[2024-01-24 11:26:13,432] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:13,435] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:13,436] [INFO] DQC Reference Directory: /var/lib/cwl/stg89c5c1e2-119a-4ef3-a2e0-89f41c5f41c5/dqc_reference
[2024-01-24 11:26:14,762] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:14,763] [INFO] Task started: Prodigal
[2024-01-24 11:26:14,764] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b986c0e-ad7a-4368-9b8d-99556f5e112c/GCF_006740705.1_ASM674070v1_genomic.fna.gz | prodigal -d GCF_006740705.1_ASM674070v1_genomic.fna/cds.fna -a GCF_006740705.1_ASM674070v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:25,656] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:25,657] [INFO] Task started: HMMsearch
[2024-01-24 11:26:25,657] [INFO] Running command: hmmsearch --tblout GCF_006740705.1_ASM674070v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89c5c1e2-119a-4ef3-a2e0-89f41c5f41c5/dqc_reference/reference_markers.hmm GCF_006740705.1_ASM674070v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:25,973] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:25,976] [INFO] Found 6/6 markers.
[2024-01-24 11:26:26,008] [INFO] Query marker FASTA was written to GCF_006740705.1_ASM674070v1_genomic.fna/markers.fasta
[2024-01-24 11:26:26,009] [INFO] Task started: Blastn
[2024-01-24 11:26:26,009] [INFO] Running command: blastn -query GCF_006740705.1_ASM674070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89c5c1e2-119a-4ef3-a2e0-89f41c5f41c5/dqc_reference/reference_markers.fasta -out GCF_006740705.1_ASM674070v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:26,668] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:26,671] [INFO] Selected 14 target genomes.
[2024-01-24 11:26:26,672] [INFO] Target genome list was writen to GCF_006740705.1_ASM674070v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:26,677] [INFO] Task started: fastANI
[2024-01-24 11:26:26,677] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b986c0e-ad7a-4368-9b8d-99556f5e112c/GCF_006740705.1_ASM674070v1_genomic.fna.gz --refList GCF_006740705.1_ASM674070v1_genomic.fna/target_genomes.txt --output GCF_006740705.1_ASM674070v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:36,461] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:36,461] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89c5c1e2-119a-4ef3-a2e0-89f41c5f41c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:36,462] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89c5c1e2-119a-4ef3-a2e0-89f41c5f41c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:36,467] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:36,468] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:36,468] [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
Salicibibacter halophilus	strain=NKC3-5	GCA_006740705.1	2502791	2502791	type	True	100.0	1251	1251	95	conclusive
Salicibibacter kimchii	strain=NKC1-1	GCA_003336365.1	2099786	2099786	type	True	84.781	845	1251	95	below_threshold
Salicibibacter cibarius	strain=NKC5-3	GCA_016495725.1	2743000	2743000	type	True	84.2682	822	1251	95	below_threshold
Salicibibacter cibi	strain=NKC21-4	GCA_016495865.1	2743001	2743001	type	True	83.4586	801	1251	95	below_threshold
Geomicrobium halophilum	strain=DSM 21769	GCA_014207655.1	549000	549000	type	True	79.4704	237	1251	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:36,469] [INFO] DFAST Taxonomy check result was written to GCF_006740705.1_ASM674070v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:36,470] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:36,470] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:36,470] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89c5c1e2-119a-4ef3-a2e0-89f41c5f41c5/dqc_reference/checkm_data
[2024-01-24 11:26:36,471] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:36,513] [INFO] Task started: CheckM
[2024-01-24 11:26:36,514] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006740705.1_ASM674070v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006740705.1_ASM674070v1_genomic.fna/checkm_input GCF_006740705.1_ASM674070v1_genomic.fna/checkm_result
[2024-01-24 11:27:13,177] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:13,179] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:13,199] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:13,200] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:13,200] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006740705.1_ASM674070v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:13,200] [INFO] Task started: Blastn
[2024-01-24 11:27:13,200] [INFO] Running command: blastn -query GCF_006740705.1_ASM674070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89c5c1e2-119a-4ef3-a2e0-89f41c5f41c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_006740705.1_ASM674070v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:14,160] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:14,165] [INFO] Selected 9 target genomes.
[2024-01-24 11:27:14,165] [INFO] Target genome list was writen to GCF_006740705.1_ASM674070v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:14,176] [INFO] Task started: fastANI
[2024-01-24 11:27:14,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b986c0e-ad7a-4368-9b8d-99556f5e112c/GCF_006740705.1_ASM674070v1_genomic.fna.gz --refList GCF_006740705.1_ASM674070v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006740705.1_ASM674070v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:21,782] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:21,792] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:21,792] [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_006740705.1	s__Salicibibacter halophilus	100.0	1251	1251	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__Salicibibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003336365.1	s__Salicibibacter kimchii	84.8077	844	1251	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__Salicibibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016495725.1	s__Salicibibacter cibarius	84.2646	821	1251	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__Salicibibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016495865.1	s__Salicibibacter cibi	83.4541	803	1251	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__Salicibibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207655.1	s__Geomicrobium halophilum	79.5207	236	1251	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__Geomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100185.1	s__Natribacillus halophilus	79.2759	444	1251	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__Natribacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:21,794] [INFO] GTDB search result was written to GCF_006740705.1_ASM674070v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:21,795] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:21,797] [INFO] DFAST_QC result json was written to GCF_006740705.1_ASM674070v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:21,797] [INFO] DFAST_QC completed!
[2024-01-24 11:27:21,797] [INFO] Total running time: 0h1m8s