[2023-06-28 11:30:30,253] [INFO] DFAST_QC pipeline started.
[2023-06-28 11:30:30,255] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 11:30:30,255] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e408b07-3445-4024-9418-51ad92fb7566/dqc_reference
[2023-06-28 11:30:31,460] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 11:30:31,461] [INFO] Task started: Prodigal
[2023-06-28 11:30:31,461] [INFO] Running command: gunzip -c /var/lib/cwl/stg50338de3-9cf8-4479-8db7-5c9b263f079a/GCA_020052025.1_ASM2005202v1_genomic.fna.gz | prodigal -d GCA_020052025.1_ASM2005202v1_genomic.fna/cds.fna -a GCA_020052025.1_ASM2005202v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 11:30:32,713] [INFO] Task succeeded: Prodigal
[2023-06-28 11:30:32,713] [INFO] Task started: HMMsearch
[2023-06-28 11:30:32,713] [INFO] Running command: hmmsearch --tblout GCA_020052025.1_ASM2005202v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e408b07-3445-4024-9418-51ad92fb7566/dqc_reference/reference_markers.hmm GCA_020052025.1_ASM2005202v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 11:30:32,829] [INFO] Task succeeded: HMMsearch
[2023-06-28 11:30:32,830] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg50338de3-9cf8-4479-8db7-5c9b263f079a/GCA_020052025.1_ASM2005202v1_genomic.fna.gz]
[2023-06-28 11:30:32,841] [INFO] Query marker FASTA was written to GCA_020052025.1_ASM2005202v1_genomic.fna/markers.fasta
[2023-06-28 11:30:32,841] [INFO] Task started: Blastn
[2023-06-28 11:30:32,841] [INFO] Running command: blastn -query GCA_020052025.1_ASM2005202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e408b07-3445-4024-9418-51ad92fb7566/dqc_reference/reference_markers.fasta -out GCA_020052025.1_ASM2005202v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:30:33,338] [INFO] Task succeeded: Blastn
[2023-06-28 11:30:33,342] [INFO] Selected 9 target genomes.
[2023-06-28 11:30:33,342] [INFO] Target genome list was writen to GCA_020052025.1_ASM2005202v1_genomic.fna/target_genomes.txt
[2023-06-28 11:30:33,343] [INFO] Task started: fastANI
[2023-06-28 11:30:33,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg50338de3-9cf8-4479-8db7-5c9b263f079a/GCA_020052025.1_ASM2005202v1_genomic.fna.gz --refList GCA_020052025.1_ASM2005202v1_genomic.fna/target_genomes.txt --output GCA_020052025.1_ASM2005202v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 11:30:39,584] [INFO] Task succeeded: fastANI
[2023-06-28 11:30:39,585] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e408b07-3445-4024-9418-51ad92fb7566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 11:30:39,585] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e408b07-3445-4024-9418-51ad92fb7566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 11:30:39,586] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 11:30:39,586] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 11:30:39,587] [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
--------------------------------------------------------------------------------
[2023-06-28 11:30:39,588] [INFO] DFAST Taxonomy check result was written to GCA_020052025.1_ASM2005202v1_genomic.fna/tc_result.tsv
[2023-06-28 11:30:39,589] [INFO] ===== Taxonomy check completed =====
[2023-06-28 11:30:39,589] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 11:30:39,589] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e408b07-3445-4024-9418-51ad92fb7566/dqc_reference/checkm_data
[2023-06-28 11:30:39,591] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 11:30:39,601] [INFO] Task started: CheckM
[2023-06-28 11:30:39,601] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020052025.1_ASM2005202v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020052025.1_ASM2005202v1_genomic.fna/checkm_input GCA_020052025.1_ASM2005202v1_genomic.fna/checkm_result
[2023-06-28 11:30:51,042] [INFO] Task succeeded: CheckM
[2023-06-28 11:30:51,043] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 42.65%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 11:30:51,060] [INFO] ===== Completeness check finished =====
[2023-06-28 11:30:51,060] [INFO] ===== Start GTDB Search =====
[2023-06-28 11:30:51,060] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020052025.1_ASM2005202v1_genomic.fna/markers.fasta)
[2023-06-28 11:30:51,061] [INFO] Task started: Blastn
[2023-06-28 11:30:51,061] [INFO] Running command: blastn -query GCA_020052025.1_ASM2005202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e408b07-3445-4024-9418-51ad92fb7566/dqc_reference/reference_markers_gtdb.fasta -out GCA_020052025.1_ASM2005202v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:30:51,627] [INFO] Task succeeded: Blastn
[2023-06-28 11:30:51,630] [INFO] Selected 9 target genomes.
[2023-06-28 11:30:51,630] [INFO] Target genome list was writen to GCA_020052025.1_ASM2005202v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 11:30:51,634] [INFO] Task started: fastANI
[2023-06-28 11:30:51,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg50338de3-9cf8-4479-8db7-5c9b263f079a/GCA_020052025.1_ASM2005202v1_genomic.fna.gz --refList GCA_020052025.1_ASM2005202v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020052025.1_ASM2005202v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 11:30:55,590] [INFO] Task succeeded: fastANI
[2023-06-28 11:30:55,595] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 11:30:55,595] [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_016208205.1	s__CG2-30-40-21 sp016208205	86.0051	102	143	d__Bacteria;p__UBA9089;c__CG2-30-40-21;o__CG2-30-40-21;f__CG2-30-40-21;g__CG2-30-40-21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018814245.1	s__CG2-30-40-21 sp018814245	83.1557	112	143	d__Bacteria;p__UBA9089;c__CG2-30-40-21;o__CG2-30-40-21;f__CG2-30-40-21;g__CG2-30-40-21	95.0	99.54	99.54	0.86	0.86	2	-
GCA_001873945.1	s__CG2-30-40-21 sp001873945	80.5546	107	143	d__Bacteria;p__UBA9089;c__CG2-30-40-21;o__CG2-30-40-21;f__CG2-30-40-21;g__CG2-30-40-21	95.0	99.45	99.27	0.82	0.80	5	-
--------------------------------------------------------------------------------
[2023-06-28 11:30:55,597] [INFO] GTDB search result was written to GCA_020052025.1_ASM2005202v1_genomic.fna/result_gtdb.tsv
[2023-06-28 11:30:55,597] [INFO] ===== GTDB Search completed =====
[2023-06-28 11:30:55,600] [INFO] DFAST_QC result json was written to GCA_020052025.1_ASM2005202v1_genomic.fna/dqc_result.json
[2023-06-28 11:30:55,600] [INFO] DFAST_QC completed!
[2023-06-28 11:30:55,600] [INFO] Total running time: 0h0m25s