[2024-01-24 11:26:10,995] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:10,997] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:10,998] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ca80d4c-b5a4-48cb-8ecc-fedfe6b56b49/dqc_reference
[2024-01-24 11:26:12,250] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:12,251] [INFO] Task started: Prodigal
[2024-01-24 11:26:12,251] [INFO] Running command: gunzip -c /var/lib/cwl/stg93734c21-b056-4b96-afe5-301c1fb96bd6/GCF_014640415.1_ASM1464041v1_genomic.fna.gz | prodigal -d GCF_014640415.1_ASM1464041v1_genomic.fna/cds.fna -a GCF_014640415.1_ASM1464041v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:29,734] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:29,735] [INFO] Task started: HMMsearch
[2024-01-24 11:26:29,735] [INFO] Running command: hmmsearch --tblout GCF_014640415.1_ASM1464041v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ca80d4c-b5a4-48cb-8ecc-fedfe6b56b49/dqc_reference/reference_markers.hmm GCF_014640415.1_ASM1464041v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:30,054] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:30,055] [INFO] Found 6/6 markers.
[2024-01-24 11:26:30,096] [INFO] Query marker FASTA was written to GCF_014640415.1_ASM1464041v1_genomic.fna/markers.fasta
[2024-01-24 11:26:30,097] [INFO] Task started: Blastn
[2024-01-24 11:26:30,097] [INFO] Running command: blastn -query GCF_014640415.1_ASM1464041v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ca80d4c-b5a4-48cb-8ecc-fedfe6b56b49/dqc_reference/reference_markers.fasta -out GCF_014640415.1_ASM1464041v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:30,741] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:30,745] [INFO] Selected 17 target genomes.
[2024-01-24 11:26:30,745] [INFO] Target genome list was writen to GCF_014640415.1_ASM1464041v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:30,755] [INFO] Task started: fastANI
[2024-01-24 11:26:30,755] [INFO] Running command: fastANI --query /var/lib/cwl/stg93734c21-b056-4b96-afe5-301c1fb96bd6/GCF_014640415.1_ASM1464041v1_genomic.fna.gz --refList GCF_014640415.1_ASM1464041v1_genomic.fna/target_genomes.txt --output GCF_014640415.1_ASM1464041v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:42,488] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:42,489] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ca80d4c-b5a4-48cb-8ecc-fedfe6b56b49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:42,489] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ca80d4c-b5a4-48cb-8ecc-fedfe6b56b49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:42,493] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:26:42,494] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:42,494] [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
Phaeocystidibacter marisrubri	strain=CGMCC 1.14954	GCA_014640415.1	1577780	1577780	type	True	100.0	1113	1113	95	conclusive
Phaeocystidibacter marisrubri	strain=JCM 30614	GCA_008933165.1	1577780	1577780	type	True	99.9991	1108	1113	95	conclusive
Phaeocystidibacter luteus	strain=LMG 25704	GCA_008933115.1	911197	911197	type	True	78.0393	175	1113	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:42,495] [INFO] DFAST Taxonomy check result was written to GCF_014640415.1_ASM1464041v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:42,496] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:42,496] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:42,496] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ca80d4c-b5a4-48cb-8ecc-fedfe6b56b49/dqc_reference/checkm_data
[2024-01-24 11:26:42,497] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:42,536] [INFO] Task started: CheckM
[2024-01-24 11:26:42,536] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014640415.1_ASM1464041v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014640415.1_ASM1464041v1_genomic.fna/checkm_input GCF_014640415.1_ASM1464041v1_genomic.fna/checkm_result
[2024-01-24 11:27:37,823] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:37,824] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:37,846] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:37,846] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:37,846] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014640415.1_ASM1464041v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:37,847] [INFO] Task started: Blastn
[2024-01-24 11:27:37,847] [INFO] Running command: blastn -query GCF_014640415.1_ASM1464041v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ca80d4c-b5a4-48cb-8ecc-fedfe6b56b49/dqc_reference/reference_markers_gtdb.fasta -out GCF_014640415.1_ASM1464041v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:38,668] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:38,672] [INFO] Selected 24 target genomes.
[2024-01-24 11:27:38,672] [INFO] Target genome list was writen to GCF_014640415.1_ASM1464041v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:38,690] [INFO] Task started: fastANI
[2024-01-24 11:27:38,691] [INFO] Running command: fastANI --query /var/lib/cwl/stg93734c21-b056-4b96-afe5-301c1fb96bd6/GCF_014640415.1_ASM1464041v1_genomic.fna.gz --refList GCF_014640415.1_ASM1464041v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014640415.1_ASM1464041v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:52,150] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:52,158] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:52,158] [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_008933165.1	s__Phaeocystidibacter marisrubri	99.9991	1108	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Phaeocystidibacter	95.0	99.07	98.14	0.97	0.95	3	conclusive
GCF_008933115.1	s__Phaeocystidibacter luteus	78.0471	174	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Phaeocystidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373425.1	s__Phaeocystidibacter sp013373425	77.1715	165	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Phaeocystidibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:52,160] [INFO] GTDB search result was written to GCF_014640415.1_ASM1464041v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:52,161] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:52,163] [INFO] DFAST_QC result json was written to GCF_014640415.1_ASM1464041v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:52,163] [INFO] DFAST_QC completed!
[2024-01-24 11:27:52,163] [INFO] Total running time: 0h1m41s