[2024-01-24 12:29:29,031] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:29,033] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:29,033] [INFO] DQC Reference Directory: /var/lib/cwl/stga512f97e-62d1-4544-880d-22e97383e6c1/dqc_reference
[2024-01-24 12:29:30,421] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:30,422] [INFO] Task started: Prodigal
[2024-01-24 12:29:30,423] [INFO] Running command: gunzip -c /var/lib/cwl/stg669af401-3d83-4bdd-a8b3-aa1405e57dd2/GCF_014636635.1_ASM1463663v1_genomic.fna.gz | prodigal -d GCF_014636635.1_ASM1463663v1_genomic.fna/cds.fna -a GCF_014636635.1_ASM1463663v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:38,790] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:38,791] [INFO] Task started: HMMsearch
[2024-01-24 12:29:38,791] [INFO] Running command: hmmsearch --tblout GCF_014636635.1_ASM1463663v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga512f97e-62d1-4544-880d-22e97383e6c1/dqc_reference/reference_markers.hmm GCF_014636635.1_ASM1463663v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:39,153] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:39,154] [INFO] Found 6/6 markers.
[2024-01-24 12:29:39,186] [INFO] Query marker FASTA was written to GCF_014636635.1_ASM1463663v1_genomic.fna/markers.fasta
[2024-01-24 12:29:39,186] [INFO] Task started: Blastn
[2024-01-24 12:29:39,186] [INFO] Running command: blastn -query GCF_014636635.1_ASM1463663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga512f97e-62d1-4544-880d-22e97383e6c1/dqc_reference/reference_markers.fasta -out GCF_014636635.1_ASM1463663v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:39,870] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:39,874] [INFO] Selected 22 target genomes.
[2024-01-24 12:29:39,875] [INFO] Target genome list was writen to GCF_014636635.1_ASM1463663v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:39,887] [INFO] Task started: fastANI
[2024-01-24 12:29:39,887] [INFO] Running command: fastANI --query /var/lib/cwl/stg669af401-3d83-4bdd-a8b3-aa1405e57dd2/GCF_014636635.1_ASM1463663v1_genomic.fna.gz --refList GCF_014636635.1_ASM1463663v1_genomic.fna/target_genomes.txt --output GCF_014636635.1_ASM1463663v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:52,553] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:52,554] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga512f97e-62d1-4544-880d-22e97383e6c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:52,554] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga512f97e-62d1-4544-880d-22e97383e6c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:52,561] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:29:52,561] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:52,561] [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 pacifica	strain=CGMCC 1.12181	GCA_014636635.1	1171543	1171543	type	True	100.0	956	958	95	conclusive
Marinicella rhabdoformis	strain=3539	GCA_009671245.1	2580566	2580566	type	True	76.9611	77	958	95	below_threshold
Marinicella sediminis	strain=F2	GCA_002000055.1	1792834	1792834	type	True	76.9508	125	958	95	below_threshold
Marinicella litoralis	strain=DSM 25488	GCA_004363335.1	644220	644220	type	True	76.7046	85	958	95	below_threshold
Marinicella litoralis	strain=KMM 3900	GCA_002591915.1	644220	644220	type	True	76.6456	86	958	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:52,564] [INFO] DFAST Taxonomy check result was written to GCF_014636635.1_ASM1463663v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:52,564] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:52,564] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:52,564] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga512f97e-62d1-4544-880d-22e97383e6c1/dqc_reference/checkm_data
[2024-01-24 12:29:52,565] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:52,599] [INFO] Task started: CheckM
[2024-01-24 12:29:52,599] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014636635.1_ASM1463663v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014636635.1_ASM1463663v1_genomic.fna/checkm_input GCF_014636635.1_ASM1463663v1_genomic.fna/checkm_result
[2024-01-24 12:30:24,383] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:24,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:24,408] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:24,408] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:24,409] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014636635.1_ASM1463663v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:24,409] [INFO] Task started: Blastn
[2024-01-24 12:30:24,409] [INFO] Running command: blastn -query GCF_014636635.1_ASM1463663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga512f97e-62d1-4544-880d-22e97383e6c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014636635.1_ASM1463663v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:25,493] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:25,497] [INFO] Selected 23 target genomes.
[2024-01-24 12:30:25,497] [INFO] Target genome list was writen to GCF_014636635.1_ASM1463663v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:25,516] [INFO] Task started: fastANI
[2024-01-24 12:30:25,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg669af401-3d83-4bdd-a8b3-aa1405e57dd2/GCF_014636635.1_ASM1463663v1_genomic.fna.gz --refList GCF_014636635.1_ASM1463663v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014636635.1_ASM1463663v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:39,161] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:39,168] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:39,168] [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_014636635.1	s__Marinicella pacifica	100.0	956	958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Marinicellaceae;g__Marinicella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_008501575.1	s__Marinicella sp008501575	79.6901	418	958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Marinicellaceae;g__Marinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009671245.1	s__Marinicella rhabdoformis	76.9611	77	958	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	76.9508	125	958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Marinicellaceae;g__Marinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002591915.1	s__Marinicella litoralis	76.6456	86	958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Marinicellaceae;g__Marinicella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:39,170] [INFO] GTDB search result was written to GCF_014636635.1_ASM1463663v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:39,170] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:39,173] [INFO] DFAST_QC result json was written to GCF_014636635.1_ASM1463663v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:39,173] [INFO] DFAST_QC completed!
[2024-01-24 12:30:39,173] [INFO] Total running time: 0h1m10s