[2024-01-24 13:49:19,419] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:19,422] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:19,423] [INFO] DQC Reference Directory: /var/lib/cwl/stgd59540e2-1af1-4b06-8f24-ae59f933e0ab/dqc_reference
[2024-01-24 13:49:20,735] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:20,736] [INFO] Task started: Prodigal
[2024-01-24 13:49:20,737] [INFO] Running command: gunzip -c /var/lib/cwl/stgaaa1025c-db53-4308-9c24-f08d40171964/GCF_030159995.1_ASM3015999v1_genomic.fna.gz | prodigal -d GCF_030159995.1_ASM3015999v1_genomic.fna/cds.fna -a GCF_030159995.1_ASM3015999v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:32,675] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:32,676] [INFO] Task started: HMMsearch
[2024-01-24 13:49:32,676] [INFO] Running command: hmmsearch --tblout GCF_030159995.1_ASM3015999v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd59540e2-1af1-4b06-8f24-ae59f933e0ab/dqc_reference/reference_markers.hmm GCF_030159995.1_ASM3015999v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:33,000] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:33,001] [INFO] Found 6/6 markers.
[2024-01-24 13:49:33,046] [INFO] Query marker FASTA was written to GCF_030159995.1_ASM3015999v1_genomic.fna/markers.fasta
[2024-01-24 13:49:33,046] [INFO] Task started: Blastn
[2024-01-24 13:49:33,046] [INFO] Running command: blastn -query GCF_030159995.1_ASM3015999v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd59540e2-1af1-4b06-8f24-ae59f933e0ab/dqc_reference/reference_markers.fasta -out GCF_030159995.1_ASM3015999v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:33,855] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:33,858] [INFO] Selected 35 target genomes.
[2024-01-24 13:49:33,858] [INFO] Target genome list was writen to GCF_030159995.1_ASM3015999v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:33,878] [INFO] Task started: fastANI
[2024-01-24 13:49:33,879] [INFO] Running command: fastANI --query /var/lib/cwl/stgaaa1025c-db53-4308-9c24-f08d40171964/GCF_030159995.1_ASM3015999v1_genomic.fna.gz --refList GCF_030159995.1_ASM3015999v1_genomic.fna/target_genomes.txt --output GCF_030159995.1_ASM3015999v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:55,717] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:55,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd59540e2-1af1-4b06-8f24-ae59f933e0ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:55,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd59540e2-1af1-4b06-8f24-ae59f933e0ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:55,723] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:49:55,723] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:49:55,723] [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
Marinomonas communis	strain=DSM 5604	GCA_004363305.1	28254	28254	type	True	76.656	52	1569	95	below_threshold
Oceanospirillum beijerinckii	strain=DSM 7166	GCA_000422425.1	64976	64976	type	True	76.5297	51	1569	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:55,725] [INFO] DFAST Taxonomy check result was written to GCF_030159995.1_ASM3015999v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:55,725] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:55,725] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:55,725] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd59540e2-1af1-4b06-8f24-ae59f933e0ab/dqc_reference/checkm_data
[2024-01-24 13:49:55,726] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:55,773] [INFO] Task started: CheckM
[2024-01-24 13:49:55,774] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030159995.1_ASM3015999v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030159995.1_ASM3015999v1_genomic.fna/checkm_input GCF_030159995.1_ASM3015999v1_genomic.fna/checkm_result
[2024-01-24 13:50:36,675] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:36,676] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:36,693] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:36,694] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:36,694] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030159995.1_ASM3015999v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:36,695] [INFO] Task started: Blastn
[2024-01-24 13:50:36,695] [INFO] Running command: blastn -query GCF_030159995.1_ASM3015999v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd59540e2-1af1-4b06-8f24-ae59f933e0ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_030159995.1_ASM3015999v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:37,811] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:37,814] [INFO] Selected 32 target genomes.
[2024-01-24 13:50:37,815] [INFO] Target genome list was writen to GCF_030159995.1_ASM3015999v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:37,842] [INFO] Task started: fastANI
[2024-01-24 13:50:37,842] [INFO] Running command: fastANI --query /var/lib/cwl/stgaaa1025c-db53-4308-9c24-f08d40171964/GCF_030159995.1_ASM3015999v1_genomic.fna.gz --refList GCF_030159995.1_ASM3015999v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030159995.1_ASM3015999v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:58,361] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:58,369] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:50:58,370] [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
GCA_015665455.1	s__JADFAD01 sp015665455	78.1987	263	1569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__JADFAD01;g__JADFAD01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363305.1	s__Marinomonas communis	76.6581	53	1569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	97.16	97.04	0.89	0.87	3	-
GCF_000422425.1	s__Oceanospirillum beijerinckii	76.5297	51	1569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	98.77	98.77	0.90	0.90	2	-
GCF_014164585.1	s__Oceanospirillum sp014164585	76.4091	56	1569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:58,371] [INFO] GTDB search result was written to GCF_030159995.1_ASM3015999v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:58,371] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:58,373] [INFO] DFAST_QC result json was written to GCF_030159995.1_ASM3015999v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:58,373] [INFO] DFAST_QC completed!
[2024-01-24 13:50:58,374] [INFO] Total running time: 0h1m39s