[2023-06-28 18:41:06,173] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:41:06,176] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:41:06,176] [INFO] DQC Reference Directory: /var/lib/cwl/stg37bd82bc-a4be-4e2b-9793-ac4fd8e57a83/dqc_reference
[2023-06-28 18:41:07,439] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:41:07,440] [INFO] Task started: Prodigal
[2023-06-28 18:41:07,440] [INFO] Running command: gunzip -c /var/lib/cwl/stg860ec679-61c1-4438-9c0b-0c3db44bda77/GCA_017647965.1_ASM1764796v1_genomic.fna.gz | prodigal -d GCA_017647965.1_ASM1764796v1_genomic.fna/cds.fna -a GCA_017647965.1_ASM1764796v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:41:09,953] [INFO] Task succeeded: Prodigal
[2023-06-28 18:41:09,953] [INFO] Task started: HMMsearch
[2023-06-28 18:41:09,954] [INFO] Running command: hmmsearch --tblout GCA_017647965.1_ASM1764796v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37bd82bc-a4be-4e2b-9793-ac4fd8e57a83/dqc_reference/reference_markers.hmm GCA_017647965.1_ASM1764796v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:41:10,177] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:41:10,178] [INFO] Found 6/6 markers.
[2023-06-28 18:41:10,197] [INFO] Query marker FASTA was written to GCA_017647965.1_ASM1764796v1_genomic.fna/markers.fasta
[2023-06-28 18:41:10,197] [INFO] Task started: Blastn
[2023-06-28 18:41:10,198] [INFO] Running command: blastn -query GCA_017647965.1_ASM1764796v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37bd82bc-a4be-4e2b-9793-ac4fd8e57a83/dqc_reference/reference_markers.fasta -out GCA_017647965.1_ASM1764796v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:41:10,786] [INFO] Task succeeded: Blastn
[2023-06-28 18:41:10,790] [INFO] Selected 18 target genomes.
[2023-06-28 18:41:10,790] [INFO] Target genome list was writen to GCA_017647965.1_ASM1764796v1_genomic.fna/target_genomes.txt
[2023-06-28 18:41:10,791] [INFO] Task started: fastANI
[2023-06-28 18:41:10,791] [INFO] Running command: fastANI --query /var/lib/cwl/stg860ec679-61c1-4438-9c0b-0c3db44bda77/GCA_017647965.1_ASM1764796v1_genomic.fna.gz --refList GCA_017647965.1_ASM1764796v1_genomic.fna/target_genomes.txt --output GCA_017647965.1_ASM1764796v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:41:18,403] [INFO] Task succeeded: fastANI
[2023-06-28 18:41:18,404] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37bd82bc-a4be-4e2b-9793-ac4fd8e57a83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:41:18,405] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37bd82bc-a4be-4e2b-9793-ac4fd8e57a83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:41:18,407] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:41:18,407] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 18:41:18,407] [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 18:41:18,409] [INFO] DFAST Taxonomy check result was written to GCA_017647965.1_ASM1764796v1_genomic.fna/tc_result.tsv
[2023-06-28 18:41:18,410] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:41:18,410] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:41:18,410] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37bd82bc-a4be-4e2b-9793-ac4fd8e57a83/dqc_reference/checkm_data
[2023-06-28 18:41:18,413] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:41:18,440] [INFO] Task started: CheckM
[2023-06-28 18:41:18,440] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017647965.1_ASM1764796v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017647965.1_ASM1764796v1_genomic.fna/checkm_input GCA_017647965.1_ASM1764796v1_genomic.fna/checkm_result
[2023-06-28 18:41:34,134] [INFO] Task succeeded: CheckM
[2023-06-28 18:41:34,135] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:41:34,158] [INFO] ===== Completeness check finished =====
[2023-06-28 18:41:34,159] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:41:34,159] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017647965.1_ASM1764796v1_genomic.fna/markers.fasta)
[2023-06-28 18:41:34,159] [INFO] Task started: Blastn
[2023-06-28 18:41:34,160] [INFO] Running command: blastn -query GCA_017647965.1_ASM1764796v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37bd82bc-a4be-4e2b-9793-ac4fd8e57a83/dqc_reference/reference_markers_gtdb.fasta -out GCA_017647965.1_ASM1764796v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:41:35,088] [INFO] Task succeeded: Blastn
[2023-06-28 18:41:35,092] [INFO] Selected 18 target genomes.
[2023-06-28 18:41:35,092] [INFO] Target genome list was writen to GCA_017647965.1_ASM1764796v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:41:35,103] [INFO] Task started: fastANI
[2023-06-28 18:41:35,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg860ec679-61c1-4438-9c0b-0c3db44bda77/GCA_017647965.1_ASM1764796v1_genomic.fna.gz --refList GCA_017647965.1_ASM1764796v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017647965.1_ASM1764796v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:41:41,751] [INFO] Task succeeded: fastANI
[2023-06-28 18:41:41,760] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 18:41:41,760] [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_017629325.1	s__RGIG1828 sp017629325	98.3789	262	339	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UMGS1810;f__UMGS1810;g__RGIG1828	95.0	98.55	98.55	0.77	0.77	2	conclusive
GCA_017437345.1	s__RGIG1828 sp017437345	82.0352	199	339	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UMGS1810;f__UMGS1810;g__RGIG1828	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017397885.1	s__RGIG1828 sp017397885	78.3806	68	339	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UMGS1810;f__UMGS1810;g__RGIG1828	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017416845.1	s__RGIG1828 sp017416845	78.0931	66	339	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UMGS1810;f__UMGS1810;g__RGIG1828	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015069015.1	s__RGIG1828 sp015069015	78.0056	88	339	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UMGS1810;f__UMGS1810;g__RGIG1828	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015068985.1	s__RGIG1828 sp015068985	77.7346	90	339	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UMGS1810;f__UMGS1810;g__RGIG1828	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016293435.1	s__RGIG1828 sp016293435	77.3105	64	339	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UMGS1810;f__UMGS1810;g__RGIG1828	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015068825.1	s__NSJ-50 sp015068825	77.0984	61	339	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UMGS1810;f__UMGS1810;g__NSJ-50	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:41:41,763] [INFO] GTDB search result was written to GCA_017647965.1_ASM1764796v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:41:41,763] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:41:41,767] [INFO] DFAST_QC result json was written to GCA_017647965.1_ASM1764796v1_genomic.fna/dqc_result.json
[2023-06-28 18:41:41,767] [INFO] DFAST_QC completed!
[2023-06-28 18:41:41,767] [INFO] Total running time: 0h0m36s