[2024-01-24 13:13:02,836] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:02,839] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:02,840] [INFO] DQC Reference Directory: /var/lib/cwl/stgb825cfea-96a0-4a03-98c7-193b0389843d/dqc_reference
[2024-01-24 13:13:04,071] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:04,072] [INFO] Task started: Prodigal
[2024-01-24 13:13:04,072] [INFO] Running command: gunzip -c /var/lib/cwl/stgfaaa897a-a1b4-4ee0-9e3e-766deaf13d4e/GCF_030550815.1_ASM3055081v1_genomic.fna.gz | prodigal -d GCF_030550815.1_ASM3055081v1_genomic.fna/cds.fna -a GCF_030550815.1_ASM3055081v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:05,547] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:05,547] [INFO] Task started: HMMsearch
[2024-01-24 13:13:05,548] [INFO] Running command: hmmsearch --tblout GCF_030550815.1_ASM3055081v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb825cfea-96a0-4a03-98c7-193b0389843d/dqc_reference/reference_markers.hmm GCF_030550815.1_ASM3055081v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:05,706] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:05,708] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgfaaa897a-a1b4-4ee0-9e3e-766deaf13d4e/GCF_030550815.1_ASM3055081v1_genomic.fna.gz]
[2024-01-24 13:13:05,720] [INFO] Query marker FASTA was written to GCF_030550815.1_ASM3055081v1_genomic.fna/markers.fasta
[2024-01-24 13:13:05,720] [INFO] Task started: Blastn
[2024-01-24 13:13:05,721] [INFO] Running command: blastn -query GCF_030550815.1_ASM3055081v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb825cfea-96a0-4a03-98c7-193b0389843d/dqc_reference/reference_markers.fasta -out GCF_030550815.1_ASM3055081v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:06,200] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:06,205] [INFO] Selected 14 target genomes.
[2024-01-24 13:13:06,205] [INFO] Target genome list was writen to GCF_030550815.1_ASM3055081v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:06,322] [INFO] Task started: fastANI
[2024-01-24 13:13:06,323] [INFO] Running command: fastANI --query /var/lib/cwl/stgfaaa897a-a1b4-4ee0-9e3e-766deaf13d4e/GCF_030550815.1_ASM3055081v1_genomic.fna.gz --refList GCF_030550815.1_ASM3055081v1_genomic.fna/target_genomes.txt --output GCF_030550815.1_ASM3055081v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:08,689] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:08,690] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb825cfea-96a0-4a03-98c7-193b0389843d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:08,690] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb825cfea-96a0-4a03-98c7-193b0389843d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:08,692] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:13:08,692] [INFO] The taxonomy check result is classified as 'no_hit'.
[2024-01-24 13:13:08,693] [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 13:13:08,694] [INFO] DFAST Taxonomy check result was written to GCF_030550815.1_ASM3055081v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:08,695] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:08,695] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:08,696] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb825cfea-96a0-4a03-98c7-193b0389843d/dqc_reference/checkm_data
[2024-01-24 13:13:08,700] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:08,711] [INFO] Task started: CheckM
[2024-01-24 13:13:08,712] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030550815.1_ASM3055081v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030550815.1_ASM3055081v1_genomic.fna/checkm_input GCF_030550815.1_ASM3055081v1_genomic.fna/checkm_result
[2024-01-24 13:13:21,554] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:21,556] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:21,575] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:21,575] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:21,576] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030550815.1_ASM3055081v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:21,576] [INFO] Task started: Blastn
[2024-01-24 13:13:21,577] [INFO] Running command: blastn -query GCF_030550815.1_ASM3055081v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb825cfea-96a0-4a03-98c7-193b0389843d/dqc_reference/reference_markers_gtdb.fasta -out GCF_030550815.1_ASM3055081v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:22,033] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:22,038] [INFO] Selected 22 target genomes.
[2024-01-24 13:13:22,038] [INFO] Target genome list was writen to GCF_030550815.1_ASM3055081v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:22,114] [INFO] Task started: fastANI
[2024-01-24 13:13:22,114] [INFO] Running command: fastANI --query /var/lib/cwl/stgfaaa897a-a1b4-4ee0-9e3e-766deaf13d4e/GCF_030550815.1_ASM3055081v1_genomic.fna.gz --refList GCF_030550815.1_ASM3055081v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030550815.1_ASM3055081v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:27,904] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:27,908] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:13:27,909] [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
--------------------------------------------------------------------------------
[2024-01-24 13:13:27,911] [INFO] GTDB search result was written to GCF_030550815.1_ASM3055081v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:27,911] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:27,913] [INFO] DFAST_QC result json was written to GCF_030550815.1_ASM3055081v1_genomic.fna/dqc_result.json
[2024-01-24 13:13:27,913] [INFO] DFAST_QC completed!
[2024-01-24 13:13:27,913] [INFO] Total running time: 0h0m25s