[2023-06-05 00:30:26,167] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:30:26,169] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:30:26,170] [INFO] DQC Reference Directory: /var/lib/cwl/stg8651a853-d4d3-408e-8fae-b75f6a882431/dqc_reference
[2023-06-05 00:30:30,132] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:30:30,133] [INFO] Task started: Prodigal
[2023-06-05 00:30:30,134] [INFO] Running command: gunzip -c /var/lib/cwl/stge24e42f9-26d3-46b7-bc01-76ea52028d9f/GCA_004375765.1_ASM437576v1_genomic.fna.gz | prodigal -d GCA_004375765.1_ASM437576v1_genomic.fna/cds.fna -a GCA_004375765.1_ASM437576v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:30:33,088] [INFO] Task succeeded: Prodigal
[2023-06-05 00:30:33,088] [INFO] Task started: HMMsearch
[2023-06-05 00:30:33,088] [INFO] Running command: hmmsearch --tblout GCA_004375765.1_ASM437576v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8651a853-d4d3-408e-8fae-b75f6a882431/dqc_reference/reference_markers.hmm GCA_004375765.1_ASM437576v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:30:33,404] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:30:33,406] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge24e42f9-26d3-46b7-bc01-76ea52028d9f/GCA_004375765.1_ASM437576v1_genomic.fna.gz]
[2023-06-05 00:30:33,427] [INFO] Query marker FASTA was written to GCA_004375765.1_ASM437576v1_genomic.fna/markers.fasta
[2023-06-05 00:30:33,428] [INFO] Task started: Blastn
[2023-06-05 00:30:33,428] [INFO] Running command: blastn -query GCA_004375765.1_ASM437576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8651a853-d4d3-408e-8fae-b75f6a882431/dqc_reference/reference_markers.fasta -out GCA_004375765.1_ASM437576v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:30:37,091] [INFO] Task succeeded: Blastn
[2023-06-05 00:30:37,095] [INFO] Selected 19 target genomes.
[2023-06-05 00:30:37,096] [INFO] Target genome list was writen to GCA_004375765.1_ASM437576v1_genomic.fna/target_genomes.txt
[2023-06-05 00:30:37,137] [INFO] Task started: fastANI
[2023-06-05 00:30:37,137] [INFO] Running command: fastANI --query /var/lib/cwl/stge24e42f9-26d3-46b7-bc01-76ea52028d9f/GCA_004375765.1_ASM437576v1_genomic.fna.gz --refList GCA_004375765.1_ASM437576v1_genomic.fna/target_genomes.txt --output GCA_004375765.1_ASM437576v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:30:48,179] [INFO] Task succeeded: fastANI
[2023-06-05 00:30:48,180] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8651a853-d4d3-408e-8fae-b75f6a882431/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:30:48,180] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8651a853-d4d3-408e-8fae-b75f6a882431/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:30:48,184] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:30:48,184] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 00:30:48,184] [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
--------------------------------------------------------------------------------
[2023-06-05 00:30:48,202] [INFO] DFAST Taxonomy check result was written to GCA_004375765.1_ASM437576v1_genomic.fna/tc_result.tsv
[2023-06-05 00:30:48,203] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:30:48,203] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:30:48,204] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8651a853-d4d3-408e-8fae-b75f6a882431/dqc_reference/checkm_data
[2023-06-05 00:30:48,209] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:30:48,225] [INFO] Task started: CheckM
[2023-06-05 00:30:48,226] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004375765.1_ASM437576v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004375765.1_ASM437576v1_genomic.fna/checkm_input GCA_004375765.1_ASM437576v1_genomic.fna/checkm_result
[2023-06-05 00:31:06,208] [INFO] Task succeeded: CheckM
[2023-06-05 00:31:06,209] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 11.40%
Strain heterogeneity: 5.56%
--------------------------------------------------------------------------------
[2023-06-05 00:31:06,235] [INFO] ===== Completeness check finished =====
[2023-06-05 00:31:06,235] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:31:06,236] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004375765.1_ASM437576v1_genomic.fna/markers.fasta)
[2023-06-05 00:31:06,236] [INFO] Task started: Blastn
[2023-06-05 00:31:06,236] [INFO] Running command: blastn -query GCA_004375765.1_ASM437576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8651a853-d4d3-408e-8fae-b75f6a882431/dqc_reference/reference_markers_gtdb.fasta -out GCA_004375765.1_ASM437576v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:31:06,993] [INFO] Task succeeded: Blastn
[2023-06-05 00:31:06,998] [INFO] Selected 20 target genomes.
[2023-06-05 00:31:06,998] [INFO] Target genome list was writen to GCA_004375765.1_ASM437576v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:31:07,262] [INFO] Task started: fastANI
[2023-06-05 00:31:07,262] [INFO] Running command: fastANI --query /var/lib/cwl/stge24e42f9-26d3-46b7-bc01-76ea52028d9f/GCA_004375765.1_ASM437576v1_genomic.fna.gz --refList GCA_004375765.1_ASM437576v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004375765.1_ASM437576v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:31:17,249] [INFO] Task succeeded: fastANI
[2023-06-05 00:31:17,256] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 00:31:17,256] [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
--------------------------------------------------------------------------------
[2023-06-05 00:31:17,259] [INFO] GTDB search result was written to GCA_004375765.1_ASM437576v1_genomic.fna/result_gtdb.tsv
[2023-06-05 00:31:17,259] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:31:17,262] [INFO] DFAST_QC result json was written to GCA_004375765.1_ASM437576v1_genomic.fna/dqc_result.json
[2023-06-05 00:31:17,262] [INFO] DFAST_QC completed!
[2023-06-05 00:31:17,262] [INFO] Total running time: 0h0m51s