[2023-06-29 19:52:57,131] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:52:57,133] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:52:57,134] [INFO] DQC Reference Directory: /var/lib/cwl/stg57eefd05-e8c6-4932-9f80-1ac8e9deedcc/dqc_reference
[2023-06-29 19:52:58,422] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:52:58,423] [INFO] Task started: Prodigal
[2023-06-29 19:52:58,423] [INFO] Running command: gunzip -c /var/lib/cwl/stge4918bff-27e9-438c-94ca-a6c2ea8ed404/GCA_016929255.1_ASM1692925v1_genomic.fna.gz | prodigal -d GCA_016929255.1_ASM1692925v1_genomic.fna/cds.fna -a GCA_016929255.1_ASM1692925v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:53:01,505] [INFO] Task succeeded: Prodigal
[2023-06-29 19:53:01,505] [INFO] Task started: HMMsearch
[2023-06-29 19:53:01,505] [INFO] Running command: hmmsearch --tblout GCA_016929255.1_ASM1692925v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57eefd05-e8c6-4932-9f80-1ac8e9deedcc/dqc_reference/reference_markers.hmm GCA_016929255.1_ASM1692925v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:53:01,704] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:53:01,706] [WARNING] Found 2/6 markers. [/var/lib/cwl/stge4918bff-27e9-438c-94ca-a6c2ea8ed404/GCA_016929255.1_ASM1692925v1_genomic.fna.gz]
[2023-06-29 19:53:01,723] [INFO] Query marker FASTA was written to GCA_016929255.1_ASM1692925v1_genomic.fna/markers.fasta
[2023-06-29 19:53:01,723] [INFO] Task started: Blastn
[2023-06-29 19:53:01,723] [INFO] Running command: blastn -query GCA_016929255.1_ASM1692925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57eefd05-e8c6-4932-9f80-1ac8e9deedcc/dqc_reference/reference_markers.fasta -out GCA_016929255.1_ASM1692925v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:53:02,255] [INFO] Task succeeded: Blastn
[2023-06-29 19:53:02,259] [INFO] Selected 5 target genomes.
[2023-06-29 19:53:02,260] [INFO] Target genome list was writen to GCA_016929255.1_ASM1692925v1_genomic.fna/target_genomes.txt
[2023-06-29 19:53:02,263] [INFO] Task started: fastANI
[2023-06-29 19:53:02,263] [INFO] Running command: fastANI --query /var/lib/cwl/stge4918bff-27e9-438c-94ca-a6c2ea8ed404/GCA_016929255.1_ASM1692925v1_genomic.fna.gz --refList GCA_016929255.1_ASM1692925v1_genomic.fna/target_genomes.txt --output GCA_016929255.1_ASM1692925v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:53:05,247] [INFO] Task succeeded: fastANI
[2023-06-29 19:53:05,248] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57eefd05-e8c6-4932-9f80-1ac8e9deedcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:53:05,248] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57eefd05-e8c6-4932-9f80-1ac8e9deedcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:53:05,250] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 19:53:05,251] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 19:53:05,251] [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
--------------------------------------------------------------------------------
[2023-06-29 19:53:05,253] [INFO] DFAST Taxonomy check result was written to GCA_016929255.1_ASM1692925v1_genomic.fna/tc_result.tsv
[2023-06-29 19:53:05,254] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:53:05,254] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:53:05,254] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57eefd05-e8c6-4932-9f80-1ac8e9deedcc/dqc_reference/checkm_data
[2023-06-29 19:53:05,258] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:53:05,274] [INFO] Task started: CheckM
[2023-06-29 19:53:05,274] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016929255.1_ASM1692925v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016929255.1_ASM1692925v1_genomic.fna/checkm_input GCA_016929255.1_ASM1692925v1_genomic.fna/checkm_result
[2023-06-29 19:53:22,418] [INFO] Task succeeded: CheckM
[2023-06-29 19:53:22,420] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 19:53:22,442] [INFO] ===== Completeness check finished =====
[2023-06-29 19:53:22,442] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:53:22,443] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016929255.1_ASM1692925v1_genomic.fna/markers.fasta)
[2023-06-29 19:53:22,443] [INFO] Task started: Blastn
[2023-06-29 19:53:22,443] [INFO] Running command: blastn -query GCA_016929255.1_ASM1692925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57eefd05-e8c6-4932-9f80-1ac8e9deedcc/dqc_reference/reference_markers_gtdb.fasta -out GCA_016929255.1_ASM1692925v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:53:23,114] [INFO] Task succeeded: Blastn
[2023-06-29 19:53:23,120] [INFO] Selected 8 target genomes.
[2023-06-29 19:53:23,120] [INFO] Target genome list was writen to GCA_016929255.1_ASM1692925v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:53:23,130] [INFO] Task started: fastANI
[2023-06-29 19:53:23,131] [INFO] Running command: fastANI --query /var/lib/cwl/stge4918bff-27e9-438c-94ca-a6c2ea8ed404/GCA_016929255.1_ASM1692925v1_genomic.fna.gz --refList GCA_016929255.1_ASM1692925v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016929255.1_ASM1692925v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:53:25,958] [INFO] Task succeeded: fastANI
[2023-06-29 19:53:25,961] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 19:53:25,962] [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_016929255.1	s__JABMQF01 sp016929255	99.9999	375	378	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Woesearchaeales;f__UBA11576;g__JABMQF01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018830225.1	s__JABMQF01 sp018830225	85.5866	265	378	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Woesearchaeales;f__UBA11576;g__JABMQF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 19:53:25,964] [INFO] GTDB search result was written to GCA_016929255.1_ASM1692925v1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:53:25,964] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:53:25,967] [INFO] DFAST_QC result json was written to GCA_016929255.1_ASM1692925v1_genomic.fna/dqc_result.json
[2023-06-29 19:53:25,967] [INFO] DFAST_QC completed!
[2023-06-29 19:53:25,967] [INFO] Total running time: 0h0m29s