[2023-06-28 07:56:55,721] [INFO] DFAST_QC pipeline started.
[2023-06-28 07:56:55,736] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 07:56:55,737] [INFO] DQC Reference Directory: /var/lib/cwl/stg078ff905-c2bb-4443-badf-8e2724c73db5/dqc_reference
[2023-06-28 07:56:57,139] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 07:56:57,140] [INFO] Task started: Prodigal
[2023-06-28 07:56:57,140] [INFO] Running command: gunzip -c /var/lib/cwl/stg56bc10bd-3287-4a40-b681-805d63f40cba/GCA_019310665.1_ASM1931066v1_genomic.fna.gz | prodigal -d GCA_019310665.1_ASM1931066v1_genomic.fna/cds.fna -a GCA_019310665.1_ASM1931066v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 07:57:05,190] [INFO] Task succeeded: Prodigal
[2023-06-28 07:57:05,191] [INFO] Task started: HMMsearch
[2023-06-28 07:57:05,191] [INFO] Running command: hmmsearch --tblout GCA_019310665.1_ASM1931066v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg078ff905-c2bb-4443-badf-8e2724c73db5/dqc_reference/reference_markers.hmm GCA_019310665.1_ASM1931066v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 07:57:05,492] [INFO] Task succeeded: HMMsearch
[2023-06-28 07:57:05,493] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg56bc10bd-3287-4a40-b681-805d63f40cba/GCA_019310665.1_ASM1931066v1_genomic.fna.gz]
[2023-06-28 07:57:05,527] [INFO] Query marker FASTA was written to GCA_019310665.1_ASM1931066v1_genomic.fna/markers.fasta
[2023-06-28 07:57:05,527] [INFO] Task started: Blastn
[2023-06-28 07:57:05,528] [INFO] Running command: blastn -query GCA_019310665.1_ASM1931066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg078ff905-c2bb-4443-badf-8e2724c73db5/dqc_reference/reference_markers.fasta -out GCA_019310665.1_ASM1931066v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 07:57:06,262] [INFO] Task succeeded: Blastn
[2023-06-28 07:57:06,266] [INFO] Selected 14 target genomes.
[2023-06-28 07:57:06,266] [INFO] Target genome list was writen to GCA_019310665.1_ASM1931066v1_genomic.fna/target_genomes.txt
[2023-06-28 07:57:06,293] [INFO] Task started: fastANI
[2023-06-28 07:57:06,293] [INFO] Running command: fastANI --query /var/lib/cwl/stg56bc10bd-3287-4a40-b681-805d63f40cba/GCA_019310665.1_ASM1931066v1_genomic.fna.gz --refList GCA_019310665.1_ASM1931066v1_genomic.fna/target_genomes.txt --output GCA_019310665.1_ASM1931066v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 07:57:17,579] [INFO] Task succeeded: fastANI
[2023-06-28 07:57:17,579] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg078ff905-c2bb-4443-badf-8e2724c73db5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 07:57:17,580] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg078ff905-c2bb-4443-badf-8e2724c73db5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 07:57:17,581] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 07:57:17,581] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 07:57:17,581] [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
--------------------------------------------------------------------------------
[2023-06-28 07:57:17,583] [INFO] DFAST Taxonomy check result was written to GCA_019310665.1_ASM1931066v1_genomic.fna/tc_result.tsv
[2023-06-28 07:57:17,584] [INFO] ===== Taxonomy check completed =====
[2023-06-28 07:57:17,584] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 07:57:17,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg078ff905-c2bb-4443-badf-8e2724c73db5/dqc_reference/checkm_data
[2023-06-28 07:57:17,587] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 07:57:17,634] [INFO] Task started: CheckM
[2023-06-28 07:57:17,634] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019310665.1_ASM1931066v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019310665.1_ASM1931066v1_genomic.fna/checkm_input GCA_019310665.1_ASM1931066v1_genomic.fna/checkm_result
[2023-06-28 07:57:47,902] [INFO] Task succeeded: CheckM
[2023-06-28 07:57:47,905] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.16%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 07:57:47,929] [INFO] ===== Completeness check finished =====
[2023-06-28 07:57:47,929] [INFO] ===== Start GTDB Search =====
[2023-06-28 07:57:47,930] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019310665.1_ASM1931066v1_genomic.fna/markers.fasta)
[2023-06-28 07:57:47,930] [INFO] Task started: Blastn
[2023-06-28 07:57:47,930] [INFO] Running command: blastn -query GCA_019310665.1_ASM1931066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg078ff905-c2bb-4443-badf-8e2724c73db5/dqc_reference/reference_markers_gtdb.fasta -out GCA_019310665.1_ASM1931066v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 07:57:48,896] [INFO] Task succeeded: Blastn
[2023-06-28 07:57:48,900] [INFO] Selected 25 target genomes.
[2023-06-28 07:57:48,900] [INFO] Target genome list was writen to GCA_019310665.1_ASM1931066v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 07:57:48,933] [INFO] Task started: fastANI
[2023-06-28 07:57:48,934] [INFO] Running command: fastANI --query /var/lib/cwl/stg56bc10bd-3287-4a40-b681-805d63f40cba/GCA_019310665.1_ASM1931066v1_genomic.fna.gz --refList GCA_019310665.1_ASM1931066v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019310665.1_ASM1931066v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 07:58:03,971] [INFO] Task succeeded: fastANI
[2023-06-28 07:58:03,975] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 07:58:03,976] [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_016219005.1	s__SpSt-501 sp016219005	76.1614	50	890	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA2174_A;g__SpSt-501	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 07:58:03,978] [INFO] GTDB search result was written to GCA_019310665.1_ASM1931066v1_genomic.fna/result_gtdb.tsv
[2023-06-28 07:58:03,978] [INFO] ===== GTDB Search completed =====
[2023-06-28 07:58:03,980] [INFO] DFAST_QC result json was written to GCA_019310665.1_ASM1931066v1_genomic.fna/dqc_result.json
[2023-06-28 07:58:03,981] [INFO] DFAST_QC completed!
[2023-06-28 07:58:03,981] [INFO] Total running time: 0h1m8s