[2024-01-24 10:47:06,551] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,558] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,559] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a073d9c-d5e8-4d76-b791-8f63ecd4c503/dqc_reference
[2024-01-24 10:47:12,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,103] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,103] [INFO] Running command: gunzip -c /var/lib/cwl/stg27f05f98-aec1-4538-8a87-7742ba39254e/GCF_002591915.1_ASM259191v1_genomic.fna.gz | prodigal -d GCF_002591915.1_ASM259191v1_genomic.fna/cds.fna -a GCF_002591915.1_ASM259191v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:21,899] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:21,899] [INFO] Task started: HMMsearch
[2024-01-24 10:47:21,899] [INFO] Running command: hmmsearch --tblout GCF_002591915.1_ASM259191v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a073d9c-d5e8-4d76-b791-8f63ecd4c503/dqc_reference/reference_markers.hmm GCF_002591915.1_ASM259191v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:22,137] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:22,138] [INFO] Found 6/6 markers.
[2024-01-24 10:47:22,164] [INFO] Query marker FASTA was written to GCF_002591915.1_ASM259191v1_genomic.fna/markers.fasta
[2024-01-24 10:47:22,165] [INFO] Task started: Blastn
[2024-01-24 10:47:22,165] [INFO] Running command: blastn -query GCF_002591915.1_ASM259191v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a073d9c-d5e8-4d76-b791-8f63ecd4c503/dqc_reference/reference_markers.fasta -out GCF_002591915.1_ASM259191v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:22,766] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:22,769] [INFO] Selected 17 target genomes.
[2024-01-24 10:47:22,769] [INFO] Target genome list was writen to GCF_002591915.1_ASM259191v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:22,779] [INFO] Task started: fastANI
[2024-01-24 10:47:22,779] [INFO] Running command: fastANI --query /var/lib/cwl/stg27f05f98-aec1-4538-8a87-7742ba39254e/GCF_002591915.1_ASM259191v1_genomic.fna.gz --refList GCF_002591915.1_ASM259191v1_genomic.fna/target_genomes.txt --output GCF_002591915.1_ASM259191v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:34,596] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:34,596] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a073d9c-d5e8-4d76-b791-8f63ecd4c503/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:34,597] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a073d9c-d5e8-4d76-b791-8f63ecd4c503/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:34,604] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:47:34,604] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:34,604] [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
Marinicella litoralis	strain=KMM 3900	GCA_002591915.1	644220	644220	type	True	100.0	1105	1106	95	conclusive
Marinicella litoralis	strain=DSM 25488	GCA_004363335.1	644220	644220	type	True	99.9947	1097	1106	95	conclusive
Marinicella rhabdoformis	strain=3539	GCA_009671245.1	2580566	2580566	type	True	77.4184	175	1106	95	below_threshold
Marinicella sediminis	strain=F2	GCA_002000055.1	1792834	1792834	type	True	77.1936	275	1106	95	below_threshold
Marinicella pacifica	strain=CGMCC 1.12181	GCA_014636635.1	1171543	1171543	type	True	76.8959	85	1106	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:34,606] [INFO] DFAST Taxonomy check result was written to GCF_002591915.1_ASM259191v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:34,606] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:34,606] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:34,607] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a073d9c-d5e8-4d76-b791-8f63ecd4c503/dqc_reference/checkm_data
[2024-01-24 10:47:34,608] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:34,642] [INFO] Task started: CheckM
[2024-01-24 10:47:34,642] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002591915.1_ASM259191v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002591915.1_ASM259191v1_genomic.fna/checkm_input GCF_002591915.1_ASM259191v1_genomic.fna/checkm_result
[2024-01-24 10:48:09,757] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:09,759] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:09,773] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:09,773] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:09,773] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002591915.1_ASM259191v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:09,774] [INFO] Task started: Blastn
[2024-01-24 10:48:09,774] [INFO] Running command: blastn -query GCF_002591915.1_ASM259191v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a073d9c-d5e8-4d76-b791-8f63ecd4c503/dqc_reference/reference_markers_gtdb.fasta -out GCF_002591915.1_ASM259191v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:10,845] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:10,848] [INFO] Selected 21 target genomes.
[2024-01-24 10:48:10,848] [INFO] Target genome list was writen to GCF_002591915.1_ASM259191v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:10,908] [INFO] Task started: fastANI
[2024-01-24 10:48:10,908] [INFO] Running command: fastANI --query /var/lib/cwl/stg27f05f98-aec1-4538-8a87-7742ba39254e/GCF_002591915.1_ASM259191v1_genomic.fna.gz --refList GCF_002591915.1_ASM259191v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002591915.1_ASM259191v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:20,950] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:20,955] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:20,955] [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_002591915.1	s__Marinicella litoralis	100.0	1105	1106	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Marinicellaceae;g__Marinicella	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_009671245.1	s__Marinicella rhabdoformis	77.4184	175	1106	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Marinicellaceae;g__Marinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000055.1	s__Marinicella sediminis	77.1837	276	1106	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Marinicellaceae;g__Marinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014636635.1	s__Marinicella pacifica	76.8959	85	1106	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Marinicellaceae;g__Marinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008501575.1	s__Marinicella sp008501575	76.6517	88	1106	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Marinicellaceae;g__Marinicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:20,957] [INFO] GTDB search result was written to GCF_002591915.1_ASM259191v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:20,957] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:20,960] [INFO] DFAST_QC result json was written to GCF_002591915.1_ASM259191v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:20,960] [INFO] DFAST_QC completed!
[2024-01-24 10:48:20,960] [INFO] Total running time: 0h1m14s