[2023-06-05 05:15:12,146] [INFO] DFAST_QC pipeline started.
[2023-06-05 05:15:12,152] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 05:15:12,152] [INFO] DQC Reference Directory: /var/lib/cwl/stg41366916-5d64-4358-9c33-e199f997e031/dqc_reference
[2023-06-05 05:15:14,897] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 05:15:14,898] [INFO] Task started: Prodigal
[2023-06-05 05:15:14,898] [INFO] Running command: gunzip -c /var/lib/cwl/stg5abe052c-086d-4801-8d6a-38467ff64177/GCA_004282745.1_ASM428274v1_genomic.fna.gz | prodigal -d GCA_004282745.1_ASM428274v1_genomic.fna/cds.fna -a GCA_004282745.1_ASM428274v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 05:15:25,113] [INFO] Task succeeded: Prodigal
[2023-06-05 05:15:25,114] [INFO] Task started: HMMsearch
[2023-06-05 05:15:25,114] [INFO] Running command: hmmsearch --tblout GCA_004282745.1_ASM428274v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41366916-5d64-4358-9c33-e199f997e031/dqc_reference/reference_markers.hmm GCA_004282745.1_ASM428274v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 05:15:25,460] [INFO] Task succeeded: HMMsearch
[2023-06-05 05:15:25,461] [INFO] Found 6/6 markers.
[2023-06-05 05:15:25,501] [INFO] Query marker FASTA was written to GCA_004282745.1_ASM428274v1_genomic.fna/markers.fasta
[2023-06-05 05:15:25,502] [INFO] Task started: Blastn
[2023-06-05 05:15:25,502] [INFO] Running command: blastn -query GCA_004282745.1_ASM428274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41366916-5d64-4358-9c33-e199f997e031/dqc_reference/reference_markers.fasta -out GCA_004282745.1_ASM428274v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:15:26,076] [INFO] Task succeeded: Blastn
[2023-06-05 05:15:26,080] [INFO] Selected 11 target genomes.
[2023-06-05 05:15:26,081] [INFO] Target genome list was writen to GCA_004282745.1_ASM428274v1_genomic.fna/target_genomes.txt
[2023-06-05 05:15:26,085] [INFO] Task started: fastANI
[2023-06-05 05:15:26,085] [INFO] Running command: fastANI --query /var/lib/cwl/stg5abe052c-086d-4801-8d6a-38467ff64177/GCA_004282745.1_ASM428274v1_genomic.fna.gz --refList GCA_004282745.1_ASM428274v1_genomic.fna/target_genomes.txt --output GCA_004282745.1_ASM428274v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 05:15:33,695] [INFO] Task succeeded: fastANI
[2023-06-05 05:15:33,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41366916-5d64-4358-9c33-e199f997e031/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 05:15:33,696] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41366916-5d64-4358-9c33-e199f997e031/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 05:15:33,697] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 05:15:33,697] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 05:15:33,698] [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 05:15:33,699] [INFO] DFAST Taxonomy check result was written to GCA_004282745.1_ASM428274v1_genomic.fna/tc_result.tsv
[2023-06-05 05:15:33,700] [INFO] ===== Taxonomy check completed =====
[2023-06-05 05:15:33,700] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 05:15:33,700] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41366916-5d64-4358-9c33-e199f997e031/dqc_reference/checkm_data
[2023-06-05 05:15:33,705] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 05:15:33,772] [INFO] Task started: CheckM
[2023-06-05 05:15:33,772] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004282745.1_ASM428274v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004282745.1_ASM428274v1_genomic.fna/checkm_input GCA_004282745.1_ASM428274v1_genomic.fna/checkm_result
[2023-06-05 05:16:09,424] [INFO] Task succeeded: CheckM
[2023-06-05 05:16:09,426] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 05:16:09,449] [INFO] ===== Completeness check finished =====
[2023-06-05 05:16:09,449] [INFO] ===== Start GTDB Search =====
[2023-06-05 05:16:09,450] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004282745.1_ASM428274v1_genomic.fna/markers.fasta)
[2023-06-05 05:16:09,450] [INFO] Task started: Blastn
[2023-06-05 05:16:09,450] [INFO] Running command: blastn -query GCA_004282745.1_ASM428274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41366916-5d64-4358-9c33-e199f997e031/dqc_reference/reference_markers_gtdb.fasta -out GCA_004282745.1_ASM428274v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:16:10,182] [INFO] Task succeeded: Blastn
[2023-06-05 05:16:10,187] [INFO] Selected 16 target genomes.
[2023-06-05 05:16:10,187] [INFO] Target genome list was writen to GCA_004282745.1_ASM428274v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 05:16:10,200] [INFO] Task started: fastANI
[2023-06-05 05:16:10,200] [INFO] Running command: fastANI --query /var/lib/cwl/stg5abe052c-086d-4801-8d6a-38467ff64177/GCA_004282745.1_ASM428274v1_genomic.fna.gz --refList GCA_004282745.1_ASM428274v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004282745.1_ASM428274v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 05:16:20,296] [INFO] Task succeeded: fastANI
[2023-06-05 05:16:20,302] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 05:16:20,303] [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_004282745.1	s__SCAELEC01 sp004282745	100.0	1476	1480	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Scalinduaceae;g__SCAELEC01	95.0	99.99	99.98	0.99	0.99	4	conclusive
GCA_017368835.1	s__Scalindua_A sediminis	76.6964	78	1480	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Scalinduaceae;g__Scalindua_A	95.0	99.30	98.63	0.78	0.60	3	-
--------------------------------------------------------------------------------
[2023-06-05 05:16:20,305] [INFO] GTDB search result was written to GCA_004282745.1_ASM428274v1_genomic.fna/result_gtdb.tsv
[2023-06-05 05:16:20,305] [INFO] ===== GTDB Search completed =====
[2023-06-05 05:16:20,308] [INFO] DFAST_QC result json was written to GCA_004282745.1_ASM428274v1_genomic.fna/dqc_result.json
[2023-06-05 05:16:20,309] [INFO] DFAST_QC completed!
[2023-06-05 05:16:20,309] [INFO] Total running time: 0h1m8s