[2023-06-28 21:36:37,920] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:36:37,923] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:36:37,923] [INFO] DQC Reference Directory: /var/lib/cwl/stgadbfd1f5-0637-4f65-9864-0f52e3b82747/dqc_reference
[2023-06-28 21:36:40,193] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:36:40,195] [INFO] Task started: Prodigal
[2023-06-28 21:36:40,196] [INFO] Running command: gunzip -c /var/lib/cwl/stg8090d993-6549-44d7-9fbd-8e92cdd7639c/GCA_017615095.1_ASM1761509v1_genomic.fna.gz | prodigal -d GCA_017615095.1_ASM1761509v1_genomic.fna/cds.fna -a GCA_017615095.1_ASM1761509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:36:43,556] [INFO] Task succeeded: Prodigal
[2023-06-28 21:36:43,556] [INFO] Task started: HMMsearch
[2023-06-28 21:36:43,556] [INFO] Running command: hmmsearch --tblout GCA_017615095.1_ASM1761509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgadbfd1f5-0637-4f65-9864-0f52e3b82747/dqc_reference/reference_markers.hmm GCA_017615095.1_ASM1761509v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:36:43,759] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:36:43,761] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8090d993-6549-44d7-9fbd-8e92cdd7639c/GCA_017615095.1_ASM1761509v1_genomic.fna.gz]
[2023-06-28 21:36:43,785] [INFO] Query marker FASTA was written to GCA_017615095.1_ASM1761509v1_genomic.fna/markers.fasta
[2023-06-28 21:36:43,785] [INFO] Task started: Blastn
[2023-06-28 21:36:43,785] [INFO] Running command: blastn -query GCA_017615095.1_ASM1761509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgadbfd1f5-0637-4f65-9864-0f52e3b82747/dqc_reference/reference_markers.fasta -out GCA_017615095.1_ASM1761509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:36:44,357] [INFO] Task succeeded: Blastn
[2023-06-28 21:36:44,362] [INFO] Selected 15 target genomes.
[2023-06-28 21:36:44,362] [INFO] Target genome list was writen to GCA_017615095.1_ASM1761509v1_genomic.fna/target_genomes.txt
[2023-06-28 21:36:44,364] [INFO] Task started: fastANI
[2023-06-28 21:36:44,364] [INFO] Running command: fastANI --query /var/lib/cwl/stg8090d993-6549-44d7-9fbd-8e92cdd7639c/GCA_017615095.1_ASM1761509v1_genomic.fna.gz --refList GCA_017615095.1_ASM1761509v1_genomic.fna/target_genomes.txt --output GCA_017615095.1_ASM1761509v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:36:53,499] [INFO] Task succeeded: fastANI
[2023-06-28 21:36:53,499] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgadbfd1f5-0637-4f65-9864-0f52e3b82747/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:36:53,500] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgadbfd1f5-0637-4f65-9864-0f52e3b82747/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:36:53,501] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 21:36:53,502] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 21:36:53,502] [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 21:36:53,504] [INFO] DFAST Taxonomy check result was written to GCA_017615095.1_ASM1761509v1_genomic.fna/tc_result.tsv
[2023-06-28 21:36:53,505] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:36:53,505] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:36:53,505] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgadbfd1f5-0637-4f65-9864-0f52e3b82747/dqc_reference/checkm_data
[2023-06-28 21:36:53,509] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:36:53,531] [INFO] Task started: CheckM
[2023-06-28 21:36:53,531] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017615095.1_ASM1761509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017615095.1_ASM1761509v1_genomic.fna/checkm_input GCA_017615095.1_ASM1761509v1_genomic.fna/checkm_result
[2023-06-28 21:37:12,019] [INFO] Task succeeded: CheckM
[2023-06-28 21:37:12,022] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 21:37:12,046] [INFO] ===== Completeness check finished =====
[2023-06-28 21:37:12,046] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:37:12,047] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017615095.1_ASM1761509v1_genomic.fna/markers.fasta)
[2023-06-28 21:37:12,047] [INFO] Task started: Blastn
[2023-06-28 21:37:12,047] [INFO] Running command: blastn -query GCA_017615095.1_ASM1761509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgadbfd1f5-0637-4f65-9864-0f52e3b82747/dqc_reference/reference_markers_gtdb.fasta -out GCA_017615095.1_ASM1761509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:37:12,846] [INFO] Task succeeded: Blastn
[2023-06-28 21:37:12,851] [INFO] Selected 13 target genomes.
[2023-06-28 21:37:12,851] [INFO] Target genome list was writen to GCA_017615095.1_ASM1761509v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:37:12,854] [INFO] Task started: fastANI
[2023-06-28 21:37:12,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg8090d993-6549-44d7-9fbd-8e92cdd7639c/GCA_017615095.1_ASM1761509v1_genomic.fna.gz --refList GCA_017615095.1_ASM1761509v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017615095.1_ASM1761509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:37:18,662] [INFO] Task succeeded: fastANI
[2023-06-28 21:37:18,680] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 21:37:18,681] [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_017615095.1	s__UBA1177 sp017615095	99.9999	455	461	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002309575.1	s__UBA1177 sp002309575	85.5586	368	461	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	97.91	97.60	0.87	0.84	4	-
GCA_017645765.1	s__UBA1177 sp017645765	78.8797	112	461	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016290135.1	s__UBA1177 sp016290135	78.7138	135	461	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002310035.1	s__UBA1177 sp002310035	78.6956	111	461	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902774115.1	s__UBA1177 sp902774115	78.5637	129	461	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	96.80	96.80	0.84	0.84	2	-
GCA_017963125.1	s__UBA1177 sp017963125	78.5383	136	461	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780365.1	s__UBA1177 sp902780365	78.4118	104	461	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235605.1	s__UBA1177 sp905235605	78.3341	139	461	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	99.00	99.00	0.87	0.87	2	-
GCA_017961325.1	s__UBA1177 sp017961325	78.2877	133	461	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002310995.1	s__UBA1177 sp002310995	77.8602	111	461	d__Bacteria;p__UBP6;c__UBA1177;o__UBA1177;f__UBA1177;g__UBA1177	95.0	99.84	99.84	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-28 21:37:18,683] [INFO] GTDB search result was written to GCA_017615095.1_ASM1761509v1_genomic.fna/result_gtdb.tsv
[2023-06-28 21:37:18,684] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:37:18,687] [INFO] DFAST_QC result json was written to GCA_017615095.1_ASM1761509v1_genomic.fna/dqc_result.json
[2023-06-28 21:37:18,688] [INFO] DFAST_QC completed!
[2023-06-28 21:37:18,688] [INFO] Total running time: 0h0m41s