[2024-01-24 13:57:43,281] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:43,284] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:43,284] [INFO] DQC Reference Directory: /var/lib/cwl/stgf46006af-99f5-4491-85eb-75e5e89faf28/dqc_reference
[2024-01-24 13:57:44,558] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:44,559] [INFO] Task started: Prodigal
[2024-01-24 13:57:44,559] [INFO] Running command: gunzip -c /var/lib/cwl/stg12712d15-199a-41dc-ae08-68236b7bf2c3/GCF_000702445.1_ASM70244v1_genomic.fna.gz | prodigal -d GCF_000702445.1_ASM70244v1_genomic.fna/cds.fna -a GCF_000702445.1_ASM70244v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:02,792] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:02,792] [INFO] Task started: HMMsearch
[2024-01-24 13:58:02,792] [INFO] Running command: hmmsearch --tblout GCF_000702445.1_ASM70244v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf46006af-99f5-4491-85eb-75e5e89faf28/dqc_reference/reference_markers.hmm GCF_000702445.1_ASM70244v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:03,109] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:03,110] [INFO] Found 6/6 markers.
[2024-01-24 13:58:03,157] [INFO] Query marker FASTA was written to GCF_000702445.1_ASM70244v1_genomic.fna/markers.fasta
[2024-01-24 13:58:03,157] [INFO] Task started: Blastn
[2024-01-24 13:58:03,157] [INFO] Running command: blastn -query GCF_000702445.1_ASM70244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf46006af-99f5-4491-85eb-75e5e89faf28/dqc_reference/reference_markers.fasta -out GCF_000702445.1_ASM70244v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:03,771] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:03,774] [INFO] Selected 25 target genomes.
[2024-01-24 13:58:03,774] [INFO] Target genome list was writen to GCF_000702445.1_ASM70244v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:03,813] [INFO] Task started: fastANI
[2024-01-24 13:58:03,813] [INFO] Running command: fastANI --query /var/lib/cwl/stg12712d15-199a-41dc-ae08-68236b7bf2c3/GCF_000702445.1_ASM70244v1_genomic.fna.gz --refList GCF_000702445.1_ASM70244v1_genomic.fna/target_genomes.txt --output GCF_000702445.1_ASM70244v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:25,227] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:25,228] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf46006af-99f5-4491-85eb-75e5e89faf28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:25,228] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf46006af-99f5-4491-85eb-75e5e89faf28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:25,233] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:25,233] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:25,233] [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
Bryobacter aggregatus	strain=MPL3	GCA_000702445.1	360054	360054	type	True	100.0	1912	1914	95	conclusive
Paludibaculum fermentans	strain=P105	GCA_015277775.1	1473598	1473598	type	True	76.5305	108	1914	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:25,235] [INFO] DFAST Taxonomy check result was written to GCF_000702445.1_ASM70244v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:25,235] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:25,235] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:25,236] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf46006af-99f5-4491-85eb-75e5e89faf28/dqc_reference/checkm_data
[2024-01-24 13:58:25,237] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:25,298] [INFO] Task started: CheckM
[2024-01-24 13:58:25,298] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000702445.1_ASM70244v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000702445.1_ASM70244v1_genomic.fna/checkm_input GCF_000702445.1_ASM70244v1_genomic.fna/checkm_result
[2024-01-24 13:59:17,562] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:17,563] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:17,583] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:17,583] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:17,583] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000702445.1_ASM70244v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:17,584] [INFO] Task started: Blastn
[2024-01-24 13:59:17,584] [INFO] Running command: blastn -query GCF_000702445.1_ASM70244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf46006af-99f5-4491-85eb-75e5e89faf28/dqc_reference/reference_markers_gtdb.fasta -out GCF_000702445.1_ASM70244v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:18,437] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:18,440] [INFO] Selected 23 target genomes.
[2024-01-24 13:59:18,440] [INFO] Target genome list was writen to GCF_000702445.1_ASM70244v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:18,595] [INFO] Task started: fastANI
[2024-01-24 13:59:18,595] [INFO] Running command: fastANI --query /var/lib/cwl/stg12712d15-199a-41dc-ae08-68236b7bf2c3/GCF_000702445.1_ASM70244v1_genomic.fna.gz --refList GCF_000702445.1_ASM70244v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000702445.1_ASM70244v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:44,487] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:44,503] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:44,504] [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_000702445.1	s__Bryobacter aggregatus	100.0	1912	1914	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Bryobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016870995.1	s__Bryobacter sp016870995	77.3401	291	1914	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Bryobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903907865.1	s__BOG-234 sp903907865	76.4312	71	1914	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__BOG-234	95.0	99.99	99.99	0.99	0.98	3	-
GCA_016716385.1	s__JADJWL01 sp016716385	76.3905	75	1914	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__JADJWL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213775.1	s__CADEFT01 sp016213775	75.9457	88	1914	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__CADEFT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003167255.1	s__PALSA-129 sp003167255	75.9311	69	1914	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__PALSA-129	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871115.1	s__DSOI01 sp016871115	75.8507	88	1914	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__DSOI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903881085.1	s__CAIRSA01 sp903881085	75.6586	89	1914	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__CAIRSA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789745.1	s__CADEFT01 sp016789745	75.6301	127	1914	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__CADEFT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268715.1	s__TMP-7 sp018268715	75.5978	102	1914	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__TMP-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213755.1	s__JACQZT01 sp016213755	75.589	59	1914	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__JACQZT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826685.1	s__CADEFT01 sp902826685	75.5574	99	1914	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__CADEFT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003164035.1	s__Bog-375 sp003164035	75.3266	55	1914	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Bog-375	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:44,506] [INFO] GTDB search result was written to GCF_000702445.1_ASM70244v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:44,506] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:44,514] [INFO] DFAST_QC result json was written to GCF_000702445.1_ASM70244v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:44,514] [INFO] DFAST_QC completed!
[2024-01-24 13:59:44,514] [INFO] Total running time: 0h2m1s