[2024-01-24 13:47:11,346] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:47:11,348] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:47:11,349] [INFO] DQC Reference Directory: /var/lib/cwl/stg2fe4d499-3c3c-46e2-853e-bbd9aea91e2c/dqc_reference
[2024-01-24 13:47:12,654] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:47:12,655] [INFO] Task started: Prodigal
[2024-01-24 13:47:12,655] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b65609e-74a1-4efb-be01-c4792d75b525/GCF_000374005.1_ASM37400v1_genomic.fna.gz | prodigal -d GCF_000374005.1_ASM37400v1_genomic.fna/cds.fna -a GCF_000374005.1_ASM37400v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:25,004] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:25,005] [INFO] Task started: HMMsearch
[2024-01-24 13:47:25,005] [INFO] Running command: hmmsearch --tblout GCF_000374005.1_ASM37400v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2fe4d499-3c3c-46e2-853e-bbd9aea91e2c/dqc_reference/reference_markers.hmm GCF_000374005.1_ASM37400v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:25,275] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:25,277] [INFO] Found 6/6 markers.
[2024-01-24 13:47:25,324] [INFO] Query marker FASTA was written to GCF_000374005.1_ASM37400v1_genomic.fna/markers.fasta
[2024-01-24 13:47:25,325] [INFO] Task started: Blastn
[2024-01-24 13:47:25,325] [INFO] Running command: blastn -query GCF_000374005.1_ASM37400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2fe4d499-3c3c-46e2-853e-bbd9aea91e2c/dqc_reference/reference_markers.fasta -out GCF_000374005.1_ASM37400v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:26,013] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:26,018] [INFO] Selected 26 target genomes.
[2024-01-24 13:47:26,019] [INFO] Target genome list was writen to GCF_000374005.1_ASM37400v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:26,040] [INFO] Task started: fastANI
[2024-01-24 13:47:26,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b65609e-74a1-4efb-be01-c4792d75b525/GCF_000374005.1_ASM37400v1_genomic.fna.gz --refList GCF_000374005.1_ASM37400v1_genomic.fna/target_genomes.txt --output GCF_000374005.1_ASM37400v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:42,113] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:42,114] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2fe4d499-3c3c-46e2-853e-bbd9aea91e2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:42,114] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2fe4d499-3c3c-46e2-853e-bbd9aea91e2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:42,121] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:42,121] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:42,121] [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
Kiloniella laminariae	strain=DSM 19542	GCA_000374005.1	454162	454162	type	True	100.0	1456	1459	95	conclusive
Kiloniella majae	strain=M56.1	GCA_002118315.1	1938558	1938558	type	True	77.7944	221	1459	95	below_threshold
Kiloniella litopenaei	strain=P1-1	GCA_000982415.1	1549748	1549748	type	True	77.6332	246	1459	95	below_threshold
Kiloniella spongiae	strain=MEBiC09566	GCA_001026905.1	1489064	1489064	type	True	77.2828	242	1459	95	below_threshold
Denitrobaculum tricleocarpae	strain=R148	GCA_007004665.1	2591009	2591009	type	True	75.2699	53	1459	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:42,122] [INFO] DFAST Taxonomy check result was written to GCF_000374005.1_ASM37400v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:42,123] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:42,123] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:42,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2fe4d499-3c3c-46e2-853e-bbd9aea91e2c/dqc_reference/checkm_data
[2024-01-24 13:47:42,126] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:42,172] [INFO] Task started: CheckM
[2024-01-24 13:47:42,173] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000374005.1_ASM37400v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000374005.1_ASM37400v1_genomic.fna/checkm_input GCF_000374005.1_ASM37400v1_genomic.fna/checkm_result
[2024-01-24 13:48:21,286] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:21,288] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:21,306] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:21,306] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:21,306] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000374005.1_ASM37400v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:21,307] [INFO] Task started: Blastn
[2024-01-24 13:48:21,307] [INFO] Running command: blastn -query GCF_000374005.1_ASM37400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2fe4d499-3c3c-46e2-853e-bbd9aea91e2c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000374005.1_ASM37400v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:22,427] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:22,431] [INFO] Selected 26 target genomes.
[2024-01-24 13:48:22,431] [INFO] Target genome list was writen to GCF_000374005.1_ASM37400v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:22,518] [INFO] Task started: fastANI
[2024-01-24 13:48:22,518] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b65609e-74a1-4efb-be01-c4792d75b525/GCF_000374005.1_ASM37400v1_genomic.fna.gz --refList GCF_000374005.1_ASM37400v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000374005.1_ASM37400v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:38,866] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:38,874] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:38,875] [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_000374005.1	s__Kiloniella laminaria	100.0	1456	1459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Kiloniella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002118315.1	s__Kiloniella majae	77.7799	222	1459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Kiloniella	95.0	97.24	97.23	0.93	0.92	3	-
GCA_002162915.1	s__Kiloniella sp002162915	77.7489	139	1459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Kiloniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000982415.1	s__Kiloniella litopenaei	77.6332	246	1459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Kiloniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900313065.1	s__Kiloniella sp900313065	77.4454	232	1459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Kiloniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001026905.1	s__Kiloniella spongiae	77.2828	242	1459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Kiloniella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:38,876] [INFO] GTDB search result was written to GCF_000374005.1_ASM37400v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:38,877] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:38,881] [INFO] DFAST_QC result json was written to GCF_000374005.1_ASM37400v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:38,881] [INFO] DFAST_QC completed!
[2024-01-24 13:48:38,881] [INFO] Total running time: 0h1m28s