[2023-06-19 05:24:52,217] [INFO] DFAST_QC pipeline started.
[2023-06-19 05:24:52,219] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 05:24:52,219] [INFO] DQC Reference Directory: /var/lib/cwl/stgeda8bce6-7e0c-4587-828a-0fe2ea2cc41d/dqc_reference
[2023-06-19 05:24:54,552] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 05:24:54,553] [INFO] Task started: Prodigal
[2023-06-19 05:24:54,554] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d5f4987-5900-4302-9b4b-3e5e79caeec3/GCA_018062885.1_ASM1806288v1_genomic.fna.gz | prodigal -d GCA_018062885.1_ASM1806288v1_genomic.fna/cds.fna -a GCA_018062885.1_ASM1806288v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 05:24:57,646] [INFO] Task succeeded: Prodigal
[2023-06-19 05:24:57,646] [INFO] Task started: HMMsearch
[2023-06-19 05:24:57,646] [INFO] Running command: hmmsearch --tblout GCA_018062885.1_ASM1806288v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeda8bce6-7e0c-4587-828a-0fe2ea2cc41d/dqc_reference/reference_markers.hmm GCA_018062885.1_ASM1806288v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 05:24:57,850] [INFO] Task succeeded: HMMsearch
[2023-06-19 05:24:57,853] [INFO] Found 6/6 markers.
[2023-06-19 05:24:57,878] [INFO] Query marker FASTA was written to GCA_018062885.1_ASM1806288v1_genomic.fna/markers.fasta
[2023-06-19 05:24:57,878] [INFO] Task started: Blastn
[2023-06-19 05:24:57,879] [INFO] Running command: blastn -query GCA_018062885.1_ASM1806288v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeda8bce6-7e0c-4587-828a-0fe2ea2cc41d/dqc_reference/reference_markers.fasta -out GCA_018062885.1_ASM1806288v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:24:59,166] [INFO] Task succeeded: Blastn
[2023-06-19 05:24:59,172] [INFO] Selected 11 target genomes.
[2023-06-19 05:24:59,172] [INFO] Target genome list was writen to GCA_018062885.1_ASM1806288v1_genomic.fna/target_genomes.txt
[2023-06-19 05:24:59,175] [INFO] Task started: fastANI
[2023-06-19 05:24:59,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d5f4987-5900-4302-9b4b-3e5e79caeec3/GCA_018062885.1_ASM1806288v1_genomic.fna.gz --refList GCA_018062885.1_ASM1806288v1_genomic.fna/target_genomes.txt --output GCA_018062885.1_ASM1806288v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 05:25:02,800] [INFO] Task succeeded: fastANI
[2023-06-19 05:25:02,800] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeda8bce6-7e0c-4587-828a-0fe2ea2cc41d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 05:25:02,801] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeda8bce6-7e0c-4587-828a-0fe2ea2cc41d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 05:25:02,802] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 05:25:02,802] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 05:25:02,802] [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
--------------------------------------------------------------------------------
[2023-06-19 05:25:02,805] [INFO] DFAST Taxonomy check result was written to GCA_018062885.1_ASM1806288v1_genomic.fna/tc_result.tsv
[2023-06-19 05:25:02,806] [INFO] ===== Taxonomy check completed =====
[2023-06-19 05:25:02,806] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 05:25:02,806] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeda8bce6-7e0c-4587-828a-0fe2ea2cc41d/dqc_reference/checkm_data
[2023-06-19 05:25:02,809] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 05:25:02,830] [INFO] Task started: CheckM
[2023-06-19 05:25:02,830] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018062885.1_ASM1806288v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018062885.1_ASM1806288v1_genomic.fna/checkm_input GCA_018062885.1_ASM1806288v1_genomic.fna/checkm_result
[2023-06-19 05:25:19,853] [INFO] Task succeeded: CheckM
[2023-06-19 05:25:19,855] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 05:25:19,886] [INFO] ===== Completeness check finished =====
[2023-06-19 05:25:19,886] [INFO] ===== Start GTDB Search =====
[2023-06-19 05:25:19,887] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018062885.1_ASM1806288v1_genomic.fna/markers.fasta)
[2023-06-19 05:25:19,887] [INFO] Task started: Blastn
[2023-06-19 05:25:19,887] [INFO] Running command: blastn -query GCA_018062885.1_ASM1806288v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeda8bce6-7e0c-4587-828a-0fe2ea2cc41d/dqc_reference/reference_markers_gtdb.fasta -out GCA_018062885.1_ASM1806288v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:25:20,658] [INFO] Task succeeded: Blastn
[2023-06-19 05:25:20,663] [INFO] Selected 13 target genomes.
[2023-06-19 05:25:20,663] [INFO] Target genome list was writen to GCA_018062885.1_ASM1806288v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 05:25:20,687] [INFO] Task started: fastANI
[2023-06-19 05:25:20,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d5f4987-5900-4302-9b4b-3e5e79caeec3/GCA_018062885.1_ASM1806288v1_genomic.fna.gz --refList GCA_018062885.1_ASM1806288v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018062885.1_ASM1806288v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 05:25:22,859] [INFO] Task succeeded: fastANI
[2023-06-19 05:25:22,869] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 05:25:22,869] [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_018062885.1	s__CAIRBL01 sp018062885	99.9999	213	214	d__Bacteria;p__Patescibacteria;c__ABY1;o__UBA1558;f__GWA2-36-10;g__CAIRBL01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903876815.1	s__CAIRBL01 sp903876815	81.5571	135	214	d__Bacteria;p__Patescibacteria;c__ABY1;o__UBA1558;f__GWA2-36-10;g__CAIRBL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903855135.1	s__GWA2-36-10 sp903855135	79.3391	102	214	d__Bacteria;p__Patescibacteria;c__ABY1;o__UBA1558;f__GWA2-36-10;g__GWA2-36-10	95.0	99.90	99.86	0.94	0.92	7	-
GCA_000991205.1	s__GWA2-36-10 sp000991205	78.5947	88	214	d__Bacteria;p__Patescibacteria;c__ABY1;o__UBA1558;f__GWA2-36-10;g__GWA2-36-10	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 05:25:22,871] [INFO] GTDB search result was written to GCA_018062885.1_ASM1806288v1_genomic.fna/result_gtdb.tsv
[2023-06-19 05:25:22,872] [INFO] ===== GTDB Search completed =====
[2023-06-19 05:25:22,874] [INFO] DFAST_QC result json was written to GCA_018062885.1_ASM1806288v1_genomic.fna/dqc_result.json
[2023-06-19 05:25:22,874] [INFO] DFAST_QC completed!
[2023-06-19 05:25:22,875] [INFO] Total running time: 0h0m31s