[2023-06-28 23:57:23,207] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:57:23,217] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:57:23,218] [INFO] DQC Reference Directory: /var/lib/cwl/stg49f0ac80-687c-4262-bc70-580ecc611d8a/dqc_reference
[2023-06-28 23:57:24,545] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:57:24,545] [INFO] Task started: Prodigal
[2023-06-28 23:57:24,546] [INFO] Running command: gunzip -c /var/lib/cwl/stg38c749fc-ae2f-4006-ad9b-5b16cf35ef0d/GCA_017435585.1_ASM1743558v1_genomic.fna.gz | prodigal -d GCA_017435585.1_ASM1743558v1_genomic.fna/cds.fna -a GCA_017435585.1_ASM1743558v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:57:26,256] [INFO] Task succeeded: Prodigal
[2023-06-28 23:57:26,256] [INFO] Task started: HMMsearch
[2023-06-28 23:57:26,256] [INFO] Running command: hmmsearch --tblout GCA_017435585.1_ASM1743558v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49f0ac80-687c-4262-bc70-580ecc611d8a/dqc_reference/reference_markers.hmm GCA_017435585.1_ASM1743558v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:57:26,470] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:57:26,471] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg38c749fc-ae2f-4006-ad9b-5b16cf35ef0d/GCA_017435585.1_ASM1743558v1_genomic.fna.gz]
[2023-06-28 23:57:26,486] [INFO] Query marker FASTA was written to GCA_017435585.1_ASM1743558v1_genomic.fna/markers.fasta
[2023-06-28 23:57:26,486] [INFO] Task started: Blastn
[2023-06-28 23:57:26,487] [INFO] Running command: blastn -query GCA_017435585.1_ASM1743558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49f0ac80-687c-4262-bc70-580ecc611d8a/dqc_reference/reference_markers.fasta -out GCA_017435585.1_ASM1743558v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:57:27,117] [INFO] Task succeeded: Blastn
[2023-06-28 23:57:27,127] [INFO] Selected 32 target genomes.
[2023-06-28 23:57:27,128] [INFO] Target genome list was writen to GCA_017435585.1_ASM1743558v1_genomic.fna/target_genomes.txt
[2023-06-28 23:57:27,140] [INFO] Task started: fastANI
[2023-06-28 23:57:27,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg38c749fc-ae2f-4006-ad9b-5b16cf35ef0d/GCA_017435585.1_ASM1743558v1_genomic.fna.gz --refList GCA_017435585.1_ASM1743558v1_genomic.fna/target_genomes.txt --output GCA_017435585.1_ASM1743558v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:57:40,296] [INFO] Task succeeded: fastANI
[2023-06-28 23:57:40,297] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49f0ac80-687c-4262-bc70-580ecc611d8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:57:40,297] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49f0ac80-687c-4262-bc70-580ecc611d8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:57:40,302] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:57:40,302] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 23:57:40,303] [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 23:57:40,309] [INFO] DFAST Taxonomy check result was written to GCA_017435585.1_ASM1743558v1_genomic.fna/tc_result.tsv
[2023-06-28 23:57:40,316] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:57:40,317] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:57:40,317] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49f0ac80-687c-4262-bc70-580ecc611d8a/dqc_reference/checkm_data
[2023-06-28 23:57:40,320] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:57:40,348] [INFO] Task started: CheckM
[2023-06-28 23:57:40,348] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017435585.1_ASM1743558v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017435585.1_ASM1743558v1_genomic.fna/checkm_input GCA_017435585.1_ASM1743558v1_genomic.fna/checkm_result
[2023-06-28 23:57:55,347] [INFO] Task succeeded: CheckM
[2023-06-28 23:57:55,348] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.15%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-28 23:57:55,373] [INFO] ===== Completeness check finished =====
[2023-06-28 23:57:55,373] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:57:55,374] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017435585.1_ASM1743558v1_genomic.fna/markers.fasta)
[2023-06-28 23:57:55,374] [INFO] Task started: Blastn
[2023-06-28 23:57:55,374] [INFO] Running command: blastn -query GCA_017435585.1_ASM1743558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49f0ac80-687c-4262-bc70-580ecc611d8a/dqc_reference/reference_markers_gtdb.fasta -out GCA_017435585.1_ASM1743558v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:57:56,161] [INFO] Task succeeded: Blastn
[2023-06-28 23:57:56,165] [INFO] Selected 33 target genomes.
[2023-06-28 23:57:56,165] [INFO] Target genome list was writen to GCA_017435585.1_ASM1743558v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:57:56,194] [INFO] Task started: fastANI
[2023-06-28 23:57:56,195] [INFO] Running command: fastANI --query /var/lib/cwl/stg38c749fc-ae2f-4006-ad9b-5b16cf35ef0d/GCA_017435585.1_ASM1743558v1_genomic.fna.gz --refList GCA_017435585.1_ASM1743558v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017435585.1_ASM1743558v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:58:03,750] [INFO] Task succeeded: fastANI
[2023-06-28 23:58:03,753] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 23:58:03,754] [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_016296945.1	s__CAG-698 sp016296945	81.557	101	245	d__Bacteria;p__Firmicutes;c__Bacilli;o__ML615J-28;f__CAG-698;g__CAG-698	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 23:58:03,756] [INFO] GTDB search result was written to GCA_017435585.1_ASM1743558v1_genomic.fna/result_gtdb.tsv
[2023-06-28 23:58:03,756] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:58:03,759] [INFO] DFAST_QC result json was written to GCA_017435585.1_ASM1743558v1_genomic.fna/dqc_result.json
[2023-06-28 23:58:03,759] [INFO] DFAST_QC completed!
[2023-06-28 23:58:03,759] [INFO] Total running time: 0h0m41s