[2023-06-18 21:21:03,178] [INFO] DFAST_QC pipeline started.
[2023-06-18 21:21:03,183] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 21:21:03,183] [INFO] DQC Reference Directory: /var/lib/cwl/stg37b7ec1a-b35a-4721-b799-bbb480c21c96/dqc_reference
[2023-06-18 21:21:04,553] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 21:21:04,553] [INFO] Task started: Prodigal
[2023-06-18 21:21:04,554] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a2f6f04-a841-4911-bf12-e3045bfe16d4/GCA_018264955.1_ASM1826495v1_genomic.fna.gz | prodigal -d GCA_018264955.1_ASM1826495v1_genomic.fna/cds.fna -a GCA_018264955.1_ASM1826495v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 21:21:11,335] [INFO] Task succeeded: Prodigal
[2023-06-18 21:21:11,336] [INFO] Task started: HMMsearch
[2023-06-18 21:21:11,336] [INFO] Running command: hmmsearch --tblout GCA_018264955.1_ASM1826495v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37b7ec1a-b35a-4721-b799-bbb480c21c96/dqc_reference/reference_markers.hmm GCA_018264955.1_ASM1826495v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 21:21:11,651] [INFO] Task succeeded: HMMsearch
[2023-06-18 21:21:11,653] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3a2f6f04-a841-4911-bf12-e3045bfe16d4/GCA_018264955.1_ASM1826495v1_genomic.fna.gz]
[2023-06-18 21:21:11,685] [INFO] Query marker FASTA was written to GCA_018264955.1_ASM1826495v1_genomic.fna/markers.fasta
[2023-06-18 21:21:11,685] [INFO] Task started: Blastn
[2023-06-18 21:21:11,686] [INFO] Running command: blastn -query GCA_018264955.1_ASM1826495v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37b7ec1a-b35a-4721-b799-bbb480c21c96/dqc_reference/reference_markers.fasta -out GCA_018264955.1_ASM1826495v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:21:12,312] [INFO] Task succeeded: Blastn
[2023-06-18 21:21:12,318] [INFO] Selected 28 target genomes.
[2023-06-18 21:21:12,318] [INFO] Target genome list was writen to GCA_018264955.1_ASM1826495v1_genomic.fna/target_genomes.txt
[2023-06-18 21:21:12,321] [INFO] Task started: fastANI
[2023-06-18 21:21:12,321] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a2f6f04-a841-4911-bf12-e3045bfe16d4/GCA_018264955.1_ASM1826495v1_genomic.fna.gz --refList GCA_018264955.1_ASM1826495v1_genomic.fna/target_genomes.txt --output GCA_018264955.1_ASM1826495v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 21:21:26,545] [INFO] Task succeeded: fastANI
[2023-06-18 21:21:26,546] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37b7ec1a-b35a-4721-b799-bbb480c21c96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 21:21:26,546] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37b7ec1a-b35a-4721-b799-bbb480c21c96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 21:21:26,552] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 21:21:26,553] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 21:21:26,553] [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
--------------------------------------------------------------------------------
[2023-06-18 21:21:26,555] [INFO] DFAST Taxonomy check result was written to GCA_018264955.1_ASM1826495v1_genomic.fna/tc_result.tsv
[2023-06-18 21:21:26,558] [INFO] ===== Taxonomy check completed =====
[2023-06-18 21:21:26,559] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 21:21:26,559] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37b7ec1a-b35a-4721-b799-bbb480c21c96/dqc_reference/checkm_data
[2023-06-18 21:21:26,563] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 21:21:26,600] [INFO] Task started: CheckM
[2023-06-18 21:21:26,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018264955.1_ASM1826495v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018264955.1_ASM1826495v1_genomic.fna/checkm_input GCA_018264955.1_ASM1826495v1_genomic.fna/checkm_result
[2023-06-18 21:21:53,332] [INFO] Task succeeded: CheckM
[2023-06-18 21:21:53,333] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.43%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 21:21:53,364] [INFO] ===== Completeness check finished =====
[2023-06-18 21:21:53,365] [INFO] ===== Start GTDB Search =====
[2023-06-18 21:21:53,365] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018264955.1_ASM1826495v1_genomic.fna/markers.fasta)
[2023-06-18 21:21:53,365] [INFO] Task started: Blastn
[2023-06-18 21:21:53,366] [INFO] Running command: blastn -query GCA_018264955.1_ASM1826495v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37b7ec1a-b35a-4721-b799-bbb480c21c96/dqc_reference/reference_markers_gtdb.fasta -out GCA_018264955.1_ASM1826495v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:21:54,170] [INFO] Task succeeded: Blastn
[2023-06-18 21:21:54,175] [INFO] Selected 24 target genomes.
[2023-06-18 21:21:54,175] [INFO] Target genome list was writen to GCA_018264955.1_ASM1826495v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 21:21:54,183] [INFO] Task started: fastANI
[2023-06-18 21:21:54,183] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a2f6f04-a841-4911-bf12-e3045bfe16d4/GCA_018264955.1_ASM1826495v1_genomic.fna.gz --refList GCA_018264955.1_ASM1826495v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018264955.1_ASM1826495v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 21:22:04,328] [INFO] Task succeeded: fastANI
[2023-06-18 21:22:04,334] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 21:22:04,335] [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_003478935.1	s__KLE1615 sp900066985	97.5823	617	774	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__KLE1615	95.0	97.20	95.19	0.86	0.78	12	conclusive
GCA_905214365.1	s__KLE1615 sp905214365	76.5205	73	774	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__KLE1615	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 21:22:04,339] [INFO] GTDB search result was written to GCA_018264955.1_ASM1826495v1_genomic.fna/result_gtdb.tsv
[2023-06-18 21:22:04,340] [INFO] ===== GTDB Search completed =====
[2023-06-18 21:22:04,342] [INFO] DFAST_QC result json was written to GCA_018264955.1_ASM1826495v1_genomic.fna/dqc_result.json
[2023-06-18 21:22:04,342] [INFO] DFAST_QC completed!
[2023-06-18 21:22:04,342] [INFO] Total running time: 0h1m1s