[2024-01-25 18:56:20,677] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:56:20,679] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:56:20,679] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4d765d0-ab85-4f23-8cfb-ac9eedcaf080/dqc_reference
[2024-01-25 18:56:21,801] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:56:21,802] [INFO] Task started: Prodigal
[2024-01-25 18:56:21,802] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f77f89b-c47f-4bbd-99d1-dcbc8d73d54e/GCF_000378345.1_ASM37834v1_genomic.fna.gz | prodigal -d GCF_000378345.1_ASM37834v1_genomic.fna/cds.fna -a GCF_000378345.1_ASM37834v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:56:29,466] [INFO] Task succeeded: Prodigal
[2024-01-25 18:56:29,467] [INFO] Task started: HMMsearch
[2024-01-25 18:56:29,467] [INFO] Running command: hmmsearch --tblout GCF_000378345.1_ASM37834v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4d765d0-ab85-4f23-8cfb-ac9eedcaf080/dqc_reference/reference_markers.hmm GCF_000378345.1_ASM37834v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:56:29,685] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:56:29,686] [INFO] Found 6/6 markers.
[2024-01-25 18:56:29,713] [INFO] Query marker FASTA was written to GCF_000378345.1_ASM37834v1_genomic.fna/markers.fasta
[2024-01-25 18:56:29,713] [INFO] Task started: Blastn
[2024-01-25 18:56:29,713] [INFO] Running command: blastn -query GCF_000378345.1_ASM37834v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4d765d0-ab85-4f23-8cfb-ac9eedcaf080/dqc_reference/reference_markers.fasta -out GCF_000378345.1_ASM37834v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:30,307] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:30,311] [INFO] Selected 22 target genomes.
[2024-01-25 18:56:30,311] [INFO] Target genome list was writen to GCF_000378345.1_ASM37834v1_genomic.fna/target_genomes.txt
[2024-01-25 18:56:30,326] [INFO] Task started: fastANI
[2024-01-25 18:56:30,327] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f77f89b-c47f-4bbd-99d1-dcbc8d73d54e/GCF_000378345.1_ASM37834v1_genomic.fna.gz --refList GCF_000378345.1_ASM37834v1_genomic.fna/target_genomes.txt --output GCF_000378345.1_ASM37834v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:56:44,367] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:44,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4d765d0-ab85-4f23-8cfb-ac9eedcaf080/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:56:44,368] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4d765d0-ab85-4f23-8cfb-ac9eedcaf080/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:56:44,372] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:56:44,372] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:56:44,372] [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
Hirschia maritima	strain=DSM 19733	GCA_000378345.1	1121961	1121961	type	True	100.0	1112	1113	95	conclusive
Hirschia baltica	strain=ATCC 49814	GCA_000023785.1	2724	2724	type	True	79.0122	335	1113	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:56:44,374] [INFO] DFAST Taxonomy check result was written to GCF_000378345.1_ASM37834v1_genomic.fna/tc_result.tsv
[2024-01-25 18:56:44,374] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:56:44,374] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:56:44,374] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4d765d0-ab85-4f23-8cfb-ac9eedcaf080/dqc_reference/checkm_data
[2024-01-25 18:56:44,375] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:56:44,411] [INFO] Task started: CheckM
[2024-01-25 18:56:44,411] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000378345.1_ASM37834v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000378345.1_ASM37834v1_genomic.fna/checkm_input GCF_000378345.1_ASM37834v1_genomic.fna/checkm_result
[2024-01-25 18:57:11,889] [INFO] Task succeeded: CheckM
[2024-01-25 18:57:11,890] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:57:11,908] [INFO] ===== Completeness check finished =====
[2024-01-25 18:57:11,909] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:57:11,909] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000378345.1_ASM37834v1_genomic.fna/markers.fasta)
[2024-01-25 18:57:11,909] [INFO] Task started: Blastn
[2024-01-25 18:57:11,909] [INFO] Running command: blastn -query GCF_000378345.1_ASM37834v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4d765d0-ab85-4f23-8cfb-ac9eedcaf080/dqc_reference/reference_markers_gtdb.fasta -out GCF_000378345.1_ASM37834v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:12,964] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:12,966] [INFO] Selected 20 target genomes.
[2024-01-25 18:57:12,966] [INFO] Target genome list was writen to GCF_000378345.1_ASM37834v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:57:13,012] [INFO] Task started: fastANI
[2024-01-25 18:57:13,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f77f89b-c47f-4bbd-99d1-dcbc8d73d54e/GCF_000378345.1_ASM37834v1_genomic.fna.gz --refList GCF_000378345.1_ASM37834v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000378345.1_ASM37834v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:57:23,831] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:23,834] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:57:23,834] [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_000378345.1	s__Hirschia maritima	100.0	1111	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hirschia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000023785.1	s__Hirschia baltica	78.9709	334	1113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hirschia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:57:23,835] [INFO] GTDB search result was written to GCF_000378345.1_ASM37834v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:57:23,836] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:57:23,837] [INFO] DFAST_QC result json was written to GCF_000378345.1_ASM37834v1_genomic.fna/dqc_result.json
[2024-01-25 18:57:23,838] [INFO] DFAST_QC completed!
[2024-01-25 18:57:23,838] [INFO] Total running time: 0h1m3s