[2024-01-25 18:58:35,567] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:58:35,568] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:58:35,569] [INFO] DQC Reference Directory: /var/lib/cwl/stg3526228e-cefe-4de7-8bb3-13031ad4c85f/dqc_reference
[2024-01-25 18:58:36,788] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:58:36,789] [INFO] Task started: Prodigal
[2024-01-25 18:58:36,789] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6aed3ff-2514-4968-b0f9-ad755389d09e/GCF_026344135.1_ASM2634413v1_genomic.fna.gz | prodigal -d GCF_026344135.1_ASM2634413v1_genomic.fna/cds.fna -a GCF_026344135.1_ASM2634413v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:58:47,959] [INFO] Task succeeded: Prodigal
[2024-01-25 18:58:47,959] [INFO] Task started: HMMsearch
[2024-01-25 18:58:47,959] [INFO] Running command: hmmsearch --tblout GCF_026344135.1_ASM2634413v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3526228e-cefe-4de7-8bb3-13031ad4c85f/dqc_reference/reference_markers.hmm GCF_026344135.1_ASM2634413v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:58:48,192] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:58:48,193] [INFO] Found 6/6 markers.
[2024-01-25 18:58:48,233] [INFO] Query marker FASTA was written to GCF_026344135.1_ASM2634413v1_genomic.fna/markers.fasta
[2024-01-25 18:58:48,234] [INFO] Task started: Blastn
[2024-01-25 18:58:48,234] [INFO] Running command: blastn -query GCF_026344135.1_ASM2634413v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3526228e-cefe-4de7-8bb3-13031ad4c85f/dqc_reference/reference_markers.fasta -out GCF_026344135.1_ASM2634413v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:48,971] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:48,973] [INFO] Selected 11 target genomes.
[2024-01-25 18:58:48,973] [INFO] Target genome list was writen to GCF_026344135.1_ASM2634413v1_genomic.fna/target_genomes.txt
[2024-01-25 18:58:48,986] [INFO] Task started: fastANI
[2024-01-25 18:58:48,986] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6aed3ff-2514-4968-b0f9-ad755389d09e/GCF_026344135.1_ASM2634413v1_genomic.fna.gz --refList GCF_026344135.1_ASM2634413v1_genomic.fna/target_genomes.txt --output GCF_026344135.1_ASM2634413v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:58:58,771] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:58,771] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3526228e-cefe-4de7-8bb3-13031ad4c85f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:58:58,771] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3526228e-cefe-4de7-8bb3-13031ad4c85f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:58:58,778] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:58:58,778] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:58:58,778] [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
Alcaligenes faecalis subsp. faecalis	strain=NBRC 13111	GCA_000739855.1	32001	511	type	True	89.6257	1124	1327	95	below_threshold
Alcaligenes faecalis	strain=DSM 30030	GCA_002443155.1	511	511	type	True	89.6013	1141	1327	95	below_threshold
Alcaligenes faecalis	strain=ATCC 8750	GCA_001298815.1	511	511	type	True	89.5877	1130	1327	95	below_threshold
Alcaligenes faecalis subsp. faecalis	strain=NBRC 13111	GCA_001748345.1	32001	511	type	True	89.5832	1129	1327	95	below_threshold
Alcaligenes pakistanensis	strain=KCTC 42083	GCA_014652815.1	1482717	1482717	type	True	87.723	1160	1327	95	below_threshold
Alcaligenes ammonioxydans	strain=HO-1	GCA_019343455.1	2582914	2582914	type	True	85.826	1024	1327	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	76.9439	174	1327	95	below_threshold
Pusillimonas maritima	strain=17-4A	GCA_003576595.1	2026239	2026239	type	True	76.4417	82	1327	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:58:58,779] [INFO] DFAST Taxonomy check result was written to GCF_026344135.1_ASM2634413v1_genomic.fna/tc_result.tsv
[2024-01-25 18:58:58,781] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:58:58,781] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:58:58,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3526228e-cefe-4de7-8bb3-13031ad4c85f/dqc_reference/checkm_data
[2024-01-25 18:58:58,782] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:58:58,823] [INFO] Task started: CheckM
[2024-01-25 18:58:58,823] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026344135.1_ASM2634413v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026344135.1_ASM2634413v1_genomic.fna/checkm_input GCF_026344135.1_ASM2634413v1_genomic.fna/checkm_result
[2024-01-25 18:59:34,161] [INFO] Task succeeded: CheckM
[2024-01-25 18:59:34,162] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:59:34,177] [INFO] ===== Completeness check finished =====
[2024-01-25 18:59:34,177] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:59:34,177] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026344135.1_ASM2634413v1_genomic.fna/markers.fasta)
[2024-01-25 18:59:34,177] [INFO] Task started: Blastn
[2024-01-25 18:59:34,177] [INFO] Running command: blastn -query GCF_026344135.1_ASM2634413v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3526228e-cefe-4de7-8bb3-13031ad4c85f/dqc_reference/reference_markers_gtdb.fasta -out GCF_026344135.1_ASM2634413v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:35,463] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:35,466] [INFO] Selected 6 target genomes.
[2024-01-25 18:59:35,466] [INFO] Target genome list was writen to GCF_026344135.1_ASM2634413v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:59:35,475] [INFO] Task started: fastANI
[2024-01-25 18:59:35,475] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6aed3ff-2514-4968-b0f9-ad755389d09e/GCF_026344135.1_ASM2634413v1_genomic.fna.gz --refList GCF_026344135.1_ASM2634413v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026344135.1_ASM2634413v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:59:42,023] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:42,028] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:59:42,029] [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
GCF_017377875.1	s__Alcaligenes sp017377875	98.109	1253	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009497775.1	s__Alcaligenes faecalis_D	90.5774	1178	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002443155.1	s__Alcaligenes faecalis	89.6047	1141	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	98.39	97.71	0.93	0.90	22	-
GCF_005311025.1	s__Alcaligenes phenolicus	89.2753	1171	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	97.79	96.15	0.91	0.86	11	-
GCF_003076515.1	s__Alcaligenes aquatilis	88.2313	1093	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	98.23	96.52	0.93	0.89	8	-
GCF_014652815.1	s__Alcaligenes pakistanensis	87.7164	1161	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	99.29	99.08	0.97	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:59:42,030] [INFO] GTDB search result was written to GCF_026344135.1_ASM2634413v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:59:42,030] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:59:42,032] [INFO] DFAST_QC result json was written to GCF_026344135.1_ASM2634413v1_genomic.fna/dqc_result.json
[2024-01-25 18:59:42,033] [INFO] DFAST_QC completed!
[2024-01-25 18:59:42,033] [INFO] Total running time: 0h1m6s