[2024-01-24 13:40:33,364] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:33,366] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:33,366] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ebd7e0f-40ed-4e72-b81e-ed75e0339dd4/dqc_reference
[2024-01-24 13:40:34,640] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:34,641] [INFO] Task started: Prodigal
[2024-01-24 13:40:34,641] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b9d9083-6b3f-43d2-a31a-6319e6b41d95/GCF_000017165.1_ASM1716v1_genomic.fna.gz | prodigal -d GCF_000017165.1_ASM1716v1_genomic.fna/cds.fna -a GCF_000017165.1_ASM1716v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:37,737] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:37,737] [INFO] Task started: HMMsearch
[2024-01-24 13:40:37,737] [INFO] Running command: hmmsearch --tblout GCF_000017165.1_ASM1716v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ebd7e0f-40ed-4e72-b81e-ed75e0339dd4/dqc_reference/reference_markers.hmm GCF_000017165.1_ASM1716v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:37,969] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:37,971] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg5b9d9083-6b3f-43d2-a31a-6319e6b41d95/GCF_000017165.1_ASM1716v1_genomic.fna.gz]
[2024-01-24 13:40:37,994] [INFO] Query marker FASTA was written to GCF_000017165.1_ASM1716v1_genomic.fna/markers.fasta
[2024-01-24 13:40:37,994] [INFO] Task started: Blastn
[2024-01-24 13:40:37,994] [INFO] Running command: blastn -query GCF_000017165.1_ASM1716v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ebd7e0f-40ed-4e72-b81e-ed75e0339dd4/dqc_reference/reference_markers.fasta -out GCF_000017165.1_ASM1716v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:38,521] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:38,525] [INFO] Selected 2 target genomes.
[2024-01-24 13:40:38,525] [INFO] Target genome list was writen to GCF_000017165.1_ASM1716v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:38,528] [INFO] Task started: fastANI
[2024-01-24 13:40:38,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b9d9083-6b3f-43d2-a31a-6319e6b41d95/GCF_000017165.1_ASM1716v1_genomic.fna.gz --refList GCF_000017165.1_ASM1716v1_genomic.fna/target_genomes.txt --output GCF_000017165.1_ASM1716v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:39,580] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:39,581] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ebd7e0f-40ed-4e72-b81e-ed75e0339dd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:39,581] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ebd7e0f-40ed-4e72-b81e-ed75e0339dd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:39,586] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:39,586] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:39,586] [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
Methanococcus vannielii	strain=SB	GCA_000017165.1	2187	2187	type	True	100.0	566	573	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:40:39,588] [INFO] DFAST Taxonomy check result was written to GCF_000017165.1_ASM1716v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:39,588] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:39,589] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:39,589] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ebd7e0f-40ed-4e72-b81e-ed75e0339dd4/dqc_reference/checkm_data
[2024-01-24 13:40:39,590] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:39,610] [INFO] Task started: CheckM
[2024-01-24 13:40:39,610] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000017165.1_ASM1716v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000017165.1_ASM1716v1_genomic.fna/checkm_input GCF_000017165.1_ASM1716v1_genomic.fna/checkm_result
[2024-01-24 13:40:57,245] [INFO] Task succeeded: CheckM
[2024-01-24 13:40:57,246] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:40:57,264] [INFO] ===== Completeness check finished =====
[2024-01-24 13:40:57,264] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:40:57,265] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000017165.1_ASM1716v1_genomic.fna/markers.fasta)
[2024-01-24 13:40:57,265] [INFO] Task started: Blastn
[2024-01-24 13:40:57,266] [INFO] Running command: blastn -query GCF_000017165.1_ASM1716v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ebd7e0f-40ed-4e72-b81e-ed75e0339dd4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000017165.1_ASM1716v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:57,842] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:57,846] [INFO] Selected 6 target genomes.
[2024-01-24 13:40:57,846] [INFO] Target genome list was writen to GCF_000017165.1_ASM1716v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:40:57,855] [INFO] Task started: fastANI
[2024-01-24 13:40:57,856] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b9d9083-6b3f-43d2-a31a-6319e6b41d95/GCF_000017165.1_ASM1716v1_genomic.fna.gz --refList GCF_000017165.1_ASM1716v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000017165.1_ASM1716v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:00,678] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:00,683] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:00,684] [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_000017165.1	s__Methanococcus vannielii	100.0	566	573	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanococcaceae;g__Methanococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000017225.1	s__Methanococcus maripaludis_A	80.064	310	573	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanococcaceae;g__Methanococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002945325.1	s__Methanococcus maripaludis	79.9542	326	573	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanococcaceae;g__Methanococcus	95.0	96.14	95.53	0.90	0.88	20	-
GCF_000016125.1	s__Methanococcus maripaludis_D	79.9192	317	573	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanococcaceae;g__Methanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018485.1	s__Methanococcus maripaludis_C	79.9178	315	573	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanococcaceae;g__Methanococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:00,685] [INFO] GTDB search result was written to GCF_000017165.1_ASM1716v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:00,686] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:00,688] [INFO] DFAST_QC result json was written to GCF_000017165.1_ASM1716v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:00,688] [INFO] DFAST_QC completed!
[2024-01-24 13:41:00,689] [INFO] Total running time: 0h0m27s