[2024-01-24 13:49:27,518] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:27,521] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:27,521] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d1b4c0c-cb02-4509-895f-32f9c9b33bbd/dqc_reference
[2024-01-24 13:49:28,823] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:28,824] [INFO] Task started: Prodigal
[2024-01-24 13:49:28,824] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f298cc0-eb57-4c9c-80bf-13b04d4dd112/GCF_004208525.1_ASM420852v1_genomic.fna.gz | prodigal -d GCF_004208525.1_ASM420852v1_genomic.fna/cds.fna -a GCF_004208525.1_ASM420852v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:53,040] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:53,040] [INFO] Task started: HMMsearch
[2024-01-24 13:49:53,040] [INFO] Running command: hmmsearch --tblout GCF_004208525.1_ASM420852v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d1b4c0c-cb02-4509-895f-32f9c9b33bbd/dqc_reference/reference_markers.hmm GCF_004208525.1_ASM420852v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:53,358] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:53,359] [INFO] Found 6/6 markers.
[2024-01-24 13:49:53,409] [INFO] Query marker FASTA was written to GCF_004208525.1_ASM420852v1_genomic.fna/markers.fasta
[2024-01-24 13:49:53,410] [INFO] Task started: Blastn
[2024-01-24 13:49:53,410] [INFO] Running command: blastn -query GCF_004208525.1_ASM420852v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d1b4c0c-cb02-4509-895f-32f9c9b33bbd/dqc_reference/reference_markers.fasta -out GCF_004208525.1_ASM420852v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:54,023] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:54,025] [INFO] Selected 7 target genomes.
[2024-01-24 13:49:54,026] [INFO] Target genome list was writen to GCF_004208525.1_ASM420852v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:54,031] [INFO] Task started: fastANI
[2024-01-24 13:49:54,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f298cc0-eb57-4c9c-80bf-13b04d4dd112/GCF_004208525.1_ASM420852v1_genomic.fna.gz --refList GCF_004208525.1_ASM420852v1_genomic.fna/target_genomes.txt --output GCF_004208525.1_ASM420852v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:02,417] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:02,417] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d1b4c0c-cb02-4509-895f-32f9c9b33bbd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:02,418] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d1b4c0c-cb02-4509-895f-32f9c9b33bbd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:02,426] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:02,426] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:02,426] [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
Sphingobacterium corticibacterium	strain=30C10-4-7	GCA_004208525.1	2484746	2484746	type	True	100.0	1701	1702	95	conclusive
Sphingobacterium micropteri	strain=DN00404	GCA_014692515.1	2763501	2763501	type	True	93.1466	1255	1702	95	below_threshold
Sphingobacterium phlebotomi	strain=SSI9	GCA_008180195.1	2605433	2605433	type	True	84.3627	1012	1702	95	below_threshold
Sphingobacterium chuzhouense	strain=KCTC 42746	GCA_014692525.1	1742264	1742264	type	True	84.0598	949	1702	95	below_threshold
Sphingobacterium arenae	strain=KCTC 32294	GCA_014692505.1	1280598	1280598	type	True	83.7598	970	1702	95	below_threshold
Sphingobacterium gobiense	strain=ACCC 05757	GCA_002980575.1	1382456	1382456	type	True	81.5441	822	1702	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:02,430] [INFO] DFAST Taxonomy check result was written to GCF_004208525.1_ASM420852v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:02,431] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:02,431] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:02,431] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d1b4c0c-cb02-4509-895f-32f9c9b33bbd/dqc_reference/checkm_data
[2024-01-24 13:50:02,433] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:02,486] [INFO] Task started: CheckM
[2024-01-24 13:50:02,486] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004208525.1_ASM420852v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004208525.1_ASM420852v1_genomic.fna/checkm_input GCF_004208525.1_ASM420852v1_genomic.fna/checkm_result
[2024-01-24 13:51:08,765] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:08,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:08,786] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:08,786] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:08,787] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004208525.1_ASM420852v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:08,787] [INFO] Task started: Blastn
[2024-01-24 13:51:08,787] [INFO] Running command: blastn -query GCF_004208525.1_ASM420852v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d1b4c0c-cb02-4509-895f-32f9c9b33bbd/dqc_reference/reference_markers_gtdb.fasta -out GCF_004208525.1_ASM420852v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:09,554] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:09,558] [INFO] Selected 6 target genomes.
[2024-01-24 13:51:09,558] [INFO] Target genome list was writen to GCF_004208525.1_ASM420852v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:09,575] [INFO] Task started: fastANI
[2024-01-24 13:51:09,576] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f298cc0-eb57-4c9c-80bf-13b04d4dd112/GCF_004208525.1_ASM420852v1_genomic.fna.gz --refList GCF_004208525.1_ASM420852v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004208525.1_ASM420852v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:16,899] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:16,911] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:16,912] [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_004208525.1	s__Sphingobacterium sp004208525	100.0	1701	1702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014692515.1	s__Sphingobacterium sp014692515	93.1517	1254	1702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008180195.1	s__Sphingobacterium phlebotomi	84.3627	1012	1702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014692525.1	s__Sphingobacterium chuzhouense	84.0601	949	1702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014692505.1	s__Sphingobacterium arenae	83.7668	969	1702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011043555.1	s__Sphingobacterium sp011043555	83.743	917	1702	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:16,913] [INFO] GTDB search result was written to GCF_004208525.1_ASM420852v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:16,914] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:16,917] [INFO] DFAST_QC result json was written to GCF_004208525.1_ASM420852v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:16,917] [INFO] DFAST_QC completed!
[2024-01-24 13:51:16,917] [INFO] Total running time: 0h1m49s