[2024-01-24 12:05:50,434] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:05:50,437] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:05:50,437] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b6fd7ee-f3bf-41c1-8cc3-0ff5e1862716/dqc_reference
[2024-01-24 12:05:52,741] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:05:52,742] [INFO] Task started: Prodigal
[2024-01-24 12:05:52,742] [INFO] Running command: gunzip -c /var/lib/cwl/stgc1888754-a90c-4769-965b-61b8f24adc8b/GCF_000297215.2_ASM29721v2_genomic.fna.gz | prodigal -d GCF_000297215.2_ASM29721v2_genomic.fna/cds.fna -a GCF_000297215.2_ASM29721v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:05:57,936] [INFO] Task succeeded: Prodigal
[2024-01-24 12:05:57,936] [INFO] Task started: HMMsearch
[2024-01-24 12:05:57,937] [INFO] Running command: hmmsearch --tblout GCF_000297215.2_ASM29721v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b6fd7ee-f3bf-41c1-8cc3-0ff5e1862716/dqc_reference/reference_markers.hmm GCF_000297215.2_ASM29721v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:05:58,143] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:05:58,146] [INFO] Found 6/6 markers.
[2024-01-24 12:05:58,173] [INFO] Query marker FASTA was written to GCF_000297215.2_ASM29721v2_genomic.fna/markers.fasta
[2024-01-24 12:05:58,174] [INFO] Task started: Blastn
[2024-01-24 12:05:58,174] [INFO] Running command: blastn -query GCF_000297215.2_ASM29721v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b6fd7ee-f3bf-41c1-8cc3-0ff5e1862716/dqc_reference/reference_markers.fasta -out GCF_000297215.2_ASM29721v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:00,693] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:00,697] [INFO] Selected 16 target genomes.
[2024-01-24 12:06:00,698] [INFO] Target genome list was writen to GCF_000297215.2_ASM29721v2_genomic.fna/target_genomes.txt
[2024-01-24 12:06:00,858] [INFO] Task started: fastANI
[2024-01-24 12:06:00,859] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1888754-a90c-4769-965b-61b8f24adc8b/GCF_000297215.2_ASM29721v2_genomic.fna.gz --refList GCF_000297215.2_ASM29721v2_genomic.fna/target_genomes.txt --output GCF_000297215.2_ASM29721v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:12,864] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:12,864] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b6fd7ee-f3bf-41c1-8cc3-0ff5e1862716/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:12,865] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b6fd7ee-f3bf-41c1-8cc3-0ff5e1862716/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:12,870] [INFO] Found 3 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:06:12,871] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:12,871] [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
Piscirickettsia salmonis	strain=LF-89	GCA_000297215.2	1238	1238	suspected-type	True	99.9577	797	880	95	conclusive
Piscirickettsia salmonis	strain=LF-89	GCA_000401515.2	1238	1238	suspected-type	True	99.7225	713	880	95	conclusive
Piscirickettsia salmonis	strain=ATCC VR-1361	GCA_000300295.4	1238	1238	suspected-type	True	95.3179	788	880	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:06:12,878] [INFO] DFAST Taxonomy check result was written to GCF_000297215.2_ASM29721v2_genomic.fna/tc_result.tsv
[2024-01-24 12:06:12,879] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:12,879] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:12,880] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b6fd7ee-f3bf-41c1-8cc3-0ff5e1862716/dqc_reference/checkm_data
[2024-01-24 12:06:12,881] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:12,911] [INFO] Task started: CheckM
[2024-01-24 12:06:12,911] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000297215.2_ASM29721v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000297215.2_ASM29721v2_genomic.fna/checkm_input GCF_000297215.2_ASM29721v2_genomic.fna/checkm_result
[2024-01-24 12:06:35,064] [INFO] Task succeeded: CheckM
[2024-01-24 12:06:35,065] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:06:35,089] [INFO] ===== Completeness check finished =====
[2024-01-24 12:06:35,090] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:06:35,090] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000297215.2_ASM29721v2_genomic.fna/markers.fasta)
[2024-01-24 12:06:35,090] [INFO] Task started: Blastn
[2024-01-24 12:06:35,090] [INFO] Running command: blastn -query GCF_000297215.2_ASM29721v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b6fd7ee-f3bf-41c1-8cc3-0ff5e1862716/dqc_reference/reference_markers_gtdb.fasta -out GCF_000297215.2_ASM29721v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:36,178] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:36,181] [INFO] Selected 21 target genomes.
[2024-01-24 12:06:36,181] [INFO] Target genome list was writen to GCF_000297215.2_ASM29721v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:06:36,196] [INFO] Task started: fastANI
[2024-01-24 12:06:36,196] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1888754-a90c-4769-965b-61b8f24adc8b/GCF_000297215.2_ASM29721v2_genomic.fna.gz --refList GCF_000297215.2_ASM29721v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000297215.2_ASM29721v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:06:48,963] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:48,967] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:06:48,967] [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_000297215.2	s__Piscirickettsia salmonis	99.9572	798	880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Piscirickettsiales;f__Piscirickettsiaceae;g__Piscirickettsia	95.0	97.52	95.10	0.92	0.81	87	conclusive
GCA_001644975.1	s__Piscirickettsia sp001644975	92.4816	691	880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Piscirickettsiales;f__Piscirickettsiaceae;g__Piscirickettsia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001720395.1	s__Piscirickettsia litoralis	78.9195	373	880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Piscirickettsiales;f__Piscirickettsiaceae;g__Piscirickettsia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:06:48,969] [INFO] GTDB search result was written to GCF_000297215.2_ASM29721v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:06:48,970] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:06:48,972] [INFO] DFAST_QC result json was written to GCF_000297215.2_ASM29721v2_genomic.fna/dqc_result.json
[2024-01-24 12:06:48,972] [INFO] DFAST_QC completed!
[2024-01-24 12:06:48,972] [INFO] Total running time: 0h0m59s