[2023-06-29 15:10:14,891] [INFO] DFAST_QC pipeline started.
[2023-06-29 15:10:14,896] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 15:10:14,896] [INFO] DQC Reference Directory: /var/lib/cwl/stg05a7ab51-b385-4943-9efe-761a2bf2fd24/dqc_reference
[2023-06-29 15:10:16,408] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 15:10:16,409] [INFO] Task started: Prodigal
[2023-06-29 15:10:16,409] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6f04472-244e-45af-b7ec-667d4dd7e393/GCA_023448095.1_ASM2344809v1_genomic.fna.gz | prodigal -d GCA_023448095.1_ASM2344809v1_genomic.fna/cds.fna -a GCA_023448095.1_ASM2344809v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 15:10:24,917] [INFO] Task succeeded: Prodigal
[2023-06-29 15:10:24,918] [INFO] Task started: HMMsearch
[2023-06-29 15:10:24,918] [INFO] Running command: hmmsearch --tblout GCA_023448095.1_ASM2344809v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05a7ab51-b385-4943-9efe-761a2bf2fd24/dqc_reference/reference_markers.hmm GCA_023448095.1_ASM2344809v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 15:10:25,265] [INFO] Task succeeded: HMMsearch
[2023-06-29 15:10:25,266] [INFO] Found 6/6 markers.
[2023-06-29 15:10:25,293] [INFO] Query marker FASTA was written to GCA_023448095.1_ASM2344809v1_genomic.fna/markers.fasta
[2023-06-29 15:10:25,294] [INFO] Task started: Blastn
[2023-06-29 15:10:25,294] [INFO] Running command: blastn -query GCA_023448095.1_ASM2344809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05a7ab51-b385-4943-9efe-761a2bf2fd24/dqc_reference/reference_markers.fasta -out GCA_023448095.1_ASM2344809v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:10:25,971] [INFO] Task succeeded: Blastn
[2023-06-29 15:10:25,974] [INFO] Selected 25 target genomes.
[2023-06-29 15:10:25,975] [INFO] Target genome list was writen to GCA_023448095.1_ASM2344809v1_genomic.fna/target_genomes.txt
[2023-06-29 15:10:25,988] [INFO] Task started: fastANI
[2023-06-29 15:10:25,988] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6f04472-244e-45af-b7ec-667d4dd7e393/GCA_023448095.1_ASM2344809v1_genomic.fna.gz --refList GCA_023448095.1_ASM2344809v1_genomic.fna/target_genomes.txt --output GCA_023448095.1_ASM2344809v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 15:10:49,320] [INFO] Task succeeded: fastANI
[2023-06-29 15:10:49,321] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05a7ab51-b385-4943-9efe-761a2bf2fd24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 15:10:49,321] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05a7ab51-b385-4943-9efe-761a2bf2fd24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 15:10:49,323] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 15:10:49,323] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 15:10:49,323] [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 15:10:49,325] [INFO] DFAST Taxonomy check result was written to GCA_023448095.1_ASM2344809v1_genomic.fna/tc_result.tsv
[2023-06-29 15:10:49,326] [INFO] ===== Taxonomy check completed =====
[2023-06-29 15:10:49,326] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 15:10:49,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05a7ab51-b385-4943-9efe-761a2bf2fd24/dqc_reference/checkm_data
[2023-06-29 15:10:49,329] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 15:10:49,377] [INFO] Task started: CheckM
[2023-06-29 15:10:49,377] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023448095.1_ASM2344809v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023448095.1_ASM2344809v1_genomic.fna/checkm_input GCA_023448095.1_ASM2344809v1_genomic.fna/checkm_result
[2023-06-29 15:11:21,270] [INFO] Task succeeded: CheckM
[2023-06-29 15:11:21,278] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 15:11:21,309] [INFO] ===== Completeness check finished =====
[2023-06-29 15:11:21,309] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:11:21,310] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023448095.1_ASM2344809v1_genomic.fna/markers.fasta)
[2023-06-29 15:11:21,310] [INFO] Task started: Blastn
[2023-06-29 15:11:21,310] [INFO] Running command: blastn -query GCA_023448095.1_ASM2344809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05a7ab51-b385-4943-9efe-761a2bf2fd24/dqc_reference/reference_markers_gtdb.fasta -out GCA_023448095.1_ASM2344809v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:11:22,244] [INFO] Task succeeded: Blastn
[2023-06-29 15:11:22,249] [INFO] Selected 14 target genomes.
[2023-06-29 15:11:22,249] [INFO] Target genome list was writen to GCA_023448095.1_ASM2344809v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:11:22,262] [INFO] Task started: fastANI
[2023-06-29 15:11:22,262] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6f04472-244e-45af-b7ec-667d4dd7e393/GCA_023448095.1_ASM2344809v1_genomic.fna.gz --refList GCA_023448095.1_ASM2344809v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023448095.1_ASM2344809v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:11:31,077] [INFO] Task succeeded: fastANI
[2023-06-29 15:11:31,089] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 15:11:31,089] [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_000437595.1	s__UBA11524 sp000437595	97.3881	769	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	97.36	96.94	0.88	0.81	39	conclusive
GCA_900769075.1	s__UBA11524 sp900769075	78.3576	241	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017399225.1	s__UBA11524 sp017399225	77.9494	216	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017481825.1	s__UBA11524 sp017481825	77.9401	229	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017465155.1	s__UBA11524 sp017465155	77.932	190	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017397765.1	s__UBA11524 sp017397765	77.9063	192	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056155.1	s__UBA11524 sp015056155	77.8764	228	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017410455.1	s__UBA11524 sp017410455	77.7824	238	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056085.1	s__UBA11524 sp015056085	77.7576	144	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017502305.1	s__UBA11524 sp017502305	77.5904	124	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017513475.1	s__UBA11524 sp017513475	77.4733	187	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017463245.1	s__UBA11524 sp017463245	77.4674	170	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056415.1	s__UBA11524 sp015056415	77.0466	124	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 15:11:31,091] [INFO] GTDB search result was written to GCA_023448095.1_ASM2344809v1_genomic.fna/result_gtdb.tsv
[2023-06-29 15:11:31,092] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:11:31,095] [INFO] DFAST_QC result json was written to GCA_023448095.1_ASM2344809v1_genomic.fna/dqc_result.json
[2023-06-29 15:11:31,095] [INFO] DFAST_QC completed!
[2023-06-29 15:11:31,095] [INFO] Total running time: 0h1m16s