[2024-01-24 13:17:47,123] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:47,126] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:47,126] [INFO] DQC Reference Directory: /var/lib/cwl/stg6305c0ec-a538-4993-8def-bc4f2c9ebb3d/dqc_reference
[2024-01-24 13:17:48,510] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:48,514] [INFO] Task started: Prodigal
[2024-01-24 13:17:48,515] [INFO] Running command: gunzip -c /var/lib/cwl/stg73b8113c-a681-4446-b38e-2a2c7eb8f68a/GCF_024808815.1_ASM2480881v1_genomic.fna.gz | prodigal -d GCF_024808815.1_ASM2480881v1_genomic.fna/cds.fna -a GCF_024808815.1_ASM2480881v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:52,410] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:52,410] [INFO] Task started: HMMsearch
[2024-01-24 13:17:52,410] [INFO] Running command: hmmsearch --tblout GCF_024808815.1_ASM2480881v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6305c0ec-a538-4993-8def-bc4f2c9ebb3d/dqc_reference/reference_markers.hmm GCF_024808815.1_ASM2480881v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:52,710] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:52,712] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg73b8113c-a681-4446-b38e-2a2c7eb8f68a/GCF_024808815.1_ASM2480881v1_genomic.fna.gz]
[2024-01-24 13:17:52,732] [INFO] Query marker FASTA was written to GCF_024808815.1_ASM2480881v1_genomic.fna/markers.fasta
[2024-01-24 13:17:52,732] [INFO] Task started: Blastn
[2024-01-24 13:17:52,732] [INFO] Running command: blastn -query GCF_024808815.1_ASM2480881v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6305c0ec-a538-4993-8def-bc4f2c9ebb3d/dqc_reference/reference_markers.fasta -out GCF_024808815.1_ASM2480881v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:53,233] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:53,237] [INFO] Selected 5 target genomes.
[2024-01-24 13:17:53,237] [INFO] Target genome list was writen to GCF_024808815.1_ASM2480881v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:53,240] [INFO] Task started: fastANI
[2024-01-24 13:17:53,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg73b8113c-a681-4446-b38e-2a2c7eb8f68a/GCF_024808815.1_ASM2480881v1_genomic.fna.gz --refList GCF_024808815.1_ASM2480881v1_genomic.fna/target_genomes.txt --output GCF_024808815.1_ASM2480881v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:55,652] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:55,652] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6305c0ec-a538-4993-8def-bc4f2c9ebb3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:55,653] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6305c0ec-a538-4993-8def-bc4f2c9ebb3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:55,657] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:55,657] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:55,657] [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
Methanosalsum natronophilum	strain=AME2	GCA_024808815.1	768733	768733	type	True	100.0	652	654	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:17:55,658] [INFO] DFAST Taxonomy check result was written to GCF_024808815.1_ASM2480881v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:55,659] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:55,659] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:55,659] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6305c0ec-a538-4993-8def-bc4f2c9ebb3d/dqc_reference/checkm_data
[2024-01-24 13:17:55,660] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:55,682] [INFO] Task started: CheckM
[2024-01-24 13:17:55,683] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024808815.1_ASM2480881v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024808815.1_ASM2480881v1_genomic.fna/checkm_input GCF_024808815.1_ASM2480881v1_genomic.fna/checkm_result
[2024-01-24 13:18:15,916] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:15,917] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:15,936] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:15,936] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:15,937] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024808815.1_ASM2480881v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:15,937] [INFO] Task started: Blastn
[2024-01-24 13:18:15,937] [INFO] Running command: blastn -query GCF_024808815.1_ASM2480881v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6305c0ec-a538-4993-8def-bc4f2c9ebb3d/dqc_reference/reference_markers_gtdb.fasta -out GCF_024808815.1_ASM2480881v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:16,403] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:16,406] [INFO] Selected 9 target genomes.
[2024-01-24 13:18:16,406] [INFO] Target genome list was writen to GCF_024808815.1_ASM2480881v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:16,414] [INFO] Task started: fastANI
[2024-01-24 13:18:16,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg73b8113c-a681-4446-b38e-2a2c7eb8f68a/GCF_024808815.1_ASM2480881v1_genomic.fna.gz --refList GCF_024808815.1_ASM2480881v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024808815.1_ASM2480881v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:19,772] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:19,775] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:19,776] [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_003555325.1	s__Methanosalsum natronophilum	99.228	449	654	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosalsum	95.0	99.02	99.02	0.86	0.86	2	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:18:19,778] [INFO] GTDB search result was written to GCF_024808815.1_ASM2480881v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:19,778] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:19,781] [INFO] DFAST_QC result json was written to GCF_024808815.1_ASM2480881v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:19,781] [INFO] DFAST_QC completed!
[2024-01-24 13:18:19,781] [INFO] Total running time: 0h0m33s