[2024-01-24 14:31:00,263] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:00,266] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:00,266] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb1f7612-584c-417d-ad89-acc30fbe7169/dqc_reference
[2024-01-24 14:31:02,102] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:02,104] [INFO] Task started: Prodigal
[2024-01-24 14:31:02,104] [INFO] Running command: gunzip -c /var/lib/cwl/stg15014e83-b3a6-42c4-ae2e-1aef0f5602a4/GCF_026344155.1_ASM2634415v1_genomic.fna.gz | prodigal -d GCF_026344155.1_ASM2634415v1_genomic.fna/cds.fna -a GCF_026344155.1_ASM2634415v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:15,335] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:15,335] [INFO] Task started: HMMsearch
[2024-01-24 14:31:15,335] [INFO] Running command: hmmsearch --tblout GCF_026344155.1_ASM2634415v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb1f7612-584c-417d-ad89-acc30fbe7169/dqc_reference/reference_markers.hmm GCF_026344155.1_ASM2634415v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:15,670] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:15,671] [INFO] Found 6/6 markers.
[2024-01-24 14:31:15,720] [INFO] Query marker FASTA was written to GCF_026344155.1_ASM2634415v1_genomic.fna/markers.fasta
[2024-01-24 14:31:15,721] [INFO] Task started: Blastn
[2024-01-24 14:31:15,721] [INFO] Running command: blastn -query GCF_026344155.1_ASM2634415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb1f7612-584c-417d-ad89-acc30fbe7169/dqc_reference/reference_markers.fasta -out GCF_026344155.1_ASM2634415v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:16,460] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:16,462] [INFO] Selected 11 target genomes.
[2024-01-24 14:31:16,463] [INFO] Target genome list was writen to GCF_026344155.1_ASM2634415v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:16,468] [INFO] Task started: fastANI
[2024-01-24 14:31:16,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg15014e83-b3a6-42c4-ae2e-1aef0f5602a4/GCF_026344155.1_ASM2634415v1_genomic.fna.gz --refList GCF_026344155.1_ASM2634415v1_genomic.fna/target_genomes.txt --output GCF_026344155.1_ASM2634415v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:26,080] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:26,080] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb1f7612-584c-417d-ad89-acc30fbe7169/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:26,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb1f7612-584c-417d-ad89-acc30fbe7169/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:26,088] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:31:26,088] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:31:26,088] [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_001748345.1	32001	511	type	True	92.6073	1191	1410	95	below_threshold
Alcaligenes faecalis subsp. faecalis	strain=NBRC 13111	GCA_000739855.1	32001	511	type	True	92.6046	1203	1410	95	below_threshold
Alcaligenes faecalis	strain=ATCC 8750	GCA_001298815.1	511	511	type	True	92.6035	1205	1410	95	below_threshold
Alcaligenes faecalis	strain=DSM 30030	GCA_002443155.1	511	511	type	True	92.5729	1205	1410	95	below_threshold
Alcaligenes ammonioxydans	strain=HO-1	GCA_019343455.1	2582914	2582914	type	True	86.9798	1045	1410	95	below_threshold
Alcaligenes pakistanensis	strain=KCTC 42083	GCA_014652815.1	1482717	1482717	type	True	86.7586	1152	1410	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	77.3001	196	1410	95	below_threshold
Pusillimonas faecipullorum	strain=CC-YST705	GCA_020539505.1	2755040	2755040	type	True	77.1372	129	1410	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	76.9445	213	1410	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	76.3935	66	1410	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:26,090] [INFO] DFAST Taxonomy check result was written to GCF_026344155.1_ASM2634415v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:26,090] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:26,090] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:26,090] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb1f7612-584c-417d-ad89-acc30fbe7169/dqc_reference/checkm_data
[2024-01-24 14:31:26,091] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:26,131] [INFO] Task started: CheckM
[2024-01-24 14:31:26,131] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026344155.1_ASM2634415v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026344155.1_ASM2634415v1_genomic.fna/checkm_input GCF_026344155.1_ASM2634415v1_genomic.fna/checkm_result
[2024-01-24 14:32:05,884] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:05,885] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:05,902] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:05,902] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:05,902] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026344155.1_ASM2634415v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:05,903] [INFO] Task started: Blastn
[2024-01-24 14:32:05,903] [INFO] Running command: blastn -query GCF_026344155.1_ASM2634415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb1f7612-584c-417d-ad89-acc30fbe7169/dqc_reference/reference_markers_gtdb.fasta -out GCF_026344155.1_ASM2634415v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:07,178] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:07,181] [INFO] Selected 5 target genomes.
[2024-01-24 14:32:07,181] [INFO] Target genome list was writen to GCF_026344155.1_ASM2634415v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:07,184] [INFO] Task started: fastANI
[2024-01-24 14:32:07,184] [INFO] Running command: fastANI --query /var/lib/cwl/stg15014e83-b3a6-42c4-ae2e-1aef0f5602a4/GCF_026344155.1_ASM2634415v1_genomic.fna.gz --refList GCF_026344155.1_ASM2634415v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026344155.1_ASM2634415v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:12,881] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:12,886] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:12,886] [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_005311025.1	s__Alcaligenes phenolicus	98.3135	1287	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	97.79	96.15	0.91	0.86	11	conclusive
GCF_009497775.1	s__Alcaligenes faecalis_D	92.7286	1228	1410	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	92.5729	1205	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	98.39	97.71	0.93	0.90	22	-
GCF_003076515.1	s__Alcaligenes aquatilis	89.681	1132	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	98.23	96.52	0.93	0.89	8	-
GCF_017377875.1	s__Alcaligenes sp017377875	89.2527	1197	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:12,887] [INFO] GTDB search result was written to GCF_026344155.1_ASM2634415v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:12,888] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:12,890] [INFO] DFAST_QC result json was written to GCF_026344155.1_ASM2634415v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:12,890] [INFO] DFAST_QC completed!
[2024-01-24 14:32:12,890] [INFO] Total running time: 0h1m13s