[2023-06-19 08:52:48,003] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:52:48,015] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:52:48,016] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa2867f9-ea02-4f62-a2ce-fae13ab037ae/dqc_reference
[2023-06-19 08:52:49,864] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:52:49,865] [INFO] Task started: Prodigal
[2023-06-19 08:52:49,865] [INFO] Running command: gunzip -c /var/lib/cwl/stg033f7c01-c810-45e4-b209-bb68950d95c5/GCA_014238875.1_ASM1423887v1_genomic.fna.gz | prodigal -d GCA_014238875.1_ASM1423887v1_genomic.fna/cds.fna -a GCA_014238875.1_ASM1423887v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:53:00,437] [INFO] Task succeeded: Prodigal
[2023-06-19 08:53:00,438] [INFO] Task started: HMMsearch
[2023-06-19 08:53:00,438] [INFO] Running command: hmmsearch --tblout GCA_014238875.1_ASM1423887v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa2867f9-ea02-4f62-a2ce-fae13ab037ae/dqc_reference/reference_markers.hmm GCA_014238875.1_ASM1423887v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:53:00,734] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:53:00,735] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg033f7c01-c810-45e4-b209-bb68950d95c5/GCA_014238875.1_ASM1423887v1_genomic.fna.gz]
[2023-06-19 08:53:00,776] [INFO] Query marker FASTA was written to GCA_014238875.1_ASM1423887v1_genomic.fna/markers.fasta
[2023-06-19 08:53:00,777] [INFO] Task started: Blastn
[2023-06-19 08:53:00,777] [INFO] Running command: blastn -query GCA_014238875.1_ASM1423887v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa2867f9-ea02-4f62-a2ce-fae13ab037ae/dqc_reference/reference_markers.fasta -out GCA_014238875.1_ASM1423887v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:53:01,434] [INFO] Task succeeded: Blastn
[2023-06-19 08:53:01,439] [INFO] Selected 31 target genomes.
[2023-06-19 08:53:01,439] [INFO] Target genome list was writen to GCA_014238875.1_ASM1423887v1_genomic.fna/target_genomes.txt
[2023-06-19 08:53:01,461] [INFO] Task started: fastANI
[2023-06-19 08:53:01,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg033f7c01-c810-45e4-b209-bb68950d95c5/GCA_014238875.1_ASM1423887v1_genomic.fna.gz --refList GCA_014238875.1_ASM1423887v1_genomic.fna/target_genomes.txt --output GCA_014238875.1_ASM1423887v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:53:34,593] [INFO] Task succeeded: fastANI
[2023-06-19 08:53:34,593] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa2867f9-ea02-4f62-a2ce-fae13ab037ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:53:34,594] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa2867f9-ea02-4f62-a2ce-fae13ab037ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:53:34,611] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:53:34,611] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 08:53:34,612] [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
--------------------------------------------------------------------------------
[2023-06-19 08:53:34,616] [INFO] DFAST Taxonomy check result was written to GCA_014238875.1_ASM1423887v1_genomic.fna/tc_result.tsv
[2023-06-19 08:53:34,619] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:53:34,620] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:53:34,620] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa2867f9-ea02-4f62-a2ce-fae13ab037ae/dqc_reference/checkm_data
[2023-06-19 08:53:34,625] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:53:34,684] [INFO] Task started: CheckM
[2023-06-19 08:53:34,685] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014238875.1_ASM1423887v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014238875.1_ASM1423887v1_genomic.fna/checkm_input GCA_014238875.1_ASM1423887v1_genomic.fna/checkm_result
[2023-06-19 08:54:09,912] [INFO] Task succeeded: CheckM
[2023-06-19 08:54:09,913] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 46.40%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:54:09,945] [INFO] ===== Completeness check finished =====
[2023-06-19 08:54:09,945] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:54:09,946] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014238875.1_ASM1423887v1_genomic.fna/markers.fasta)
[2023-06-19 08:54:09,946] [INFO] Task started: Blastn
[2023-06-19 08:54:09,946] [INFO] Running command: blastn -query GCA_014238875.1_ASM1423887v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa2867f9-ea02-4f62-a2ce-fae13ab037ae/dqc_reference/reference_markers_gtdb.fasta -out GCA_014238875.1_ASM1423887v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:54:10,970] [INFO] Task succeeded: Blastn
[2023-06-19 08:54:10,975] [INFO] Selected 33 target genomes.
[2023-06-19 08:54:10,976] [INFO] Target genome list was writen to GCA_014238875.1_ASM1423887v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:54:10,991] [INFO] Task started: fastANI
[2023-06-19 08:54:10,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg033f7c01-c810-45e4-b209-bb68950d95c5/GCA_014238875.1_ASM1423887v1_genomic.fna.gz --refList GCA_014238875.1_ASM1423887v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014238875.1_ASM1423887v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:54:40,386] [INFO] Task succeeded: fastANI
[2023-06-19 08:54:40,388] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 08:54:40,388] [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
--------------------------------------------------------------------------------
[2023-06-19 08:54:40,391] [INFO] GTDB search result was written to GCA_014238875.1_ASM1423887v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:54:40,392] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:54:40,394] [INFO] DFAST_QC result json was written to GCA_014238875.1_ASM1423887v1_genomic.fna/dqc_result.json
[2023-06-19 08:54:40,395] [INFO] DFAST_QC completed!
[2023-06-19 08:54:40,395] [INFO] Total running time: 0h1m52s