[2023-06-28 12:33:30,621] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:33:30,622] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:33:30,622] [INFO] DQC Reference Directory: /var/lib/cwl/stgede8fd81-5ca1-4fa6-a246-8752740998cb/dqc_reference
[2023-06-28 12:33:31,822] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:33:31,823] [INFO] Task started: Prodigal
[2023-06-28 12:33:31,823] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4b6d8db-451b-4e04-bff5-80022109e96a/GCA_017413945.1_ASM1741394v1_genomic.fna.gz | prodigal -d GCA_017413945.1_ASM1741394v1_genomic.fna/cds.fna -a GCA_017413945.1_ASM1741394v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:33:33,662] [INFO] Task succeeded: Prodigal
[2023-06-28 12:33:33,663] [INFO] Task started: HMMsearch
[2023-06-28 12:33:33,663] [INFO] Running command: hmmsearch --tblout GCA_017413945.1_ASM1741394v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgede8fd81-5ca1-4fa6-a246-8752740998cb/dqc_reference/reference_markers.hmm GCA_017413945.1_ASM1741394v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:33:33,856] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:33:33,858] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgd4b6d8db-451b-4e04-bff5-80022109e96a/GCA_017413945.1_ASM1741394v1_genomic.fna.gz]
[2023-06-28 12:33:33,876] [INFO] Query marker FASTA was written to GCA_017413945.1_ASM1741394v1_genomic.fna/markers.fasta
[2023-06-28 12:33:33,876] [INFO] Task started: Blastn
[2023-06-28 12:33:33,876] [INFO] Running command: blastn -query GCA_017413945.1_ASM1741394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgede8fd81-5ca1-4fa6-a246-8752740998cb/dqc_reference/reference_markers.fasta -out GCA_017413945.1_ASM1741394v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:33:34,392] [INFO] Task succeeded: Blastn
[2023-06-28 12:33:34,396] [INFO] Selected 10 target genomes.
[2023-06-28 12:33:34,397] [INFO] Target genome list was writen to GCA_017413945.1_ASM1741394v1_genomic.fna/target_genomes.txt
[2023-06-28 12:33:34,398] [INFO] Task started: fastANI
[2023-06-28 12:33:34,398] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4b6d8db-451b-4e04-bff5-80022109e96a/GCA_017413945.1_ASM1741394v1_genomic.fna.gz --refList GCA_017413945.1_ASM1741394v1_genomic.fna/target_genomes.txt --output GCA_017413945.1_ASM1741394v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:33:40,443] [INFO] Task succeeded: fastANI
[2023-06-28 12:33:40,443] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgede8fd81-5ca1-4fa6-a246-8752740998cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:33:40,444] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgede8fd81-5ca1-4fa6-a246-8752740998cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:33:40,446] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:33:40,446] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:33:40,446] [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 12:33:40,449] [INFO] DFAST Taxonomy check result was written to GCA_017413945.1_ASM1741394v1_genomic.fna/tc_result.tsv
[2023-06-28 12:33:40,450] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:33:40,450] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:33:40,450] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgede8fd81-5ca1-4fa6-a246-8752740998cb/dqc_reference/checkm_data
[2023-06-28 12:33:40,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:33:40,475] [INFO] Task started: CheckM
[2023-06-28 12:33:40,475] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017413945.1_ASM1741394v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017413945.1_ASM1741394v1_genomic.fna/checkm_input GCA_017413945.1_ASM1741394v1_genomic.fna/checkm_result
[2023-06-28 12:33:53,865] [INFO] Task succeeded: CheckM
[2023-06-28 12:33:53,866] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:33:53,888] [INFO] ===== Completeness check finished =====
[2023-06-28 12:33:53,889] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:33:53,889] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017413945.1_ASM1741394v1_genomic.fna/markers.fasta)
[2023-06-28 12:33:53,890] [INFO] Task started: Blastn
[2023-06-28 12:33:53,890] [INFO] Running command: blastn -query GCA_017413945.1_ASM1741394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgede8fd81-5ca1-4fa6-a246-8752740998cb/dqc_reference/reference_markers_gtdb.fasta -out GCA_017413945.1_ASM1741394v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:33:54,492] [INFO] Task succeeded: Blastn
[2023-06-28 12:33:54,497] [INFO] Selected 8 target genomes.
[2023-06-28 12:33:54,497] [INFO] Target genome list was writen to GCA_017413945.1_ASM1741394v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:33:54,502] [INFO] Task started: fastANI
[2023-06-28 12:33:54,502] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4b6d8db-451b-4e04-bff5-80022109e96a/GCA_017413945.1_ASM1741394v1_genomic.fna.gz --refList GCA_017413945.1_ASM1741394v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017413945.1_ASM1741394v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:33:58,761] [INFO] Task succeeded: fastANI
[2023-06-28 12:33:58,766] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:33:58,766] [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_017450105.1	s__RUG12461 sp017450105	97.6974	170	179	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG12461	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016286115.1	s__RUG12461 sp016286115	78.0754	83	179	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG12461	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:33:58,770] [INFO] GTDB search result was written to GCA_017413945.1_ASM1741394v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:33:58,770] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:33:58,773] [INFO] DFAST_QC result json was written to GCA_017413945.1_ASM1741394v1_genomic.fna/dqc_result.json
[2023-06-28 12:33:58,773] [INFO] DFAST_QC completed!
[2023-06-28 12:33:58,773] [INFO] Total running time: 0h0m28s