[2023-06-13 11:50:37,295] [INFO] DFAST_QC pipeline started.
[2023-06-13 11:50:37,299] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 11:50:37,299] [INFO] DQC Reference Directory: /var/lib/cwl/stg958f6939-898f-4c3e-9482-750164aa081c/dqc_reference
[2023-06-13 11:50:38,721] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 11:50:38,722] [INFO] Task started: Prodigal
[2023-06-13 11:50:38,722] [INFO] Running command: gunzip -c /var/lib/cwl/stg35a66118-afaa-4056-a537-741da473b596/GCA_022508375.1_ASM2250837v1_genomic.fna.gz | prodigal -d GCA_022508375.1_ASM2250837v1_genomic.fna/cds.fna -a GCA_022508375.1_ASM2250837v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 11:50:43,276] [INFO] Task succeeded: Prodigal
[2023-06-13 11:50:43,276] [INFO] Task started: HMMsearch
[2023-06-13 11:50:43,276] [INFO] Running command: hmmsearch --tblout GCA_022508375.1_ASM2250837v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg958f6939-898f-4c3e-9482-750164aa081c/dqc_reference/reference_markers.hmm GCA_022508375.1_ASM2250837v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 11:50:43,510] [INFO] Task succeeded: HMMsearch
[2023-06-13 11:50:43,511] [INFO] Found 6/6 markers.
[2023-06-13 11:50:43,541] [INFO] Query marker FASTA was written to GCA_022508375.1_ASM2250837v1_genomic.fna/markers.fasta
[2023-06-13 11:50:43,542] [INFO] Task started: Blastn
[2023-06-13 11:50:43,542] [INFO] Running command: blastn -query GCA_022508375.1_ASM2250837v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg958f6939-898f-4c3e-9482-750164aa081c/dqc_reference/reference_markers.fasta -out GCA_022508375.1_ASM2250837v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:50:44,125] [INFO] Task succeeded: Blastn
[2023-06-13 11:50:44,129] [INFO] Selected 16 target genomes.
[2023-06-13 11:50:44,129] [INFO] Target genome list was writen to GCA_022508375.1_ASM2250837v1_genomic.fna/target_genomes.txt
[2023-06-13 11:50:44,132] [INFO] Task started: fastANI
[2023-06-13 11:50:44,132] [INFO] Running command: fastANI --query /var/lib/cwl/stg35a66118-afaa-4056-a537-741da473b596/GCA_022508375.1_ASM2250837v1_genomic.fna.gz --refList GCA_022508375.1_ASM2250837v1_genomic.fna/target_genomes.txt --output GCA_022508375.1_ASM2250837v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 11:50:55,802] [INFO] Task succeeded: fastANI
[2023-06-13 11:50:55,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg958f6939-898f-4c3e-9482-750164aa081c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 11:50:55,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg958f6939-898f-4c3e-9482-750164aa081c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 11:50:55,804] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 11:50:55,804] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 11:50:55,804] [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
--------------------------------------------------------------------------------
[2023-06-13 11:50:55,806] [INFO] DFAST Taxonomy check result was written to GCA_022508375.1_ASM2250837v1_genomic.fna/tc_result.tsv
[2023-06-13 11:50:55,807] [INFO] ===== Taxonomy check completed =====
[2023-06-13 11:50:55,807] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 11:50:55,807] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg958f6939-898f-4c3e-9482-750164aa081c/dqc_reference/checkm_data
[2023-06-13 11:50:55,810] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 11:50:55,829] [INFO] Task started: CheckM
[2023-06-13 11:50:55,830] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022508375.1_ASM2250837v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022508375.1_ASM2250837v1_genomic.fna/checkm_input GCA_022508375.1_ASM2250837v1_genomic.fna/checkm_result
[2023-06-13 11:51:16,697] [INFO] Task succeeded: CheckM
[2023-06-13 11:51:16,699] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.68%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 11:51:16,721] [INFO] ===== Completeness check finished =====
[2023-06-13 11:51:16,722] [INFO] ===== Start GTDB Search =====
[2023-06-13 11:51:16,722] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022508375.1_ASM2250837v1_genomic.fna/markers.fasta)
[2023-06-13 11:51:16,722] [INFO] Task started: Blastn
[2023-06-13 11:51:16,722] [INFO] Running command: blastn -query GCA_022508375.1_ASM2250837v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg958f6939-898f-4c3e-9482-750164aa081c/dqc_reference/reference_markers_gtdb.fasta -out GCA_022508375.1_ASM2250837v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:51:17,506] [INFO] Task succeeded: Blastn
[2023-06-13 11:51:17,511] [INFO] Selected 23 target genomes.
[2023-06-13 11:51:17,511] [INFO] Target genome list was writen to GCA_022508375.1_ASM2250837v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 11:51:17,518] [INFO] Task started: fastANI
[2023-06-13 11:51:17,518] [INFO] Running command: fastANI --query /var/lib/cwl/stg35a66118-afaa-4056-a537-741da473b596/GCA_022508375.1_ASM2250837v1_genomic.fna.gz --refList GCA_022508375.1_ASM2250837v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022508375.1_ASM2250837v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 11:51:25,001] [INFO] Task succeeded: fastANI
[2023-06-13 11:51:25,008] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 11:51:25,008] [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_000433775.1	s__Fimimonas gallinarum	77.0427	70	531	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-314;g__Fimimonas	95.0	98.11	97.98	0.92	0.91	5	-
GCA_900769665.1	s__Fimimonas sp900769665	76.9389	69	531	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-314;g__Fimimonas	95.0	96.81	96.81	0.74	0.74	2	-
GCA_003537755.1	s__Fimimonas sp003537755	76.9112	63	531	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-314;g__Fimimonas	95.0	97.28	97.18	0.87	0.84	4	-
GCA_910586905.1	s__Fimimonas sp910586905	76.8108	59	531	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-314;g__Fimimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017409765.1	s__Fimimonas sp017409765	76.5561	58	531	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-314;g__Fimimonas	95.0	96.35	95.81	0.87	0.85	5	-
GCA_910586625.1	s__Fimimonas sp910586625	76.5055	78	531	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-314;g__Fimimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 11:51:25,010] [INFO] GTDB search result was written to GCA_022508375.1_ASM2250837v1_genomic.fna/result_gtdb.tsv
[2023-06-13 11:51:25,011] [INFO] ===== GTDB Search completed =====
[2023-06-13 11:51:25,014] [INFO] DFAST_QC result json was written to GCA_022508375.1_ASM2250837v1_genomic.fna/dqc_result.json
[2023-06-13 11:51:25,014] [INFO] DFAST_QC completed!
[2023-06-13 11:51:25,014] [INFO] Total running time: 0h0m48s