367925	76.6875	53	391	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__DSXH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873835.1	s__DSXH01 sp016873835	76.64	66	391	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__DSXH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011368355.1	s__Ignavibacterium album_A	76.1608	50	391	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__Ignavibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016234355.1	s__Fen-1258 sp016234355	76.0719	57	391	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__Fen-1258	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716225.1	s__GCA-2746605 sp016716225	75.9469	68	391	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__GCA-2746605	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012026935.1	s__Fen-1258 sp012026935	75.8496	78	391	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__Fen-1258	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003155655.1	s__Fen-1258 sp003155655	75.7059	59	391	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__Fen-1258	95.0	99.91	99.91	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-29 20:14:31,090] [INFO] GTDB search result was written to GCA_021824435.1_ASM2182443v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:14:31,091] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:14:31,094] [INFO] DFAST_QC result json was written to GCA_021824435.1_ASM2182443v1_genomic.fna/dqc_result.json
[2023-06-29 20:14:31,094] [INFO] DFAST_QC completed!
[2023-06-29 20:14:31,094] [INFO] Total running time: 0h0m36s