[2024-01-24 10:57:12,857] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:12,859] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:12,859] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6f3b6dc-5d0e-4746-b386-e9f04c0a29bd/dqc_reference
[2024-01-24 10:57:14,283] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:14,283] [INFO] Task started: Prodigal
[2024-01-24 10:57:14,284] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd46e6cc-168e-4b95-a928-5781a88376f5/GCF_018398935.1_ASM1839893v1_genomic.fna.gz | prodigal -d GCF_018398935.1_ASM1839893v1_genomic.fna/cds.fna -a GCF_018398935.1_ASM1839893v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:32,955] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:32,956] [INFO] Task started: HMMsearch
[2024-01-24 10:57:32,956] [INFO] Running command: hmmsearch --tblout GCF_018398935.1_ASM1839893v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6f3b6dc-5d0e-4746-b386-e9f04c0a29bd/dqc_reference/reference_markers.hmm GCF_018398935.1_ASM1839893v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:33,324] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:33,325] [INFO] Found 6/6 markers.
[2024-01-24 10:57:33,385] [INFO] Query marker FASTA was written to GCF_018398935.1_ASM1839893v1_genomic.fna/markers.fasta
[2024-01-24 10:57:33,385] [INFO] Task started: Blastn
[2024-01-24 10:57:33,385] [INFO] Running command: blastn -query GCF_018398935.1_ASM1839893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6f3b6dc-5d0e-4746-b386-e9f04c0a29bd/dqc_reference/reference_markers.fasta -out GCF_018398935.1_ASM1839893v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:34,027] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:34,030] [INFO] Selected 24 target genomes.
[2024-01-24 10:57:34,031] [INFO] Target genome list was writen to GCF_018398935.1_ASM1839893v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:34,053] [INFO] Task started: fastANI
[2024-01-24 10:57:34,053] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd46e6cc-168e-4b95-a928-5781a88376f5/GCF_018398935.1_ASM1839893v1_genomic.fna.gz --refList GCF_018398935.1_ASM1839893v1_genomic.fna/target_genomes.txt --output GCF_018398935.1_ASM1839893v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:00,186] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:00,186] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6f3b6dc-5d0e-4746-b386-e9f04c0a29bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:00,187] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6f3b6dc-5d0e-4746-b386-e9f04c0a29bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:00,194] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:00,194] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:00,194] [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
Telmatocola sphagniphila	strain=SP2T	GCA_018398935.1	1123043	1123043	type	True	100.0	2197	2197	95	conclusive
Limnoglobus roseus	strain=PX52	GCA_008254045.1	2598579	2598579	type	True	76.3934	56	2197	95	below_threshold
Fimbriiglobus ruber	strain=SP5	GCA_002197845.1	1908690	1908690	type	True	76.0705	62	2197	95	below_threshold
Tuwongella immobilis		GCA_901538355.1	692036	692036	type	True	76.0639	63	2197	95	below_threshold
Zavarzinella formosa	strain=DSM 19928	GCA_000255705.1	360055	360055	type	True	75.807	93	2197	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:00,196] [INFO] DFAST Taxonomy check result was written to GCF_018398935.1_ASM1839893v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:00,197] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:00,197] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:00,197] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6f3b6dc-5d0e-4746-b386-e9f04c0a29bd/dqc_reference/checkm_data
[2024-01-24 10:58:00,198] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:00,259] [INFO] Task started: CheckM
[2024-01-24 10:58:00,260] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018398935.1_ASM1839893v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018398935.1_ASM1839893v1_genomic.fna/checkm_input GCF_018398935.1_ASM1839893v1_genomic.fna/checkm_result
[2024-01-24 10:58:52,921] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:52,923] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:52,942] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:52,942] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:52,943] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018398935.1_ASM1839893v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:52,943] [INFO] Task started: Blastn
[2024-01-24 10:58:52,943] [INFO] Running command: blastn -query GCF_018398935.1_ASM1839893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6f3b6dc-5d0e-4746-b386-e9f04c0a29bd/dqc_reference/reference_markers_gtdb.fasta -out GCF_018398935.1_ASM1839893v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:53,755] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:53,759] [INFO] Selected 24 target genomes.
[2024-01-24 10:58:53,759] [INFO] Target genome list was writen to GCF_018398935.1_ASM1839893v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:53,806] [INFO] Task started: fastANI
[2024-01-24 10:58:53,806] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd46e6cc-168e-4b95-a928-5781a88376f5/GCF_018398935.1_ASM1839893v1_genomic.fna.gz --refList GCF_018398935.1_ASM1839893v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018398935.1_ASM1839893v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:16,923] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:16,929] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:16,929] [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_018398935.1	s__Telmatocola sphagniphila	100.0	2197	2197	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Telmatocola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002197845.1	s__Fimbriiglobus ruber	76.1553	59	2197	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Fimbriiglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011331615.1	s__DSRJ01 sp011331615	76.054	50	2197	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__DSRJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000255705.1	s__Zavarzinella formosa	75.7971	92	2197	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Zavarzinella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:16,930] [INFO] GTDB search result was written to GCF_018398935.1_ASM1839893v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:16,931] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:16,933] [INFO] DFAST_QC result json was written to GCF_018398935.1_ASM1839893v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:16,933] [INFO] DFAST_QC completed!
[2024-01-24 10:59:16,933] [INFO] Total running time: 0h2m4s