[2023-06-30 11:59:43,428] [INFO] DFAST_QC pipeline started.
[2023-06-30 11:59:43,430] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 11:59:43,430] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f9bf8ee-edd0-47cd-95a4-3f3468515072/dqc_reference
[2023-06-30 11:59:44,698] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 11:59:44,699] [INFO] Task started: Prodigal
[2023-06-30 11:59:44,699] [INFO] Running command: gunzip -c /var/lib/cwl/stg17ba01e9-a945-4bae-a3c9-b58288669088/GCA_024402995.1_ASM2440299v1_genomic.fna.gz | prodigal -d GCA_024402995.1_ASM2440299v1_genomic.fna/cds.fna -a GCA_024402995.1_ASM2440299v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 11:59:48,345] [INFO] Task succeeded: Prodigal
[2023-06-30 11:59:48,346] [INFO] Task started: HMMsearch
[2023-06-30 11:59:48,346] [INFO] Running command: hmmsearch --tblout GCA_024402995.1_ASM2440299v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f9bf8ee-edd0-47cd-95a4-3f3468515072/dqc_reference/reference_markers.hmm GCA_024402995.1_ASM2440299v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 11:59:48,579] [INFO] Task succeeded: HMMsearch
[2023-06-30 11:59:48,581] [INFO] Found 6/6 markers.
[2023-06-30 11:59:48,605] [INFO] Query marker FASTA was written to GCA_024402995.1_ASM2440299v1_genomic.fna/markers.fasta
[2023-06-30 11:59:48,605] [INFO] Task started: Blastn
[2023-06-30 11:59:48,605] [INFO] Running command: blastn -query GCA_024402995.1_ASM2440299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f9bf8ee-edd0-47cd-95a4-3f3468515072/dqc_reference/reference_markers.fasta -out GCA_024402995.1_ASM2440299v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:59:49,185] [INFO] Task succeeded: Blastn
[2023-06-30 11:59:49,191] [INFO] Selected 14 target genomes.
[2023-06-30 11:59:49,191] [INFO] Target genome list was writen to GCA_024402995.1_ASM2440299v1_genomic.fna/target_genomes.txt
[2023-06-30 11:59:49,194] [INFO] Task started: fastANI
[2023-06-30 11:59:49,194] [INFO] Running command: fastANI --query /var/lib/cwl/stg17ba01e9-a945-4bae-a3c9-b58288669088/GCA_024402995.1_ASM2440299v1_genomic.fna.gz --refList GCA_024402995.1_ASM2440299v1_genomic.fna/target_genomes.txt --output GCA_024402995.1_ASM2440299v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 11:59:57,494] [INFO] Task succeeded: fastANI
[2023-06-30 11:59:57,495] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f9bf8ee-edd0-47cd-95a4-3f3468515072/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 11:59:57,495] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f9bf8ee-edd0-47cd-95a4-3f3468515072/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 11:59:57,497] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 11:59:57,498] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 11:59:57,498] [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 11:59:57,500] [INFO] DFAST Taxonomy check result was written to GCA_024402995.1_ASM2440299v1_genomic.fna/tc_result.tsv
[2023-06-30 11:59:57,501] [INFO] ===== Taxonomy check completed =====
[2023-06-30 11:59:57,501] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 11:59:57,502] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f9bf8ee-edd0-47cd-95a4-3f3468515072/dqc_reference/checkm_data
[2023-06-30 11:59:57,505] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 11:59:57,527] [INFO] Task started: CheckM
[2023-06-30 11:59:57,527] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024402995.1_ASM2440299v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024402995.1_ASM2440299v1_genomic.fna/checkm_input GCA_024402995.1_ASM2440299v1_genomic.fna/checkm_result
[2023-06-30 12:00:16,199] [INFO] Task succeeded: CheckM
[2023-06-30 12:00:16,201] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 12:00:16,220] [INFO] ===== Completeness check finished =====
[2023-06-30 12:00:16,220] [INFO] ===== Start GTDB Search =====
[2023-06-30 12:00:16,221] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024402995.1_ASM2440299v1_genomic.fna/markers.fasta)
[2023-06-30 12:00:16,221] [INFO] Task started: Blastn
[2023-06-30 12:00:16,221] [INFO] Running command: blastn -query GCA_024402995.1_ASM2440299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f9bf8ee-edd0-47cd-95a4-3f3468515072/dqc_reference/reference_markers_gtdb.fasta -out GCA_024402995.1_ASM2440299v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:00:17,087] [INFO] Task succeeded: Blastn
[2023-06-30 12:00:17,092] [INFO] Selected 23 target genomes.
[2023-06-30 12:00:17,092] [INFO] Target genome list was writen to GCA_024402995.1_ASM2440299v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 12:00:17,105] [INFO] Task started: fastANI
[2023-06-30 12:00:17,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg17ba01e9-a945-4bae-a3c9-b58288669088/GCA_024402995.1_ASM2440299v1_genomic.fna.gz --refList GCA_024402995.1_ASM2440299v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024402995.1_ASM2440299v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 12:00:25,528] [INFO] Task succeeded: fastANI
[2023-06-30 12:00:25,535] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 12:00:25,535] [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_902773665.1	s__RUG11894 sp902773665	77.6472	61	513	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG11894	95.0	97.59	96.15	0.91	0.88	4	-
GCA_017626845.1	s__RUG11894 sp017626845	77.4436	60	513	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG11894	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 12:00:25,538] [INFO] GTDB search result was written to GCA_024402995.1_ASM2440299v1_genomic.fna/result_gtdb.tsv
[2023-06-30 12:00:25,539] [INFO] ===== GTDB Search completed =====
[2023-06-30 12:00:25,544] [INFO] DFAST_QC result json was written to GCA_024402995.1_ASM2440299v1_genomic.fna/dqc_result.json
[2023-06-30 12:00:25,544] [INFO] DFAST_QC completed!
[2023-06-30 12:00:25,544] [INFO] Total running time: 0h0m42s