[2023-06-30 06:33:11,976] [INFO] DFAST_QC pipeline started.
[2023-06-30 06:33:12,003] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 06:33:12,003] [INFO] DQC Reference Directory: /var/lib/cwl/stg722a7796-d4de-42a3-a90f-d932a2cf5d18/dqc_reference
[2023-06-30 06:33:13,314] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 06:33:13,316] [INFO] Task started: Prodigal
[2023-06-30 06:33:13,317] [INFO] Running command: gunzip -c /var/lib/cwl/stg96475d4c-ce0a-4048-8cce-4e1f64e57801/GCA_016293975.1_ASM1629397v1_genomic.fna.gz | prodigal -d GCA_016293975.1_ASM1629397v1_genomic.fna/cds.fna -a GCA_016293975.1_ASM1629397v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 06:33:17,434] [INFO] Task succeeded: Prodigal
[2023-06-30 06:33:17,434] [INFO] Task started: HMMsearch
[2023-06-30 06:33:17,435] [INFO] Running command: hmmsearch --tblout GCA_016293975.1_ASM1629397v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg722a7796-d4de-42a3-a90f-d932a2cf5d18/dqc_reference/reference_markers.hmm GCA_016293975.1_ASM1629397v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 06:33:17,699] [INFO] Task succeeded: HMMsearch
[2023-06-30 06:33:17,700] [INFO] Found 6/6 markers.
[2023-06-30 06:33:17,731] [INFO] Query marker FASTA was written to GCA_016293975.1_ASM1629397v1_genomic.fna/markers.fasta
[2023-06-30 06:33:17,732] [INFO] Task started: Blastn
[2023-06-30 06:33:17,732] [INFO] Running command: blastn -query GCA_016293975.1_ASM1629397v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg722a7796-d4de-42a3-a90f-d932a2cf5d18/dqc_reference/reference_markers.fasta -out GCA_016293975.1_ASM1629397v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:33:18,339] [INFO] Task succeeded: Blastn
[2023-06-30 06:33:18,343] [INFO] Selected 23 target genomes.
[2023-06-30 06:33:18,343] [INFO] Target genome list was writen to GCA_016293975.1_ASM1629397v1_genomic.fna/target_genomes.txt
[2023-06-30 06:33:18,348] [INFO] Task started: fastANI
[2023-06-30 06:33:18,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg96475d4c-ce0a-4048-8cce-4e1f64e57801/GCA_016293975.1_ASM1629397v1_genomic.fna.gz --refList GCA_016293975.1_ASM1629397v1_genomic.fna/target_genomes.txt --output GCA_016293975.1_ASM1629397v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 06:33:32,118] [INFO] Task succeeded: fastANI
[2023-06-30 06:33:32,118] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg722a7796-d4de-42a3-a90f-d932a2cf5d18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 06:33:32,118] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg722a7796-d4de-42a3-a90f-d932a2cf5d18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 06:33:32,120] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 06:33:32,120] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 06:33:32,120] [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 06:33:32,122] [INFO] DFAST Taxonomy check result was written to GCA_016293975.1_ASM1629397v1_genomic.fna/tc_result.tsv
[2023-06-30 06:33:32,123] [INFO] ===== Taxonomy check completed =====
[2023-06-30 06:33:32,123] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 06:33:32,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg722a7796-d4de-42a3-a90f-d932a2cf5d18/dqc_reference/checkm_data
[2023-06-30 06:33:32,127] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 06:33:32,148] [INFO] Task started: CheckM
[2023-06-30 06:33:32,149] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016293975.1_ASM1629397v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016293975.1_ASM1629397v1_genomic.fna/checkm_input GCA_016293975.1_ASM1629397v1_genomic.fna/checkm_result
[2023-06-30 06:33:51,886] [INFO] Task succeeded: CheckM
[2023-06-30 06:33:51,888] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 06:33:51,923] [INFO] ===== Completeness check finished =====
[2023-06-30 06:33:51,923] [INFO] ===== Start GTDB Search =====
[2023-06-30 06:33:51,924] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016293975.1_ASM1629397v1_genomic.fna/markers.fasta)
[2023-06-30 06:33:51,925] [INFO] Task started: Blastn
[2023-06-30 06:33:51,925] [INFO] Running command: blastn -query GCA_016293975.1_ASM1629397v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg722a7796-d4de-42a3-a90f-d932a2cf5d18/dqc_reference/reference_markers_gtdb.fasta -out GCA_016293975.1_ASM1629397v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:33:52,918] [INFO] Task succeeded: Blastn
[2023-06-30 06:33:52,923] [INFO] Selected 26 target genomes.
[2023-06-30 06:33:52,923] [INFO] Target genome list was writen to GCA_016293975.1_ASM1629397v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 06:33:52,931] [INFO] Task started: fastANI
[2023-06-30 06:33:52,931] [INFO] Running command: fastANI --query /var/lib/cwl/stg96475d4c-ce0a-4048-8cce-4e1f64e57801/GCA_016293975.1_ASM1629397v1_genomic.fna.gz --refList GCA_016293975.1_ASM1629397v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016293975.1_ASM1629397v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 06:34:02,661] [INFO] Task succeeded: fastANI
[2023-06-30 06:34:02,666] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 06:34:02,666] [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_016293975.1	s__RGIG1693 sp016293975	100.0	503	503	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RGIG1693	95.0	99.67	99.67	0.98	0.98	2	conclusive
--------------------------------------------------------------------------------
[2023-06-30 06:34:02,669] [INFO] GTDB search result was written to GCA_016293975.1_ASM1629397v1_genomic.fna/result_gtdb.tsv
[2023-06-30 06:34:02,669] [INFO] ===== GTDB Search completed =====
[2023-06-30 06:34:02,672] [INFO] DFAST_QC result json was written to GCA_016293975.1_ASM1629397v1_genomic.fna/dqc_result.json
[2023-06-30 06:34:02,673] [INFO] DFAST_QC completed!
[2023-06-30 06:34:02,673] [INFO] Total running time: 0h0m51s