[2023-06-30 05:03:17,173] [INFO] DFAST_QC pipeline started.
[2023-06-30 05:03:17,179] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 05:03:17,179] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a22edba-7111-4eb1-b897-d839652c19cc/dqc_reference
[2023-06-30 05:03:18,376] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 05:03:18,377] [INFO] Task started: Prodigal
[2023-06-30 05:03:18,377] [INFO] Running command: gunzip -c /var/lib/cwl/stgf907bfba-7ed4-4868-8e0f-521b1ba04665/GCA_019306345.1_ASM1930634v1_genomic.fna.gz | prodigal -d GCA_019306345.1_ASM1930634v1_genomic.fna/cds.fna -a GCA_019306345.1_ASM1930634v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 05:03:26,112] [INFO] Task succeeded: Prodigal
[2023-06-30 05:03:26,113] [INFO] Task started: HMMsearch
[2023-06-30 05:03:26,113] [INFO] Running command: hmmsearch --tblout GCA_019306345.1_ASM1930634v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a22edba-7111-4eb1-b897-d839652c19cc/dqc_reference/reference_markers.hmm GCA_019306345.1_ASM1930634v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 05:03:26,387] [INFO] Task succeeded: HMMsearch
[2023-06-30 05:03:26,390] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf907bfba-7ed4-4868-8e0f-521b1ba04665/GCA_019306345.1_ASM1930634v1_genomic.fna.gz]
[2023-06-30 05:03:26,429] [INFO] Query marker FASTA was written to GCA_019306345.1_ASM1930634v1_genomic.fna/markers.fasta
[2023-06-30 05:03:26,429] [INFO] Task started: Blastn
[2023-06-30 05:03:26,429] [INFO] Running command: blastn -query GCA_019306345.1_ASM1930634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a22edba-7111-4eb1-b897-d839652c19cc/dqc_reference/reference_markers.fasta -out GCA_019306345.1_ASM1930634v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:03:27,014] [INFO] Task succeeded: Blastn
[2023-06-30 05:03:27,019] [INFO] Selected 16 target genomes.
[2023-06-30 05:03:27,020] [INFO] Target genome list was writen to GCA_019306345.1_ASM1930634v1_genomic.fna/target_genomes.txt
[2023-06-30 05:03:27,023] [INFO] Task started: fastANI
[2023-06-30 05:03:27,023] [INFO] Running command: fastANI --query /var/lib/cwl/stgf907bfba-7ed4-4868-8e0f-521b1ba04665/GCA_019306345.1_ASM1930634v1_genomic.fna.gz --refList GCA_019306345.1_ASM1930634v1_genomic.fna/target_genomes.txt --output GCA_019306345.1_ASM1930634v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 05:03:36,577] [INFO] Task succeeded: fastANI
[2023-06-30 05:03:36,578] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a22edba-7111-4eb1-b897-d839652c19cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 05:03:36,578] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a22edba-7111-4eb1-b897-d839652c19cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 05:03:36,580] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 05:03:36,580] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 05:03:36,580] [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 05:03:36,583] [INFO] DFAST Taxonomy check result was written to GCA_019306345.1_ASM1930634v1_genomic.fna/tc_result.tsv
[2023-06-30 05:03:36,584] [INFO] ===== Taxonomy check completed =====
[2023-06-30 05:03:36,584] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 05:03:36,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a22edba-7111-4eb1-b897-d839652c19cc/dqc_reference/checkm_data
[2023-06-30 05:03:36,587] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 05:03:36,628] [INFO] Task started: CheckM
[2023-06-30 05:03:36,628] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019306345.1_ASM1930634v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019306345.1_ASM1930634v1_genomic.fna/checkm_input GCA_019306345.1_ASM1930634v1_genomic.fna/checkm_result
[2023-06-30 05:04:06,504] [INFO] Task succeeded: CheckM
[2023-06-30 05:04:06,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.39%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 05:04:06,528] [INFO] ===== Completeness check finished =====
[2023-06-30 05:04:06,529] [INFO] ===== Start GTDB Search =====
[2023-06-30 05:04:06,529] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019306345.1_ASM1930634v1_genomic.fna/markers.fasta)
[2023-06-30 05:04:06,529] [INFO] Task started: Blastn
[2023-06-30 05:04:06,530] [INFO] Running command: blastn -query GCA_019306345.1_ASM1930634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a22edba-7111-4eb1-b897-d839652c19cc/dqc_reference/reference_markers_gtdb.fasta -out GCA_019306345.1_ASM1930634v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:04:07,344] [INFO] Task succeeded: Blastn
[2023-06-30 05:04:07,348] [INFO] Selected 21 target genomes.
[2023-06-30 05:04:07,348] [INFO] Target genome list was writen to GCA_019306345.1_ASM1930634v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 05:04:07,401] [INFO] Task started: fastANI
[2023-06-30 05:04:07,402] [INFO] Running command: fastANI --query /var/lib/cwl/stgf907bfba-7ed4-4868-8e0f-521b1ba04665/GCA_019306345.1_ASM1930634v1_genomic.fna.gz --refList GCA_019306345.1_ASM1930634v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019306345.1_ASM1930634v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 05:04:19,489] [INFO] Task succeeded: fastANI
[2023-06-30 05:04:19,496] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 05:04:19,497] [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_014382905.1	s__Desulfacyla sp014382905	76.4576	72	924	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__Desulfatiglandaceae;g__Desulfacyla	95.0	98.82	98.20	0.84	0.79	5	-
GCA_014382715.1	s__Desulfacyla euxinica	76.2688	58	924	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__Desulfatiglandaceae;g__Desulfacyla	95.0	99.00	98.56	0.73	0.65	3	-
--------------------------------------------------------------------------------
[2023-06-30 05:04:19,499] [INFO] GTDB search result was written to GCA_019306345.1_ASM1930634v1_genomic.fna/result_gtdb.tsv
[2023-06-30 05:04:19,500] [INFO] ===== GTDB Search completed =====
[2023-06-30 05:04:19,503] [INFO] DFAST_QC result json was written to GCA_019306345.1_ASM1930634v1_genomic.fna/dqc_result.json
[2023-06-30 05:04:19,503] [INFO] DFAST_QC completed!
[2023-06-30 05:04:19,503] [INFO] Total running time: 0h1m2s