[2024-01-24 13:31:35,636] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:35,641] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:35,642] [INFO] DQC Reference Directory: /var/lib/cwl/stg5fbbda7d-e8ce-49b0-a170-6d1cc7fed6ff/dqc_reference
[2024-01-24 13:31:37,099] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:37,100] [INFO] Task started: Prodigal
[2024-01-24 13:31:37,100] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe45c9bd-0516-4dc0-8871-85f729e4311b/GCF_003353065.1_ASM335306v1_genomic.fna.gz | prodigal -d GCF_003353065.1_ASM335306v1_genomic.fna/cds.fna -a GCF_003353065.1_ASM335306v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:00,571] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:00,571] [INFO] Task started: HMMsearch
[2024-01-24 13:32:00,571] [INFO] Running command: hmmsearch --tblout GCF_003353065.1_ASM335306v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5fbbda7d-e8ce-49b0-a170-6d1cc7fed6ff/dqc_reference/reference_markers.hmm GCF_003353065.1_ASM335306v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:00,870] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:00,871] [INFO] Found 6/6 markers.
[2024-01-24 13:32:00,907] [INFO] Query marker FASTA was written to GCF_003353065.1_ASM335306v1_genomic.fna/markers.fasta
[2024-01-24 13:32:00,907] [INFO] Task started: Blastn
[2024-01-24 13:32:00,907] [INFO] Running command: blastn -query GCF_003353065.1_ASM335306v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fbbda7d-e8ce-49b0-a170-6d1cc7fed6ff/dqc_reference/reference_markers.fasta -out GCF_003353065.1_ASM335306v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:01,559] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:01,562] [INFO] Selected 20 target genomes.
[2024-01-24 13:32:01,562] [INFO] Target genome list was writen to GCF_003353065.1_ASM335306v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:01,583] [INFO] Task started: fastANI
[2024-01-24 13:32:01,583] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe45c9bd-0516-4dc0-8871-85f729e4311b/GCF_003353065.1_ASM335306v1_genomic.fna.gz --refList GCF_003353065.1_ASM335306v1_genomic.fna/target_genomes.txt --output GCF_003353065.1_ASM335306v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:15,157] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:15,158] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5fbbda7d-e8ce-49b0-a170-6d1cc7fed6ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:15,158] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5fbbda7d-e8ce-49b0-a170-6d1cc7fed6ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:15,160] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:32:15,160] [INFO] The taxonomy check result is classified as 'no_hit'.
[2024-01-24 13:32:15,160] [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
--------------------------------------------------------------------------------
[2024-01-24 13:32:15,161] [INFO] DFAST Taxonomy check result was written to GCF_003353065.1_ASM335306v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:15,162] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:15,162] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:15,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5fbbda7d-e8ce-49b0-a170-6d1cc7fed6ff/dqc_reference/checkm_data
[2024-01-24 13:32:15,165] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:15,215] [INFO] Task started: CheckM
[2024-01-24 13:32:15,215] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003353065.1_ASM335306v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003353065.1_ASM335306v1_genomic.fna/checkm_input GCF_003353065.1_ASM335306v1_genomic.fna/checkm_result
[2024-01-24 13:33:21,610] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:21,612] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:21,642] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:21,642] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:21,643] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003353065.1_ASM335306v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:21,643] [INFO] Task started: Blastn
[2024-01-24 13:33:21,643] [INFO] Running command: blastn -query GCF_003353065.1_ASM335306v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fbbda7d-e8ce-49b0-a170-6d1cc7fed6ff/dqc_reference/reference_markers_gtdb.fasta -out GCF_003353065.1_ASM335306v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:22,551] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:22,554] [INFO] Selected 21 target genomes.
[2024-01-24 13:33:22,554] [INFO] Target genome list was writen to GCF_003353065.1_ASM335306v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:22,596] [INFO] Task started: fastANI
[2024-01-24 13:33:22,596] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe45c9bd-0516-4dc0-8871-85f729e4311b/GCF_003353065.1_ASM335306v1_genomic.fna.gz --refList GCF_003353065.1_ASM335306v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003353065.1_ASM335306v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:35,419] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:35,427] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:35,427] [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_003353065.1	s__Cyclonatronum proteinivorum	100.0	1430	1431	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__PXAI01;g__Cyclonatronum	95.0	99.77	99.77	1.00	1.00	2	conclusive
GCA_003555145.1	s__Cyclonatronum sp003555145	76.4805	105	1431	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__PXAI01;g__Cyclonatronum	95.0	98.75	98.75	0.87	0.87	2	-
GCA_003566395.1	s__Cyclonatronum sp003566395	76.0334	95	1431	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__PXAI01;g__Cyclonatronum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:35,429] [INFO] GTDB search result was written to GCF_003353065.1_ASM335306v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:35,430] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:35,432] [INFO] DFAST_QC result json was written to GCF_003353065.1_ASM335306v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:35,432] [INFO] DFAST_QC completed!
[2024-01-24 13:33:35,432] [INFO] Total running time: 0h1m60s