[2023-06-29 12:37:52,806] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:37:52,809] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:37:52,809] [INFO] DQC Reference Directory: /var/lib/cwl/stg21ea525f-edcf-4524-9c06-a679728b7740/dqc_reference
[2023-06-29 12:37:54,222] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:37:54,224] [INFO] Task started: Prodigal
[2023-06-29 12:37:54,225] [INFO] Running command: gunzip -c /var/lib/cwl/stgfde7ae53-5915-4767-87aa-7124bfe8fc85/GCA_021633665.1_ASM2163366v1_genomic.fna.gz | prodigal -d GCA_021633665.1_ASM2163366v1_genomic.fna/cds.fna -a GCA_021633665.1_ASM2163366v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:37:57,977] [INFO] Task succeeded: Prodigal
[2023-06-29 12:37:57,977] [INFO] Task started: HMMsearch
[2023-06-29 12:37:57,977] [INFO] Running command: hmmsearch --tblout GCA_021633665.1_ASM2163366v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21ea525f-edcf-4524-9c06-a679728b7740/dqc_reference/reference_markers.hmm GCA_021633665.1_ASM2163366v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:37:58,236] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:37:58,237] [INFO] Found 6/6 markers.
[2023-06-29 12:37:58,255] [INFO] Query marker FASTA was written to GCA_021633665.1_ASM2163366v1_genomic.fna/markers.fasta
[2023-06-29 12:37:58,256] [INFO] Task started: Blastn
[2023-06-29 12:37:58,256] [INFO] Running command: blastn -query GCA_021633665.1_ASM2163366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21ea525f-edcf-4524-9c06-a679728b7740/dqc_reference/reference_markers.fasta -out GCA_021633665.1_ASM2163366v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:37:58,864] [INFO] Task succeeded: Blastn
[2023-06-29 12:37:58,868] [INFO] Selected 30 target genomes.
[2023-06-29 12:37:58,869] [INFO] Target genome list was writen to GCA_021633665.1_ASM2163366v1_genomic.fna/target_genomes.txt
[2023-06-29 12:37:58,870] [INFO] Task started: fastANI
[2023-06-29 12:37:58,870] [INFO] Running command: fastANI --query /var/lib/cwl/stgfde7ae53-5915-4767-87aa-7124bfe8fc85/GCA_021633665.1_ASM2163366v1_genomic.fna.gz --refList GCA_021633665.1_ASM2163366v1_genomic.fna/target_genomes.txt --output GCA_021633665.1_ASM2163366v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:38:20,014] [INFO] Task succeeded: fastANI
[2023-06-29 12:38:20,015] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21ea525f-edcf-4524-9c06-a679728b7740/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:38:20,015] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21ea525f-edcf-4524-9c06-a679728b7740/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:38:20,017] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:38:20,017] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 12:38:20,017] [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 12:38:20,019] [INFO] DFAST Taxonomy check result was written to GCA_021633665.1_ASM2163366v1_genomic.fna/tc_result.tsv
[2023-06-29 12:38:20,020] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:38:20,020] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:38:20,021] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21ea525f-edcf-4524-9c06-a679728b7740/dqc_reference/checkm_data
[2023-06-29 12:38:20,025] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:38:20,048] [INFO] Task started: CheckM
[2023-06-29 12:38:20,048] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021633665.1_ASM2163366v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021633665.1_ASM2163366v1_genomic.fna/checkm_input GCA_021633665.1_ASM2163366v1_genomic.fna/checkm_result
[2023-06-29 12:38:38,830] [INFO] Task succeeded: CheckM
[2023-06-29 12:38:38,831] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:38:38,873] [INFO] ===== Completeness check finished =====
[2023-06-29 12:38:38,873] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:38:38,874] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021633665.1_ASM2163366v1_genomic.fna/markers.fasta)
[2023-06-29 12:38:38,874] [INFO] Task started: Blastn
[2023-06-29 12:38:38,874] [INFO] Running command: blastn -query GCA_021633665.1_ASM2163366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21ea525f-edcf-4524-9c06-a679728b7740/dqc_reference/reference_markers_gtdb.fasta -out GCA_021633665.1_ASM2163366v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:38:39,668] [INFO] Task succeeded: Blastn
[2023-06-29 12:38:39,673] [INFO] Selected 19 target genomes.
[2023-06-29 12:38:39,673] [INFO] Target genome list was writen to GCA_021633665.1_ASM2163366v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:38:39,675] [INFO] Task started: fastANI
[2023-06-29 12:38:39,675] [INFO] Running command: fastANI --query /var/lib/cwl/stgfde7ae53-5915-4767-87aa-7124bfe8fc85/GCA_021633665.1_ASM2163366v1_genomic.fna.gz --refList GCA_021633665.1_ASM2163366v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021633665.1_ASM2163366v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:38:46,968] [INFO] Task succeeded: fastANI
[2023-06-29 12:38:46,978] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 12:38:46,978] [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_004557245.1	s__SFEL01 sp004557245	96.3476	404	447	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__SFEL01	95.0	97.48	96.14	0.90	0.84	17	conclusive
GCA_016292635.1	s__SFEL01 sp016292635	78.8208	166	447	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__SFEL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017547885.1	s__SFEL01 sp017547885	78.7117	145	447	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__SFEL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543475.1	s__Pelethousia gallinarum	77.4965	62	447	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__Pelethousia	95.0	98.78	98.45	0.84	0.76	5	-
GCA_900542615.1	s__Pelethousia sp900542615	77.0368	64	447	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__Pelethousia	95.0	100.00	100.00	0.99	0.99	2	-
GCA_004558525.1	s__Phil1 sp004558525	76.6589	56	447	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__Phil1	95.0	98.96	98.54	0.91	0.86	6	-
--------------------------------------------------------------------------------
[2023-06-29 12:38:46,980] [INFO] GTDB search result was written to GCA_021633665.1_ASM2163366v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:38:46,980] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:38:46,983] [INFO] DFAST_QC result json was written to GCA_021633665.1_ASM2163366v1_genomic.fna/dqc_result.json
[2023-06-29 12:38:46,983] [INFO] DFAST_QC completed!
[2023-06-29 12:38:46,983] [INFO] Total running time: 0h0m54s