[2023-06-18 18:10:13,124] [INFO] DFAST_QC pipeline started.
[2023-06-18 18:10:13,126] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 18:10:13,126] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf4b993b-7833-4b66-aafd-eac7d340ac0e/dqc_reference
[2023-06-18 18:10:15,132] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 18:10:15,133] [INFO] Task started: Prodigal
[2023-06-18 18:10:15,133] [INFO] Running command: gunzip -c /var/lib/cwl/stge4a55482-d0f6-4009-be85-cbdec8281c93/GCA_013334735.1_ASM1333473v1_genomic.fna.gz | prodigal -d GCA_013334735.1_ASM1333473v1_genomic.fna/cds.fna -a GCA_013334735.1_ASM1333473v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 18:10:27,324] [INFO] Task succeeded: Prodigal
[2023-06-18 18:10:27,325] [INFO] Task started: HMMsearch
[2023-06-18 18:10:27,325] [INFO] Running command: hmmsearch --tblout GCA_013334735.1_ASM1333473v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf4b993b-7833-4b66-aafd-eac7d340ac0e/dqc_reference/reference_markers.hmm GCA_013334735.1_ASM1333473v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 18:10:27,583] [INFO] Task succeeded: HMMsearch
[2023-06-18 18:10:27,585] [INFO] Found 6/6 markers.
[2023-06-18 18:10:27,626] [INFO] Query marker FASTA was written to GCA_013334735.1_ASM1333473v1_genomic.fna/markers.fasta
[2023-06-18 18:10:27,626] [INFO] Task started: Blastn
[2023-06-18 18:10:27,626] [INFO] Running command: blastn -query GCA_013334735.1_ASM1333473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf4b993b-7833-4b66-aafd-eac7d340ac0e/dqc_reference/reference_markers.fasta -out GCA_013334735.1_ASM1333473v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:10:28,239] [INFO] Task succeeded: Blastn
[2023-06-18 18:10:28,244] [INFO] Selected 34 target genomes.
[2023-06-18 18:10:28,245] [INFO] Target genome list was writen to GCA_013334735.1_ASM1333473v1_genomic.fna/target_genomes.txt
[2023-06-18 18:10:28,274] [INFO] Task started: fastANI
[2023-06-18 18:10:28,274] [INFO] Running command: fastANI --query /var/lib/cwl/stge4a55482-d0f6-4009-be85-cbdec8281c93/GCA_013334735.1_ASM1333473v1_genomic.fna.gz --refList GCA_013334735.1_ASM1333473v1_genomic.fna/target_genomes.txt --output GCA_013334735.1_ASM1333473v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 18:10:47,866] [INFO] Task succeeded: fastANI
[2023-06-18 18:10:47,866] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf4b993b-7833-4b66-aafd-eac7d340ac0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 18:10:47,867] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf4b993b-7833-4b66-aafd-eac7d340ac0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 18:10:47,869] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 18:10:47,869] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 18:10:47,870] [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
--------------------------------------------------------------------------------
[2023-06-18 18:10:47,872] [INFO] DFAST Taxonomy check result was written to GCA_013334735.1_ASM1333473v1_genomic.fna/tc_result.tsv
[2023-06-18 18:10:47,873] [INFO] ===== Taxonomy check completed =====
[2023-06-18 18:10:47,874] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 18:10:47,874] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf4b993b-7833-4b66-aafd-eac7d340ac0e/dqc_reference/checkm_data
[2023-06-18 18:10:47,879] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 18:10:47,922] [INFO] Task started: CheckM
[2023-06-18 18:10:47,923] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013334735.1_ASM1333473v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013334735.1_ASM1333473v1_genomic.fna/checkm_input GCA_013334735.1_ASM1333473v1_genomic.fna/checkm_result
[2023-06-18 18:11:27,017] [INFO] Task succeeded: CheckM
[2023-06-18 18:11:27,019] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.62%
Contamintation: 5.07%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 18:11:27,049] [INFO] ===== Completeness check finished =====
[2023-06-18 18:11:27,050] [INFO] ===== Start GTDB Search =====
[2023-06-18 18:11:27,050] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013334735.1_ASM1333473v1_genomic.fna/markers.fasta)
[2023-06-18 18:11:27,051] [INFO] Task started: Blastn
[2023-06-18 18:11:27,051] [INFO] Running command: blastn -query GCA_013334735.1_ASM1333473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf4b993b-7833-4b66-aafd-eac7d340ac0e/dqc_reference/reference_markers_gtdb.fasta -out GCA_013334735.1_ASM1333473v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:11:27,858] [INFO] Task succeeded: Blastn
[2023-06-18 18:11:27,868] [INFO] Selected 23 target genomes.
[2023-06-18 18:11:27,869] [INFO] Target genome list was writen to GCA_013334735.1_ASM1333473v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 18:11:27,882] [INFO] Task started: fastANI
[2023-06-18 18:11:27,883] [INFO] Running command: fastANI --query /var/lib/cwl/stge4a55482-d0f6-4009-be85-cbdec8281c93/GCA_013334735.1_ASM1333473v1_genomic.fna.gz --refList GCA_013334735.1_ASM1333473v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013334735.1_ASM1333473v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 18:11:42,614] [INFO] Task succeeded: fastANI
[2023-06-18 18:11:42,621] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 18:11:42,622] [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_013334735.1	s__CAINEZ01 sp013334735	100.0	844	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__CG2-30-32-10;g__CAINEZ01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903847905.1	s__CAINEZ01 sp903847905	76.6642	131	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__CG2-30-32-10;g__CAINEZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903889915.1	s__CAINEZ01 sp903889915	76.3586	67	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__CG2-30-32-10;g__CAINEZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 18:11:42,624] [INFO] GTDB search result was written to GCA_013334735.1_ASM1333473v1_genomic.fna/result_gtdb.tsv
[2023-06-18 18:11:42,624] [INFO] ===== GTDB Search completed =====
[2023-06-18 18:11:42,627] [INFO] DFAST_QC result json was written to GCA_013334735.1_ASM1333473v1_genomic.fna/dqc_result.json
[2023-06-18 18:11:42,627] [INFO] DFAST_QC completed!
[2023-06-18 18:11:42,627] [INFO] Total running time: 0h1m30s