[2024-01-25 19:57:35,824] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:57:35,828] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:57:35,828] [INFO] DQC Reference Directory: /var/lib/cwl/stg430c9f61-07d2-4607-a1b6-9c0048a732b8/dqc_reference
[2024-01-25 19:57:36,976] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:57:36,976] [INFO] Task started: Prodigal
[2024-01-25 19:57:36,977] [INFO] Running command: gunzip -c /var/lib/cwl/stg39982b25-49e2-4d7c-b5ba-a48f306118f8/GCF_014701235.1_ASM1470123v1_genomic.fna.gz | prodigal -d GCF_014701235.1_ASM1470123v1_genomic.fna/cds.fna -a GCF_014701235.1_ASM1470123v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:57:41,770] [INFO] Task succeeded: Prodigal
[2024-01-25 19:57:41,771] [INFO] Task started: HMMsearch
[2024-01-25 19:57:41,771] [INFO] Running command: hmmsearch --tblout GCF_014701235.1_ASM1470123v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg430c9f61-07d2-4607-a1b6-9c0048a732b8/dqc_reference/reference_markers.hmm GCF_014701235.1_ASM1470123v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:57:41,971] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:57:41,972] [INFO] Found 6/6 markers.
[2024-01-25 19:57:41,994] [INFO] Query marker FASTA was written to GCF_014701235.1_ASM1470123v1_genomic.fna/markers.fasta
[2024-01-25 19:57:41,994] [INFO] Task started: Blastn
[2024-01-25 19:57:41,995] [INFO] Running command: blastn -query GCF_014701235.1_ASM1470123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg430c9f61-07d2-4607-a1b6-9c0048a732b8/dqc_reference/reference_markers.fasta -out GCF_014701235.1_ASM1470123v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:42,539] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:42,541] [INFO] Selected 14 target genomes.
[2024-01-25 19:57:42,542] [INFO] Target genome list was writen to GCF_014701235.1_ASM1470123v1_genomic.fna/target_genomes.txt
[2024-01-25 19:57:42,554] [INFO] Task started: fastANI
[2024-01-25 19:57:42,555] [INFO] Running command: fastANI --query /var/lib/cwl/stg39982b25-49e2-4d7c-b5ba-a48f306118f8/GCF_014701235.1_ASM1470123v1_genomic.fna.gz --refList GCF_014701235.1_ASM1470123v1_genomic.fna/target_genomes.txt --output GCF_014701235.1_ASM1470123v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:57:50,988] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:50,988] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg430c9f61-07d2-4607-a1b6-9c0048a732b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:57:50,989] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg430c9f61-07d2-4607-a1b6-9c0048a732b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:57:50,992] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:57:50,992] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:57:50,992] [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
Dissulfurispira thermophila	strain=T55J	GCA_014701235.1	2715679	2715679	type	True	100.0	790	790	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 19:57:50,998] [INFO] DFAST Taxonomy check result was written to GCF_014701235.1_ASM1470123v1_genomic.fna/tc_result.tsv
[2024-01-25 19:57:50,999] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:57:50,999] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:57:50,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg430c9f61-07d2-4607-a1b6-9c0048a732b8/dqc_reference/checkm_data
[2024-01-25 19:57:51,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:57:51,026] [INFO] Task started: CheckM
[2024-01-25 19:57:51,026] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014701235.1_ASM1470123v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014701235.1_ASM1470123v1_genomic.fna/checkm_input GCF_014701235.1_ASM1470123v1_genomic.fna/checkm_result
[2024-01-25 19:58:10,807] [INFO] Task succeeded: CheckM
[2024-01-25 19:58:10,808] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:58:10,823] [INFO] ===== Completeness check finished =====
[2024-01-25 19:58:10,823] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:58:10,824] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014701235.1_ASM1470123v1_genomic.fna/markers.fasta)
[2024-01-25 19:58:10,824] [INFO] Task started: Blastn
[2024-01-25 19:58:10,824] [INFO] Running command: blastn -query GCF_014701235.1_ASM1470123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg430c9f61-07d2-4607-a1b6-9c0048a732b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_014701235.1_ASM1470123v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:11,541] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:11,544] [INFO] Selected 20 target genomes.
[2024-01-25 19:58:11,544] [INFO] Target genome list was writen to GCF_014701235.1_ASM1470123v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:58:11,566] [INFO] Task started: fastANI
[2024-01-25 19:58:11,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg39982b25-49e2-4d7c-b5ba-a48f306118f8/GCF_014701235.1_ASM1470123v1_genomic.fna.gz --refList GCF_014701235.1_ASM1470123v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014701235.1_ASM1470123v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:58:20,810] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:20,815] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:58:20,815] [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_014701235.1	s__Dissulfurispira thermophila	100.0	790	790	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__Dissulfurispiraceae;g__Dissulfurispira	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002299835.1	s__UBA665 sp002299835	76.8004	137	790	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__Dissulfurispiraceae;g__UBA665	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016212685.1	s__GWB2-47-37 sp016212685	76.6627	83	790	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__Dissulfurispiraceae;g__GWB2-47-37	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001803635.1	s__GWB2-47-37 sp001803635	76.301	74	790	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__Dissulfurispiraceae;g__GWB2-47-37	95.0	99.75	99.58	0.92	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-25 19:58:20,819] [INFO] GTDB search result was written to GCF_014701235.1_ASM1470123v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:58:20,820] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:58:20,821] [INFO] DFAST_QC result json was written to GCF_014701235.1_ASM1470123v1_genomic.fna/dqc_result.json
[2024-01-25 19:58:20,822] [INFO] DFAST_QC completed!
[2024-01-25 19:58:20,822] [INFO] Total running time: 0h0m45s