[2024-01-24 10:57:13,105] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:13,106] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:13,106] [INFO] DQC Reference Directory: /var/lib/cwl/stg2157b768-f58e-4744-a7dc-e9e3eecf1a2b/dqc_reference
[2024-01-24 10:57:14,620] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:14,621] [INFO] Task started: Prodigal
[2024-01-24 10:57:14,621] [INFO] Running command: gunzip -c /var/lib/cwl/stg6be0af0d-cf6a-41a0-9805-d48cab70e719/GCF_003336225.1_ASM333622v1_genomic.fna.gz | prodigal -d GCF_003336225.1_ASM333622v1_genomic.fna/cds.fna -a GCF_003336225.1_ASM333622v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:25,791] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:25,791] [INFO] Task started: HMMsearch
[2024-01-24 10:57:25,792] [INFO] Running command: hmmsearch --tblout GCF_003336225.1_ASM333622v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2157b768-f58e-4744-a7dc-e9e3eecf1a2b/dqc_reference/reference_markers.hmm GCF_003336225.1_ASM333622v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:26,082] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:26,084] [INFO] Found 6/6 markers.
[2024-01-24 10:57:26,125] [INFO] Query marker FASTA was written to GCF_003336225.1_ASM333622v1_genomic.fna/markers.fasta
[2024-01-24 10:57:26,125] [INFO] Task started: Blastn
[2024-01-24 10:57:26,125] [INFO] Running command: blastn -query GCF_003336225.1_ASM333622v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2157b768-f58e-4744-a7dc-e9e3eecf1a2b/dqc_reference/reference_markers.fasta -out GCF_003336225.1_ASM333622v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:26,990] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:26,994] [INFO] Selected 34 target genomes.
[2024-01-24 10:57:26,995] [INFO] Target genome list was writen to GCF_003336225.1_ASM333622v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:27,006] [INFO] Task started: fastANI
[2024-01-24 10:57:27,007] [INFO] Running command: fastANI --query /var/lib/cwl/stg6be0af0d-cf6a-41a0-9805-d48cab70e719/GCF_003336225.1_ASM333622v1_genomic.fna.gz --refList GCF_003336225.1_ASM333622v1_genomic.fna/target_genomes.txt --output GCF_003336225.1_ASM333622v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:49,670] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:49,671] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2157b768-f58e-4744-a7dc-e9e3eecf1a2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:49,671] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2157b768-f58e-4744-a7dc-e9e3eecf1a2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:49,675] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:57:49,675] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:57:49,676] [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
Ferrimonas lipolytica	strain=S7	GCA_012295575.1	2724191	2724191	type	True	76.2456	55	1421	95	below_threshold
Ferrimonas aestuarii	strain=IMCC35002	GCA_005116665.1	2569539	2569539	type	True	76.0121	52	1421	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:49,677] [INFO] DFAST Taxonomy check result was written to GCF_003336225.1_ASM333622v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:49,677] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:49,678] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:49,678] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2157b768-f58e-4744-a7dc-e9e3eecf1a2b/dqc_reference/checkm_data
[2024-01-24 10:57:49,679] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:49,720] [INFO] Task started: CheckM
[2024-01-24 10:57:49,720] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003336225.1_ASM333622v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003336225.1_ASM333622v1_genomic.fna/checkm_input GCF_003336225.1_ASM333622v1_genomic.fna/checkm_result
[2024-01-24 10:58:27,553] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:27,555] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:27,571] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:27,572] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:27,572] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003336225.1_ASM333622v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:27,572] [INFO] Task started: Blastn
[2024-01-24 10:58:27,573] [INFO] Running command: blastn -query GCF_003336225.1_ASM333622v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2157b768-f58e-4744-a7dc-e9e3eecf1a2b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003336225.1_ASM333622v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:28,827] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:28,832] [INFO] Selected 29 target genomes.
[2024-01-24 10:58:28,832] [INFO] Target genome list was writen to GCF_003336225.1_ASM333622v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:28,854] [INFO] Task started: fastANI
[2024-01-24 10:58:28,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg6be0af0d-cf6a-41a0-9805-d48cab70e719/GCF_003336225.1_ASM333622v1_genomic.fna.gz --refList GCF_003336225.1_ASM333622v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003336225.1_ASM333622v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:49,127] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:49,136] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:49,137] [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_004336975.1	s__Corallincola luteus	98.1067	1275	1421	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Neiellaceae;g__Corallincola	95.0	98.11	98.10	0.91	0.90	3	conclusive
GCF_900115495.1	s__Enterovibrio norvegicus	76.7911	50	1421	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	97.84	95.33	0.92	0.87	14	-
GCF_012295575.1	s__Ferrimonas lipolytica	76.2491	55	1421	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116665.1	s__Ferrimonas sp005116665	75.9884	53	1421	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:49,138] [INFO] GTDB search result was written to GCF_003336225.1_ASM333622v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:49,139] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:49,141] [INFO] DFAST_QC result json was written to GCF_003336225.1_ASM333622v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:49,141] [INFO] DFAST_QC completed!
[2024-01-24 10:58:49,142] [INFO] Total running time: 0h1m36s