[2024-01-24 12:14:34,593] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:34,600] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:34,600] [INFO] DQC Reference Directory: /var/lib/cwl/stg80817dca-c52a-48db-90a7-7e3d5d4ab4ff/dqc_reference
[2024-01-24 12:14:35,862] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,862] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,863] [INFO] Running command: gunzip -c /var/lib/cwl/stg2dc8b923-a384-4363-a06a-6410b9e9caea/GCF_006539325.1_ASM653932v1_genomic.fna.gz | prodigal -d GCF_006539325.1_ASM653932v1_genomic.fna/cds.fna -a GCF_006539325.1_ASM653932v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:43,719] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:43,720] [INFO] Task started: HMMsearch
[2024-01-24 12:14:43,720] [INFO] Running command: hmmsearch --tblout GCF_006539325.1_ASM653932v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80817dca-c52a-48db-90a7-7e3d5d4ab4ff/dqc_reference/reference_markers.hmm GCF_006539325.1_ASM653932v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:43,992] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:43,993] [INFO] Found 6/6 markers.
[2024-01-24 12:14:44,020] [INFO] Query marker FASTA was written to GCF_006539325.1_ASM653932v1_genomic.fna/markers.fasta
[2024-01-24 12:14:44,021] [INFO] Task started: Blastn
[2024-01-24 12:14:44,021] [INFO] Running command: blastn -query GCF_006539325.1_ASM653932v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80817dca-c52a-48db-90a7-7e3d5d4ab4ff/dqc_reference/reference_markers.fasta -out GCF_006539325.1_ASM653932v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:44,759] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:44,762] [INFO] Selected 11 target genomes.
[2024-01-24 12:14:44,762] [INFO] Target genome list was writen to GCF_006539325.1_ASM653932v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:44,778] [INFO] Task started: fastANI
[2024-01-24 12:14:44,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dc8b923-a384-4363-a06a-6410b9e9caea/GCF_006539325.1_ASM653932v1_genomic.fna.gz --refList GCF_006539325.1_ASM653932v1_genomic.fna/target_genomes.txt --output GCF_006539325.1_ASM653932v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:51,954] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:51,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80817dca-c52a-48db-90a7-7e3d5d4ab4ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:51,955] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80817dca-c52a-48db-90a7-7e3d5d4ab4ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:51,961] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:14:51,961] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:51,961] [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
Acetobacter orleanensis	strain=NBRC 13752	GCA_006539325.1	104099	104099	type	True	100.0	958	959	95	conclusive
Acetobacter orleanensis	strain=LMG 1583	GCA_001581005.1	104099	104099	type	True	99.9856	945	959	95	conclusive
Acetobacter orleanensis	strain=JCM 7639T	GCA_000964205.1	104099	104099	type	True	99.984	929	959	95	conclusive
Acetobacter persici	strain=JCM 25330	GCA_000613905.1	1076596	1076596	type	True	85.2105	684	959	95	below_threshold
Acetobacter malorum	strain=LMG 1746	GCA_001580615.1	178901	178901	suspected-type	True	85.1181	708	959	95	below_threshold
Acetobacter cerevisiae	strain=LMG 1625	GCA_001580535.1	178900	178900	type	True	85.0524	693	959	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	77.981	272	959	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:51,962] [INFO] DFAST Taxonomy check result was written to GCF_006539325.1_ASM653932v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:51,963] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:51,963] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:51,963] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80817dca-c52a-48db-90a7-7e3d5d4ab4ff/dqc_reference/checkm_data
[2024-01-24 12:14:51,964] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:51,993] [INFO] Task started: CheckM
[2024-01-24 12:14:51,994] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006539325.1_ASM653932v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006539325.1_ASM653932v1_genomic.fna/checkm_input GCF_006539325.1_ASM653932v1_genomic.fna/checkm_result
[2024-01-24 12:15:18,279] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:18,281] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:18,298] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:18,298] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:18,299] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006539325.1_ASM653932v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:18,299] [INFO] Task started: Blastn
[2024-01-24 12:15:18,299] [INFO] Running command: blastn -query GCF_006539325.1_ASM653932v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80817dca-c52a-48db-90a7-7e3d5d4ab4ff/dqc_reference/reference_markers_gtdb.fasta -out GCF_006539325.1_ASM653932v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:19,465] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:19,468] [INFO] Selected 7 target genomes.
[2024-01-24 12:15:19,468] [INFO] Target genome list was writen to GCF_006539325.1_ASM653932v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:19,472] [INFO] Task started: fastANI
[2024-01-24 12:15:19,473] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dc8b923-a384-4363-a06a-6410b9e9caea/GCF_006539325.1_ASM653932v1_genomic.fna.gz --refList GCF_006539325.1_ASM653932v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006539325.1_ASM653932v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:24,621] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:24,627] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:24,627] [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_001581005.1	s__Acetobacter orleanensis	99.9856	945	959	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	99.99	99.99	0.99	0.99	4	conclusive
GCF_000613905.1	s__Acetobacter persici	85.2175	683	959	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.00	95.85	0.80	0.79	8	-
GCF_001580615.1	s__Acetobacter malorum	85.103	709	959	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	95.98	95.83	0.82	0.80	5	-
GCF_001580535.1	s__Acetobacter cerevisiae	85.0524	693	959	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.52	96.47	0.88	0.86	4	-
GCF_002153605.1	s__Acetobacter malorum_A	85.0269	681	959	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.53	96.53	0.89	0.89	2	-
GCF_011516935.1	s__Acetobacter farinalis	82.9632	642	959	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000963945.1	s__Acetobacter indonesiensis	79.3702	420	959	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.28	96.85	0.92	0.88	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:24,628] [INFO] GTDB search result was written to GCF_006539325.1_ASM653932v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:24,629] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:24,632] [INFO] DFAST_QC result json was written to GCF_006539325.1_ASM653932v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:24,632] [INFO] DFAST_QC completed!
[2024-01-24 12:15:24,632] [INFO] Total running time: 0h0m50s