[2024-01-25 17:54:35,707] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:54:35,708] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:54:35,708] [INFO] DQC Reference Directory: /var/lib/cwl/stg54258567-a10c-4812-8108-cc4ecf19094a/dqc_reference
[2024-01-25 17:54:36,862] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:54:36,863] [INFO] Task started: Prodigal
[2024-01-25 17:54:36,863] [INFO] Running command: gunzip -c /var/lib/cwl/stge3ba83b3-3909-4683-84fe-c4e1ba3ffe41/GCF_025631005.1_ASM2563100v1_genomic.fna.gz | prodigal -d GCF_025631005.1_ASM2563100v1_genomic.fna/cds.fna -a GCF_025631005.1_ASM2563100v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:54:49,640] [INFO] Task succeeded: Prodigal
[2024-01-25 17:54:49,641] [INFO] Task started: HMMsearch
[2024-01-25 17:54:49,641] [INFO] Running command: hmmsearch --tblout GCF_025631005.1_ASM2563100v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54258567-a10c-4812-8108-cc4ecf19094a/dqc_reference/reference_markers.hmm GCF_025631005.1_ASM2563100v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:54:49,898] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:54:49,899] [INFO] Found 6/6 markers.
[2024-01-25 17:54:49,931] [INFO] Query marker FASTA was written to GCF_025631005.1_ASM2563100v1_genomic.fna/markers.fasta
[2024-01-25 17:54:49,932] [INFO] Task started: Blastn
[2024-01-25 17:54:49,932] [INFO] Running command: blastn -query GCF_025631005.1_ASM2563100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54258567-a10c-4812-8108-cc4ecf19094a/dqc_reference/reference_markers.fasta -out GCF_025631005.1_ASM2563100v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:50,550] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:50,555] [INFO] Selected 30 target genomes.
[2024-01-25 17:54:50,556] [INFO] Target genome list was writen to GCF_025631005.1_ASM2563100v1_genomic.fna/target_genomes.txt
[2024-01-25 17:54:50,607] [INFO] Task started: fastANI
[2024-01-25 17:54:50,607] [INFO] Running command: fastANI --query /var/lib/cwl/stge3ba83b3-3909-4683-84fe-c4e1ba3ffe41/GCF_025631005.1_ASM2563100v1_genomic.fna.gz --refList GCF_025631005.1_ASM2563100v1_genomic.fna/target_genomes.txt --output GCF_025631005.1_ASM2563100v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:55:15,248] [INFO] Task succeeded: fastANI
[2024-01-25 17:55:15,248] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54258567-a10c-4812-8108-cc4ecf19094a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:55:15,248] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54258567-a10c-4812-8108-cc4ecf19094a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:55:15,253] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:55:15,253] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:55:15,253] [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
Sediminibacterium ginsengisoli	strain=DSM 22335	GCA_900167075.1	413434	413434	type	True	76.5683	50	1068	95	below_threshold
Ilyomonas limi	strain=17mud1-8	GCA_005233845.1	2575867	2575867	type	True	76.4728	50	1068	95	below_threshold
Parafilimonas terrae	strain=DSM 28286	GCA_900115755.1	1465490	1465490	type	True	76.3971	60	1068	95	below_threshold
Deminuibacter soli	strain=K23C18032701	GCA_003412455.1	2291815	2291815	type	True	76.0353	59	1068	95	below_threshold
Panacibacter microcysteis	strain=DH6	GCA_015831355.1	2793269	2793269	type	True	75.8825	50	1068	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:55:15,255] [INFO] DFAST Taxonomy check result was written to GCF_025631005.1_ASM2563100v1_genomic.fna/tc_result.tsv
[2024-01-25 17:55:15,255] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:55:15,255] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:55:15,256] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54258567-a10c-4812-8108-cc4ecf19094a/dqc_reference/checkm_data
[2024-01-25 17:55:15,256] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:55:15,291] [INFO] Task started: CheckM
[2024-01-25 17:55:15,291] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025631005.1_ASM2563100v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025631005.1_ASM2563100v1_genomic.fna/checkm_input GCF_025631005.1_ASM2563100v1_genomic.fna/checkm_result
[2024-01-25 17:55:53,395] [INFO] Task succeeded: CheckM
[2024-01-25 17:55:53,396] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:55:53,419] [INFO] ===== Completeness check finished =====
[2024-01-25 17:55:53,419] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:55:53,420] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025631005.1_ASM2563100v1_genomic.fna/markers.fasta)
[2024-01-25 17:55:53,421] [INFO] Task started: Blastn
[2024-01-25 17:55:53,421] [INFO] Running command: blastn -query GCF_025631005.1_ASM2563100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54258567-a10c-4812-8108-cc4ecf19094a/dqc_reference/reference_markers_gtdb.fasta -out GCF_025631005.1_ASM2563100v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:55:54,243] [INFO] Task succeeded: Blastn
[2024-01-25 17:55:54,246] [INFO] Selected 32 target genomes.
[2024-01-25 17:55:54,247] [INFO] Target genome list was writen to GCF_025631005.1_ASM2563100v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:55:54,303] [INFO] Task started: fastANI
[2024-01-25 17:55:54,303] [INFO] Running command: fastANI --query /var/lib/cwl/stge3ba83b3-3909-4683-84fe-c4e1ba3ffe41/GCF_025631005.1_ASM2563100v1_genomic.fna.gz --refList GCF_025631005.1_ASM2563100v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025631005.1_ASM2563100v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:56:16,664] [INFO] Task succeeded: fastANI
[2024-01-25 17:56:16,668] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:56:16,668] [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_900167075.1	s__Sediminibacterium ginsengisoli	76.5683	50	1068	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005233845.1	s__Ilyomonas limi	76.4728	50	1068	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ilyomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003412455.1	s__Deminuibacter soli	76.0353	59	1068	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Deminuibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015831355.1	s__Panacibacter sp015831355	75.8825	50	1068	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Panacibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:56:16,669] [INFO] GTDB search result was written to GCF_025631005.1_ASM2563100v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:56:16,670] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:56:16,677] [INFO] DFAST_QC result json was written to GCF_025631005.1_ASM2563100v1_genomic.fna/dqc_result.json
[2024-01-25 17:56:16,677] [INFO] DFAST_QC completed!
[2024-01-25 17:56:16,677] [INFO] Total running time: 0h1m41s