[2023-06-29 09:19:47,064] [INFO] DFAST_QC pipeline started.
[2023-06-29 09:19:47,067] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 09:19:47,067] [INFO] DQC Reference Directory: /var/lib/cwl/stgcee407c1-3885-4673-9be3-3d299a3afe6a/dqc_reference
[2023-06-29 09:19:48,352] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 09:19:48,353] [INFO] Task started: Prodigal
[2023-06-29 09:19:48,353] [INFO] Running command: gunzip -c /var/lib/cwl/stg166e0446-bfc3-45d5-882e-84045b6bca4c/GCA_020052415.1_ASM2005241v1_genomic.fna.gz | prodigal -d GCA_020052415.1_ASM2005241v1_genomic.fna/cds.fna -a GCA_020052415.1_ASM2005241v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 09:20:07,366] [INFO] Task succeeded: Prodigal
[2023-06-29 09:20:07,366] [INFO] Task started: HMMsearch
[2023-06-29 09:20:07,367] [INFO] Running command: hmmsearch --tblout GCA_020052415.1_ASM2005241v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcee407c1-3885-4673-9be3-3d299a3afe6a/dqc_reference/reference_markers.hmm GCA_020052415.1_ASM2005241v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 09:20:07,731] [INFO] Task succeeded: HMMsearch
[2023-06-29 09:20:07,733] [INFO] Found 6/6 markers.
[2023-06-29 09:20:07,775] [INFO] Query marker FASTA was written to GCA_020052415.1_ASM2005241v1_genomic.fna/markers.fasta
[2023-06-29 09:20:07,776] [INFO] Task started: Blastn
[2023-06-29 09:20:07,776] [INFO] Running command: blastn -query GCA_020052415.1_ASM2005241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcee407c1-3885-4673-9be3-3d299a3afe6a/dqc_reference/reference_markers.fasta -out GCA_020052415.1_ASM2005241v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:20:08,379] [INFO] Task succeeded: Blastn
[2023-06-29 09:20:08,388] [INFO] Selected 30 target genomes.
[2023-06-29 09:20:08,389] [INFO] Target genome list was writen to GCA_020052415.1_ASM2005241v1_genomic.fna/target_genomes.txt
[2023-06-29 09:20:08,395] [INFO] Task started: fastANI
[2023-06-29 09:20:08,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg166e0446-bfc3-45d5-882e-84045b6bca4c/GCA_020052415.1_ASM2005241v1_genomic.fna.gz --refList GCA_020052415.1_ASM2005241v1_genomic.fna/target_genomes.txt --output GCA_020052415.1_ASM2005241v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 09:20:29,529] [INFO] Task succeeded: fastANI
[2023-06-29 09:20:29,530] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcee407c1-3885-4673-9be3-3d299a3afe6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 09:20:29,530] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcee407c1-3885-4673-9be3-3d299a3afe6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 09:20:29,532] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 09:20:29,533] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 09:20:29,533] [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
--------------------------------------------------------------------------------
[2023-06-29 09:20:29,535] [INFO] DFAST Taxonomy check result was written to GCA_020052415.1_ASM2005241v1_genomic.fna/tc_result.tsv
[2023-06-29 09:20:29,536] [INFO] ===== Taxonomy check completed =====
[2023-06-29 09:20:29,536] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 09:20:29,537] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcee407c1-3885-4673-9be3-3d299a3afe6a/dqc_reference/checkm_data
[2023-06-29 09:20:29,541] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 09:20:29,590] [INFO] Task started: CheckM
[2023-06-29 09:20:29,591] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020052415.1_ASM2005241v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020052415.1_ASM2005241v1_genomic.fna/checkm_input GCA_020052415.1_ASM2005241v1_genomic.fna/checkm_result
[2023-06-29 09:21:26,749] [INFO] Task succeeded: CheckM
[2023-06-29 09:21:26,751] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 09:21:26,787] [INFO] ===== Completeness check finished =====
[2023-06-29 09:21:26,787] [INFO] ===== Start GTDB Search =====
[2023-06-29 09:21:26,787] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020052415.1_ASM2005241v1_genomic.fna/markers.fasta)
[2023-06-29 09:21:26,788] [INFO] Task started: Blastn
[2023-06-29 09:21:26,788] [INFO] Running command: blastn -query GCA_020052415.1_ASM2005241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcee407c1-3885-4673-9be3-3d299a3afe6a/dqc_reference/reference_markers_gtdb.fasta -out GCA_020052415.1_ASM2005241v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:21:27,560] [INFO] Task succeeded: Blastn
[2023-06-29 09:21:27,565] [INFO] Selected 33 target genomes.
[2023-06-29 09:21:27,565] [INFO] Target genome list was writen to GCA_020052415.1_ASM2005241v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 09:21:27,580] [INFO] Task started: fastANI
[2023-06-29 09:21:27,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg166e0446-bfc3-45d5-882e-84045b6bca4c/GCA_020052415.1_ASM2005241v1_genomic.fna.gz --refList GCA_020052415.1_ASM2005241v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020052415.1_ASM2005241v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 09:21:47,774] [INFO] Task succeeded: fastANI
[2023-06-29 09:21:47,779] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 09:21:47,779] [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_016783885.1	s__JAADJA01 sp016783885	75.7636	90	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__JAADJA01;g__JAADJA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903944895.1	s__CAJATL01 sp903944895	75.221	52	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__4484-276;g__CAJATL01	95.0	99.79	99.79	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-06-29 09:21:47,781] [INFO] GTDB search result was written to GCA_020052415.1_ASM2005241v1_genomic.fna/result_gtdb.tsv
[2023-06-29 09:21:47,782] [INFO] ===== GTDB Search completed =====
[2023-06-29 09:21:47,784] [INFO] DFAST_QC result json was written to GCA_020052415.1_ASM2005241v1_genomic.fna/dqc_result.json
[2023-06-29 09:21:47,785] [INFO] DFAST_QC completed!
[2023-06-29 09:21:47,785] [INFO] Total running time: 0h2m1s