[2023-06-30 22:42:37,921] [INFO] DFAST_QC pipeline started.
[2023-06-30 22:42:37,927] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 22:42:37,928] [INFO] DQC Reference Directory: /var/lib/cwl/stg01c5124d-6cdd-494e-9922-0ed3910c1b2c/dqc_reference
[2023-06-30 22:42:39,443] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 22:42:39,444] [INFO] Task started: Prodigal
[2023-06-30 22:42:39,444] [INFO] Running command: gunzip -c /var/lib/cwl/stg5fd2a732-6c35-4c4a-afdc-8cfe9830f114/GCA_024275535.1_ASM2427553v1_genomic.fna.gz | prodigal -d GCA_024275535.1_ASM2427553v1_genomic.fna/cds.fna -a GCA_024275535.1_ASM2427553v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 22:42:46,416] [INFO] Task succeeded: Prodigal
[2023-06-30 22:42:46,416] [INFO] Task started: HMMsearch
[2023-06-30 22:42:46,416] [INFO] Running command: hmmsearch --tblout GCA_024275535.1_ASM2427553v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01c5124d-6cdd-494e-9922-0ed3910c1b2c/dqc_reference/reference_markers.hmm GCA_024275535.1_ASM2427553v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 22:42:46,685] [INFO] Task succeeded: HMMsearch
[2023-06-30 22:42:46,686] [INFO] Found 6/6 markers.
[2023-06-30 22:42:46,719] [INFO] Query marker FASTA was written to GCA_024275535.1_ASM2427553v1_genomic.fna/markers.fasta
[2023-06-30 22:42:46,720] [INFO] Task started: Blastn
[2023-06-30 22:42:46,720] [INFO] Running command: blastn -query GCA_024275535.1_ASM2427553v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01c5124d-6cdd-494e-9922-0ed3910c1b2c/dqc_reference/reference_markers.fasta -out GCA_024275535.1_ASM2427553v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:42:47,286] [INFO] Task succeeded: Blastn
[2023-06-30 22:42:47,290] [INFO] Selected 23 target genomes.
[2023-06-30 22:42:47,291] [INFO] Target genome list was writen to GCA_024275535.1_ASM2427553v1_genomic.fna/target_genomes.txt
[2023-06-30 22:42:47,294] [INFO] Task started: fastANI
[2023-06-30 22:42:47,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fd2a732-6c35-4c4a-afdc-8cfe9830f114/GCA_024275535.1_ASM2427553v1_genomic.fna.gz --refList GCA_024275535.1_ASM2427553v1_genomic.fna/target_genomes.txt --output GCA_024275535.1_ASM2427553v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 22:42:59,833] [INFO] Task succeeded: fastANI
[2023-06-30 22:42:59,833] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01c5124d-6cdd-494e-9922-0ed3910c1b2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 22:42:59,834] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01c5124d-6cdd-494e-9922-0ed3910c1b2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 22:42:59,835] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 22:42:59,835] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 22:42:59,836] [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
--------------------------------------------------------------------------------
[2023-06-30 22:42:59,838] [INFO] DFAST Taxonomy check result was written to GCA_024275535.1_ASM2427553v1_genomic.fna/tc_result.tsv
[2023-06-30 22:42:59,838] [INFO] ===== Taxonomy check completed =====
[2023-06-30 22:42:59,838] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 22:42:59,839] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01c5124d-6cdd-494e-9922-0ed3910c1b2c/dqc_reference/checkm_data
[2023-06-30 22:42:59,841] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 22:42:59,881] [INFO] Task started: CheckM
[2023-06-30 22:42:59,881] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024275535.1_ASM2427553v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024275535.1_ASM2427553v1_genomic.fna/checkm_input GCA_024275535.1_ASM2427553v1_genomic.fna/checkm_result
[2023-06-30 22:43:27,477] [INFO] Task succeeded: CheckM
[2023-06-30 22:43:27,478] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 17.13%
Strain heterogeneity: 35.29%
--------------------------------------------------------------------------------
[2023-06-30 22:43:27,508] [INFO] ===== Completeness check finished =====
[2023-06-30 22:43:27,509] [INFO] ===== Start GTDB Search =====
[2023-06-30 22:43:27,509] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024275535.1_ASM2427553v1_genomic.fna/markers.fasta)
[2023-06-30 22:43:27,509] [INFO] Task started: Blastn
[2023-06-30 22:43:27,510] [INFO] Running command: blastn -query GCA_024275535.1_ASM2427553v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01c5124d-6cdd-494e-9922-0ed3910c1b2c/dqc_reference/reference_markers_gtdb.fasta -out GCA_024275535.1_ASM2427553v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:43:28,311] [INFO] Task succeeded: Blastn
[2023-06-30 22:43:28,316] [INFO] Selected 30 target genomes.
[2023-06-30 22:43:28,317] [INFO] Target genome list was writen to GCA_024275535.1_ASM2427553v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 22:43:28,334] [INFO] Task started: fastANI
[2023-06-30 22:43:28,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fd2a732-6c35-4c4a-afdc-8cfe9830f114/GCA_024275535.1_ASM2427553v1_genomic.fna.gz --refList GCA_024275535.1_ASM2427553v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024275535.1_ASM2427553v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 22:43:45,695] [INFO] Task succeeded: fastANI
[2023-06-30 22:43:45,700] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 22:43:45,700] [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_011369465.1	s__DRQG01 sp011369465	77.7502	301	918	d__Bacteria;p__Calditrichota;c__Calditrichia;o__Calditrichales;f__Calditrichaceae;g__DRQG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 22:43:45,703] [INFO] GTDB search result was written to GCA_024275535.1_ASM2427553v1_genomic.fna/result_gtdb.tsv
[2023-06-30 22:43:45,703] [INFO] ===== GTDB Search completed =====
[2023-06-30 22:43:45,705] [INFO] DFAST_QC result json was written to GCA_024275535.1_ASM2427553v1_genomic.fna/dqc_result.json
[2023-06-30 22:43:45,706] [INFO] DFAST_QC completed!
[2023-06-30 22:43:45,706] [INFO] Total running time: 0h1m8s