[2024-01-24 14:39:14,799] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:14,801] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:14,801] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c0b1f8f-17ee-492a-ae69-300db503f960/dqc_reference
[2024-01-24 14:39:16,175] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:16,176] [INFO] Task started: Prodigal
[2024-01-24 14:39:16,176] [INFO] Running command: gunzip -c /var/lib/cwl/stg9134856d-29f1-4846-bfbf-31c1ae2023ce/GCF_025995175.1_ASM2599517v1_genomic.fna.gz | prodigal -d GCF_025995175.1_ASM2599517v1_genomic.fna/cds.fna -a GCF_025995175.1_ASM2599517v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:27,111] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:27,112] [INFO] Task started: HMMsearch
[2024-01-24 14:39:27,112] [INFO] Running command: hmmsearch --tblout GCF_025995175.1_ASM2599517v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c0b1f8f-17ee-492a-ae69-300db503f960/dqc_reference/reference_markers.hmm GCF_025995175.1_ASM2599517v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:27,410] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:27,412] [INFO] Found 6/6 markers.
[2024-01-24 14:39:27,445] [INFO] Query marker FASTA was written to GCF_025995175.1_ASM2599517v1_genomic.fna/markers.fasta
[2024-01-24 14:39:27,446] [INFO] Task started: Blastn
[2024-01-24 14:39:27,446] [INFO] Running command: blastn -query GCF_025995175.1_ASM2599517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c0b1f8f-17ee-492a-ae69-300db503f960/dqc_reference/reference_markers.fasta -out GCF_025995175.1_ASM2599517v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:28,218] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:28,221] [INFO] Selected 18 target genomes.
[2024-01-24 14:39:28,222] [INFO] Target genome list was writen to GCF_025995175.1_ASM2599517v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:28,229] [INFO] Task started: fastANI
[2024-01-24 14:39:28,229] [INFO] Running command: fastANI --query /var/lib/cwl/stg9134856d-29f1-4846-bfbf-31c1ae2023ce/GCF_025995175.1_ASM2599517v1_genomic.fna.gz --refList GCF_025995175.1_ASM2599517v1_genomic.fna/target_genomes.txt --output GCF_025995175.1_ASM2599517v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:41,761] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:41,762] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c0b1f8f-17ee-492a-ae69-300db503f960/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:41,762] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c0b1f8f-17ee-492a-ae69-300db503f960/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:41,771] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:39:41,772] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:39:41,772] [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
Asaia bogorensis	strain=NBRC 16594	GCA_007989265.1	91915	91915	suspected-type	True	83.0063	689	1147	95	below_threshold
Asaia bogorensis	strain=NBRC 16594	GCA_001547995.1	91915	91915	suspected-type	True	82.9114	680	1147	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	82.0904	672	1147	95	below_threshold
Asaia siamensis	strain=CCM 7132	GCA_014635085.1	110479	110479	type	True	82.0024	672	1147	95	below_threshold
Asaia platycodi	strain=JCM 25414	GCA_000614545.1	610243	610243	type	True	81.6303	622	1147	95	below_threshold
Asaia astilbis	strain=JCM 15831	GCA_000613845.1	610244	610244	type	True	80.3305	501	1147	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	77.6099	177	1147	95	below_threshold
Bradyrhizobium mercantei	strain=SEMIA 6399	GCA_001982635.1	1904807	1904807	type	True	76.007	59	1147	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:41,779] [INFO] DFAST Taxonomy check result was written to GCF_025995175.1_ASM2599517v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:41,780] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:41,780] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:41,780] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c0b1f8f-17ee-492a-ae69-300db503f960/dqc_reference/checkm_data
[2024-01-24 14:39:41,781] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:41,824] [INFO] Task started: CheckM
[2024-01-24 14:39:41,825] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025995175.1_ASM2599517v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025995175.1_ASM2599517v1_genomic.fna/checkm_input GCF_025995175.1_ASM2599517v1_genomic.fna/checkm_result
[2024-01-24 14:40:18,151] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:18,152] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:18,172] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:18,172] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:18,173] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025995175.1_ASM2599517v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:18,173] [INFO] Task started: Blastn
[2024-01-24 14:40:18,173] [INFO] Running command: blastn -query GCF_025995175.1_ASM2599517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c0b1f8f-17ee-492a-ae69-300db503f960/dqc_reference/reference_markers_gtdb.fasta -out GCF_025995175.1_ASM2599517v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:19,403] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:19,406] [INFO] Selected 14 target genomes.
[2024-01-24 14:40:19,406] [INFO] Target genome list was writen to GCF_025995175.1_ASM2599517v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:19,417] [INFO] Task started: fastANI
[2024-01-24 14:40:19,417] [INFO] Running command: fastANI --query /var/lib/cwl/stg9134856d-29f1-4846-bfbf-31c1ae2023ce/GCF_025995175.1_ASM2599517v1_genomic.fna.gz --refList GCF_025995175.1_ASM2599517v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025995175.1_ASM2599517v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:28,337] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:28,345] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:40:28,346] [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_003994335.1	s__Asaia sp003994335	89.9935	809	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001547995.1	s__Asaia bogorensis	82.9202	679	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	96.55	95.04	0.93	0.88	6	-
GCF_900465345.1	s__Asaia bogorensis_A	82.8155	660	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635085.1	s__Asaia siamensis	82.01	671	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000614545.1	s__Asaia platycodi	81.6279	623	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613885.1	s__Asaia prunellae	80.7258	519	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007988945.1	s__Swaminathania salitolerans	80.5903	483	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Swaminathania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613845.1	s__Asaia astilbis	80.3234	502	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:28,348] [INFO] GTDB search result was written to GCF_025995175.1_ASM2599517v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:28,348] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:28,352] [INFO] DFAST_QC result json was written to GCF_025995175.1_ASM2599517v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:28,352] [INFO] DFAST_QC completed!
[2024-01-24 14:40:28,352] [INFO] Total running time: 0h1m14s