[2023-06-26 23:15:19,921] [INFO] DFAST_QC pipeline started.
[2023-06-26 23:15:19,923] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 23:15:19,923] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3c173cd-04e2-4671-9f13-718334483f64/dqc_reference
[2023-06-26 23:15:21,226] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 23:15:21,227] [INFO] Task started: Prodigal
[2023-06-26 23:15:21,228] [INFO] Running command: gunzip -c /var/lib/cwl/stgf6ba0e4c-0f26-4790-beaa-d4751570c9c2/GCA_002691485.1_ASM269148v1_genomic.fna.gz | prodigal -d GCA_002691485.1_ASM269148v1_genomic.fna/cds.fna -a GCA_002691485.1_ASM269148v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 23:15:24,382] [INFO] Task succeeded: Prodigal
[2023-06-26 23:15:24,382] [INFO] Task started: HMMsearch
[2023-06-26 23:15:24,382] [INFO] Running command: hmmsearch --tblout GCA_002691485.1_ASM269148v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3c173cd-04e2-4671-9f13-718334483f64/dqc_reference/reference_markers.hmm GCA_002691485.1_ASM269148v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 23:15:24,549] [INFO] Task succeeded: HMMsearch
[2023-06-26 23:15:24,550] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf6ba0e4c-0f26-4790-beaa-d4751570c9c2/GCA_002691485.1_ASM269148v1_genomic.fna.gz]
[2023-06-26 23:15:24,569] [INFO] Query marker FASTA was written to GCA_002691485.1_ASM269148v1_genomic.fna/markers.fasta
[2023-06-26 23:15:24,569] [INFO] Task started: Blastn
[2023-06-26 23:15:24,569] [INFO] Running command: blastn -query GCA_002691485.1_ASM269148v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3c173cd-04e2-4671-9f13-718334483f64/dqc_reference/reference_markers.fasta -out GCA_002691485.1_ASM269148v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:15:25,211] [INFO] Task succeeded: Blastn
[2023-06-26 23:15:25,214] [INFO] Selected 25 target genomes.
[2023-06-26 23:15:25,215] [INFO] Target genome list was writen to GCA_002691485.1_ASM269148v1_genomic.fna/target_genomes.txt
[2023-06-26 23:15:25,218] [INFO] Task started: fastANI
[2023-06-26 23:15:25,218] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6ba0e4c-0f26-4790-beaa-d4751570c9c2/GCA_002691485.1_ASM269148v1_genomic.fna.gz --refList GCA_002691485.1_ASM269148v1_genomic.fna/target_genomes.txt --output GCA_002691485.1_ASM269148v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 23:15:38,338] [INFO] Task succeeded: fastANI
[2023-06-26 23:15:38,338] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3c173cd-04e2-4671-9f13-718334483f64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 23:15:38,338] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3c173cd-04e2-4671-9f13-718334483f64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 23:15:38,340] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 23:15:38,340] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-26 23:15:38,340] [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
--------------------------------------------------------------------------------
[2023-06-26 23:15:38,342] [INFO] DFAST Taxonomy check result was written to GCA_002691485.1_ASM269148v1_genomic.fna/tc_result.tsv
[2023-06-26 23:15:38,343] [INFO] ===== Taxonomy check completed =====
[2023-06-26 23:15:38,343] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 23:15:38,343] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3c173cd-04e2-4671-9f13-718334483f64/dqc_reference/checkm_data
[2023-06-26 23:15:38,346] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 23:15:38,360] [INFO] Task started: CheckM
[2023-06-26 23:15:38,361] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002691485.1_ASM269148v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002691485.1_ASM269148v1_genomic.fna/checkm_input GCA_002691485.1_ASM269148v1_genomic.fna/checkm_result
[2023-06-26 23:15:55,569] [INFO] Task succeeded: CheckM
[2023-06-26 23:15:55,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-26 23:15:55,590] [INFO] ===== Completeness check finished =====
[2023-06-26 23:15:55,590] [INFO] ===== Start GTDB Search =====
[2023-06-26 23:15:55,590] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002691485.1_ASM269148v1_genomic.fna/markers.fasta)
[2023-06-26 23:15:55,591] [INFO] Task started: Blastn
[2023-06-26 23:15:55,591] [INFO] Running command: blastn -query GCA_002691485.1_ASM269148v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3c173cd-04e2-4671-9f13-718334483f64/dqc_reference/reference_markers_gtdb.fasta -out GCA_002691485.1_ASM269148v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:15:56,467] [INFO] Task succeeded: Blastn
[2023-06-26 23:15:56,471] [INFO] Selected 18 target genomes.
[2023-06-26 23:15:56,471] [INFO] Target genome list was writen to GCA_002691485.1_ASM269148v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 23:15:56,480] [INFO] Task started: fastANI
[2023-06-26 23:15:56,480] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6ba0e4c-0f26-4790-beaa-d4751570c9c2/GCA_002691485.1_ASM269148v1_genomic.fna.gz --refList GCA_002691485.1_ASM269148v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002691485.1_ASM269148v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 23:16:05,273] [INFO] Task succeeded: fastANI
[2023-06-26 23:16:05,366] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-26 23:16:05,367] [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_009886945.1	s__HIMB30 sp002691485	96.718	311	365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	97.88	95.73	0.81	0.62	14	conclusive
GCA_008087055.1	s__HIMB30 sp008087055	79.2594	173	365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010024125.1	s__HIMB30 sp010024125	79.1205	148	365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	98.50	98.43	0.79	0.78	4	-
GCA_002705325.1	s__HIMB30 sp002705325	78.6988	118	365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	97.62	96.19	0.76	0.70	4	-
GCA_000227525.2	s__HIMB30 sp000227525	78.682	140	365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	98.38	98.38	0.91	0.91	2	-
GCA_902536515.1	s__HIMB30 sp902536515	77.4669	62	365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-26 23:16:05,369] [INFO] GTDB search result was written to GCA_002691485.1_ASM269148v1_genomic.fna/result_gtdb.tsv
[2023-06-26 23:16:05,369] [INFO] ===== GTDB Search completed =====
[2023-06-26 23:16:05,372] [INFO] DFAST_QC result json was written to GCA_002691485.1_ASM269148v1_genomic.fna/dqc_result.json
[2023-06-26 23:16:05,372] [INFO] DFAST_QC completed!
[2023-06-26 23:16:05,372] [INFO] Total running time: 0h0m45s