[2023-06-28 12:02:49,577] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:02:49,580] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:02:49,580] [INFO] DQC Reference Directory: /var/lib/cwl/stga80d9235-7983-4eaf-a914-fdeacfc3427d/dqc_reference
[2023-06-28 12:02:50,889] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:02:50,890] [INFO] Task started: Prodigal
[2023-06-28 12:02:50,890] [INFO] Running command: gunzip -c /var/lib/cwl/stge3e10a4b-aff4-4499-89b2-1be47d1b1e6d/GCA_012839585.1_ASM1283958v1_genomic.fna.gz | prodigal -d GCA_012839585.1_ASM1283958v1_genomic.fna/cds.fna -a GCA_012839585.1_ASM1283958v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:02:56,406] [INFO] Task succeeded: Prodigal
[2023-06-28 12:02:56,407] [INFO] Task started: HMMsearch
[2023-06-28 12:02:56,407] [INFO] Running command: hmmsearch --tblout GCA_012839585.1_ASM1283958v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga80d9235-7983-4eaf-a914-fdeacfc3427d/dqc_reference/reference_markers.hmm GCA_012839585.1_ASM1283958v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:02:56,675] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:02:56,677] [INFO] Found 6/6 markers.
[2023-06-28 12:02:56,704] [INFO] Query marker FASTA was written to GCA_012839585.1_ASM1283958v1_genomic.fna/markers.fasta
[2023-06-28 12:02:56,705] [INFO] Task started: Blastn
[2023-06-28 12:02:56,705] [INFO] Running command: blastn -query GCA_012839585.1_ASM1283958v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga80d9235-7983-4eaf-a914-fdeacfc3427d/dqc_reference/reference_markers.fasta -out GCA_012839585.1_ASM1283958v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:02:57,377] [INFO] Task succeeded: Blastn
[2023-06-28 12:02:57,382] [INFO] Selected 28 target genomes.
[2023-06-28 12:02:57,383] [INFO] Target genome list was writen to GCA_012839585.1_ASM1283958v1_genomic.fna/target_genomes.txt
[2023-06-28 12:02:57,394] [INFO] Task started: fastANI
[2023-06-28 12:02:57,394] [INFO] Running command: fastANI --query /var/lib/cwl/stge3e10a4b-aff4-4499-89b2-1be47d1b1e6d/GCA_012839585.1_ASM1283958v1_genomic.fna.gz --refList GCA_012839585.1_ASM1283958v1_genomic.fna/target_genomes.txt --output GCA_012839585.1_ASM1283958v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:03:14,815] [INFO] Task succeeded: fastANI
[2023-06-28 12:03:14,816] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga80d9235-7983-4eaf-a914-fdeacfc3427d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:03:14,816] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga80d9235-7983-4eaf-a914-fdeacfc3427d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:03:14,822] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:03:14,823] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:03:14,823] [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
Paenalcaligenes hominis	strain=CCM 7698	GCA_014635265.1	643674	643674	type	True	78.7186	213	693	95	below_threshold
Paenalcaligenes hominis	strain=DSM 26613	GCA_011927625.1	643674	643674	type	True	78.6695	216	693	95	below_threshold
Paenalcaligenes niemegkensis	strain=NGK35	GCA_022230885.1	2895469	2895469	type	True	77.1323	71	693	95	below_threshold
Alcaligenes ammonioxydans	strain=HO-1	GCA_019343455.1	2582914	2582914	type	True	76.8545	64	693	95	below_threshold
Alcaligenes pakistanensis	strain=KCTC 42083	GCA_014652815.1	1482717	1482717	type	True	76.406	70	693	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:03:14,827] [INFO] DFAST Taxonomy check result was written to GCA_012839585.1_ASM1283958v1_genomic.fna/tc_result.tsv
[2023-06-28 12:03:14,827] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:03:14,828] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:03:14,828] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga80d9235-7983-4eaf-a914-fdeacfc3427d/dqc_reference/checkm_data
[2023-06-28 12:03:14,829] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:03:14,864] [INFO] Task started: CheckM
[2023-06-28 12:03:14,864] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_012839585.1_ASM1283958v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_012839585.1_ASM1283958v1_genomic.fna/checkm_input GCA_012839585.1_ASM1283958v1_genomic.fna/checkm_result
[2023-06-28 12:03:38,516] [INFO] Task succeeded: CheckM
[2023-06-28 12:03:38,517] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.80%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:03:38,539] [INFO] ===== Completeness check finished =====
[2023-06-28 12:03:38,540] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:03:38,540] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_012839585.1_ASM1283958v1_genomic.fna/markers.fasta)
[2023-06-28 12:03:38,541] [INFO] Task started: Blastn
[2023-06-28 12:03:38,541] [INFO] Running command: blastn -query GCA_012839585.1_ASM1283958v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga80d9235-7983-4eaf-a914-fdeacfc3427d/dqc_reference/reference_markers_gtdb.fasta -out GCA_012839585.1_ASM1283958v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:03:39,609] [INFO] Task succeeded: Blastn
[2023-06-28 12:03:39,613] [INFO] Selected 25 target genomes.
[2023-06-28 12:03:39,613] [INFO] Target genome list was writen to GCA_012839585.1_ASM1283958v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:03:39,667] [INFO] Task started: fastANI
[2023-06-28 12:03:39,668] [INFO] Running command: fastANI --query /var/lib/cwl/stge3e10a4b-aff4-4499-89b2-1be47d1b1e6d/GCA_012839585.1_ASM1283958v1_genomic.fna.gz --refList GCA_012839585.1_ASM1283958v1_genomic.fna/target_genomes_gtdb.txt --output GCA_012839585.1_ASM1283958v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:03:53,949] [INFO] Task succeeded: fastANI
[2023-06-28 12:03:53,962] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:03:53,962] [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_012839585.1	s__Paenalcaligenes sp012839585	100.0	686	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paenalcaligenes	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011927625.1	s__Paenalcaligenes hominis	78.6695	216	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paenalcaligenes	95.0	98.31	96.62	0.96	0.92	3	-
GCA_012518715.1	s__Paenalcaligenes sp012518715	78.4875	185	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paenalcaligenes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011290505.1	s__Paenalcaligenes suwonensis	76.9315	88	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paenalcaligenes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004791645.1	s__Paenalcaligenes sp004791645	76.7957	90	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paenalcaligenes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009497775.1	s__Alcaligenes faecalis_D	76.7443	72	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005311025.1	s__Alcaligenes phenolicus	76.6201	60	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	97.79	96.15	0.91	0.86	11	-
GCA_013416445.1	s__Candidimonas_A sp013416445	75.9362	53	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:03:53,964] [INFO] GTDB search result was written to GCA_012839585.1_ASM1283958v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:03:53,965] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:03:53,970] [INFO] DFAST_QC result json was written to GCA_012839585.1_ASM1283958v1_genomic.fna/dqc_result.json
[2023-06-28 12:03:53,970] [INFO] DFAST_QC completed!
[2023-06-28 12:03:53,971] [INFO] Total running time: 0h1m4s