[2023-06-27 18:56:06,743] [INFO] DFAST_QC pipeline started.
[2023-06-27 18:56:06,746] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 18:56:06,746] [INFO] DQC Reference Directory: /var/lib/cwl/stgded1dfa7-cb91-45ac-9d5b-d15e488caed5/dqc_reference
[2023-06-27 18:56:08,005] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 18:56:08,006] [INFO] Task started: Prodigal
[2023-06-27 18:56:08,007] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4c8fabc-9399-4a7e-9f01-2354b3fed69d/GCA_026705165.1_ASM2670516v1_genomic.fna.gz | prodigal -d GCA_026705165.1_ASM2670516v1_genomic.fna/cds.fna -a GCA_026705165.1_ASM2670516v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 18:56:16,832] [INFO] Task succeeded: Prodigal
[2023-06-27 18:56:16,833] [INFO] Task started: HMMsearch
[2023-06-27 18:56:16,833] [INFO] Running command: hmmsearch --tblout GCA_026705165.1_ASM2670516v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgded1dfa7-cb91-45ac-9d5b-d15e488caed5/dqc_reference/reference_markers.hmm GCA_026705165.1_ASM2670516v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 18:56:17,098] [INFO] Task succeeded: HMMsearch
[2023-06-27 18:56:17,100] [INFO] Found 6/6 markers.
[2023-06-27 18:56:17,138] [INFO] Query marker FASTA was written to GCA_026705165.1_ASM2670516v1_genomic.fna/markers.fasta
[2023-06-27 18:56:17,139] [INFO] Task started: Blastn
[2023-06-27 18:56:17,139] [INFO] Running command: blastn -query GCA_026705165.1_ASM2670516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgded1dfa7-cb91-45ac-9d5b-d15e488caed5/dqc_reference/reference_markers.fasta -out GCA_026705165.1_ASM2670516v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:56:17,800] [INFO] Task succeeded: Blastn
[2023-06-27 18:56:17,805] [INFO] Selected 15 target genomes.
[2023-06-27 18:56:17,805] [INFO] Target genome list was writen to GCA_026705165.1_ASM2670516v1_genomic.fna/target_genomes.txt
[2023-06-27 18:56:17,811] [INFO] Task started: fastANI
[2023-06-27 18:56:17,811] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4c8fabc-9399-4a7e-9f01-2354b3fed69d/GCA_026705165.1_ASM2670516v1_genomic.fna.gz --refList GCA_026705165.1_ASM2670516v1_genomic.fna/target_genomes.txt --output GCA_026705165.1_ASM2670516v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 18:56:26,684] [INFO] Task succeeded: fastANI
[2023-06-27 18:56:26,685] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgded1dfa7-cb91-45ac-9d5b-d15e488caed5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 18:56:26,685] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgded1dfa7-cb91-45ac-9d5b-d15e488caed5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 18:56:26,690] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 18:56:26,691] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 18:56:26,691] [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
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	74.8138	51	998	95	below_threshold
Nocardia harenae	strain=NBRC 108248	GCA_001612885.1	358707	358707	type	True	74.7426	59	998	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 18:56:26,693] [INFO] DFAST Taxonomy check result was written to GCA_026705165.1_ASM2670516v1_genomic.fna/tc_result.tsv
[2023-06-27 18:56:26,694] [INFO] ===== Taxonomy check completed =====
[2023-06-27 18:56:26,694] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 18:56:26,695] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgded1dfa7-cb91-45ac-9d5b-d15e488caed5/dqc_reference/checkm_data
[2023-06-27 18:56:26,696] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 18:56:26,729] [INFO] Task started: CheckM
[2023-06-27 18:56:26,729] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026705165.1_ASM2670516v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026705165.1_ASM2670516v1_genomic.fna/checkm_input GCA_026705165.1_ASM2670516v1_genomic.fna/checkm_result
[2023-06-27 18:56:57,605] [INFO] Task succeeded: CheckM
[2023-06-27 18:56:57,606] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 18:56:57,631] [INFO] ===== Completeness check finished =====
[2023-06-27 18:56:57,632] [INFO] ===== Start GTDB Search =====
[2023-06-27 18:56:57,632] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026705165.1_ASM2670516v1_genomic.fna/markers.fasta)
[2023-06-27 18:56:57,633] [INFO] Task started: Blastn
[2023-06-27 18:56:57,633] [INFO] Running command: blastn -query GCA_026705165.1_ASM2670516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgded1dfa7-cb91-45ac-9d5b-d15e488caed5/dqc_reference/reference_markers_gtdb.fasta -out GCA_026705165.1_ASM2670516v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:56:58,489] [INFO] Task succeeded: Blastn
[2023-06-27 18:56:58,493] [INFO] Selected 15 target genomes.
[2023-06-27 18:56:58,493] [INFO] Target genome list was writen to GCA_026705165.1_ASM2670516v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 18:56:58,506] [INFO] Task started: fastANI
[2023-06-27 18:56:58,506] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4c8fabc-9399-4a7e-9f01-2354b3fed69d/GCA_026705165.1_ASM2670516v1_genomic.fna.gz --refList GCA_026705165.1_ASM2670516v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026705165.1_ASM2670516v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 18:57:08,073] [INFO] Task succeeded: fastANI
[2023-06-27 18:57:08,080] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 18:57:08,080] [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_009838735.1	s__Bin125 sp009838735	95.5106	880	998	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Bin125;f__Bin125;g__Bin125	95.0	96.51	95.66	0.92	0.90	7	conclusive
GCA_009838915.1	s__Bin125 sp009838915	82.4251	628	998	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Bin125;f__Bin125;g__Bin125	95.0	98.62	97.86	0.96	0.92	7	-
GCA_002239025.1	s__Bin125 sp002239025	79.8714	616	998	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Bin125;f__Bin125;g__Bin125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007571275.1	s__Bin125 sp007571275	79.3685	418	998	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Bin125;f__Bin125;g__Bin125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016866055.1	s__VGNK01 sp016866055	75.7417	70	998	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__VGNK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814555.1	s__Lysobacter tengchongensis	74.8138	51	998	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-27 18:57:08,082] [INFO] GTDB search result was written to GCA_026705165.1_ASM2670516v1_genomic.fna/result_gtdb.tsv
[2023-06-27 18:57:08,083] [INFO] ===== GTDB Search completed =====
[2023-06-27 18:57:08,087] [INFO] DFAST_QC result json was written to GCA_026705165.1_ASM2670516v1_genomic.fna/dqc_result.json
[2023-06-27 18:57:08,087] [INFO] DFAST_QC completed!
[2023-06-27 18:57:08,088] [INFO] Total running time: 0h1m1s