[2023-06-29 14:06:18,245] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:06:18,249] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:06:18,250] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f3f15ba-a7d1-47c0-8a59-db8b27b516db/dqc_reference
[2023-06-29 14:06:19,586] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:06:19,587] [INFO] Task started: Prodigal
[2023-06-29 14:06:19,587] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d373d9e-216b-4f23-bab4-489ceb77b0d3/GCA_021817645.1_ASM2181764v1_genomic.fna.gz | prodigal -d GCA_021817645.1_ASM2181764v1_genomic.fna/cds.fna -a GCA_021817645.1_ASM2181764v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:06:26,950] [INFO] Task succeeded: Prodigal
[2023-06-29 14:06:26,951] [INFO] Task started: HMMsearch
[2023-06-29 14:06:26,951] [INFO] Running command: hmmsearch --tblout GCA_021817645.1_ASM2181764v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f3f15ba-a7d1-47c0-8a59-db8b27b516db/dqc_reference/reference_markers.hmm GCA_021817645.1_ASM2181764v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:06:27,220] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:06:27,221] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg2d373d9e-216b-4f23-bab4-489ceb77b0d3/GCA_021817645.1_ASM2181764v1_genomic.fna.gz]
[2023-06-29 14:06:27,248] [INFO] Query marker FASTA was written to GCA_021817645.1_ASM2181764v1_genomic.fna/markers.fasta
[2023-06-29 14:06:27,248] [INFO] Task started: Blastn
[2023-06-29 14:06:27,249] [INFO] Running command: blastn -query GCA_021817645.1_ASM2181764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f3f15ba-a7d1-47c0-8a59-db8b27b516db/dqc_reference/reference_markers.fasta -out GCA_021817645.1_ASM2181764v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:06:27,893] [INFO] Task succeeded: Blastn
[2023-06-29 14:06:27,897] [INFO] Selected 19 target genomes.
[2023-06-29 14:06:27,897] [INFO] Target genome list was writen to GCA_021817645.1_ASM2181764v1_genomic.fna/target_genomes.txt
[2023-06-29 14:06:27,900] [INFO] Task started: fastANI
[2023-06-29 14:06:27,900] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d373d9e-216b-4f23-bab4-489ceb77b0d3/GCA_021817645.1_ASM2181764v1_genomic.fna.gz --refList GCA_021817645.1_ASM2181764v1_genomic.fna/target_genomes.txt --output GCA_021817645.1_ASM2181764v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:06:40,751] [INFO] Task succeeded: fastANI
[2023-06-29 14:06:40,751] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f3f15ba-a7d1-47c0-8a59-db8b27b516db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:06:40,752] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f3f15ba-a7d1-47c0-8a59-db8b27b516db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:06:40,753] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:06:40,753] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 14:06:40,754] [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 14:06:40,756] [INFO] DFAST Taxonomy check result was written to GCA_021817645.1_ASM2181764v1_genomic.fna/tc_result.tsv
[2023-06-29 14:06:40,756] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:06:40,756] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:06:40,757] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f3f15ba-a7d1-47c0-8a59-db8b27b516db/dqc_reference/checkm_data
[2023-06-29 14:06:40,760] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:06:40,797] [INFO] Task started: CheckM
[2023-06-29 14:06:40,798] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021817645.1_ASM2181764v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021817645.1_ASM2181764v1_genomic.fna/checkm_input GCA_021817645.1_ASM2181764v1_genomic.fna/checkm_result
[2023-06-29 14:07:07,996] [INFO] Task succeeded: CheckM
[2023-06-29 14:07:07,998] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:07:08,019] [INFO] ===== Completeness check finished =====
[2023-06-29 14:07:08,020] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:07:08,020] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021817645.1_ASM2181764v1_genomic.fna/markers.fasta)
[2023-06-29 14:07:08,021] [INFO] Task started: Blastn
[2023-06-29 14:07:08,021] [INFO] Running command: blastn -query GCA_021817645.1_ASM2181764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f3f15ba-a7d1-47c0-8a59-db8b27b516db/dqc_reference/reference_markers_gtdb.fasta -out GCA_021817645.1_ASM2181764v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:07:08,844] [INFO] Task succeeded: Blastn
[2023-06-29 14:07:08,856] [INFO] Selected 10 target genomes.
[2023-06-29 14:07:08,856] [INFO] Target genome list was writen to GCA_021817645.1_ASM2181764v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:07:08,862] [INFO] Task started: fastANI
[2023-06-29 14:07:08,862] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d373d9e-216b-4f23-bab4-489ceb77b0d3/GCA_021817645.1_ASM2181764v1_genomic.fna.gz --refList GCA_021817645.1_ASM2181764v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021817645.1_ASM2181764v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:07:14,888] [INFO] Task succeeded: fastANI
[2023-06-29 14:07:14,900] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 14:07:14,900] [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_016208235.1	s__SURF-52 sp016208235	82.236	440	857	d__Bacteria;p__Desulfobacterota;c__Desulfobaccia;o__Desulfobaccales;f__0-14-0-80-60-11;g__SURF-52	95.0	98.97	98.97	0.86	0.86	2	-
GCA_003599195.1	s__SURF-52 sp003599195	80.5231	464	857	d__Bacteria;p__Desulfobacterota;c__Desulfobaccia;o__Desulfobaccales;f__0-14-0-80-60-11;g__SURF-52	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002779455.1	s__0-14-0-80-60-11 sp002779455	78.6572	220	857	d__Bacteria;p__Desulfobacterota;c__Desulfobaccia;o__Desulfobaccales;f__0-14-0-80-60-11;g__0-14-0-80-60-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875015.1	s__0-14-0-80-60-11 sp016875015	78.2896	273	857	d__Bacteria;p__Desulfobacterota;c__Desulfobaccia;o__Desulfobaccales;f__0-14-0-80-60-11;g__0-14-0-80-60-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874915.1	s__0-14-0-80-60-11 sp016874915	78.1029	259	857	d__Bacteria;p__Desulfobacterota;c__Desulfobaccia;o__Desulfobaccales;f__0-14-0-80-60-11;g__0-14-0-80-60-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874975.1	s__VGSQ01 sp016874975	77.8532	224	857	d__Bacteria;p__Desulfobacterota;c__Desulfobaccia;o__Desulfobaccales;f__0-14-0-80-60-11;g__VGSQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874945.1	s__0-14-0-80-60-11 sp016874945	77.7995	222	857	d__Bacteria;p__Desulfobacterota;c__Desulfobaccia;o__Desulfobaccales;f__0-14-0-80-60-11;g__0-14-0-80-60-11	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 14:07:14,903] [INFO] GTDB search result was written to GCA_021817645.1_ASM2181764v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:07:14,903] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:07:14,906] [INFO] DFAST_QC result json was written to GCA_021817645.1_ASM2181764v1_genomic.fna/dqc_result.json
[2023-06-29 14:07:14,906] [INFO] DFAST_QC completed!
[2023-06-29 14:07:14,906] [INFO] Total running time: 0h0m57s