[2023-06-30 04:49:30,464] [INFO] DFAST_QC pipeline started.
[2023-06-30 04:49:30,467] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 04:49:30,467] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd52d294-d9b4-4b9a-b1fe-02be28d9054d/dqc_reference
[2023-06-30 04:49:31,667] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 04:49:31,668] [INFO] Task started: Prodigal
[2023-06-30 04:49:31,668] [INFO] Running command: gunzip -c /var/lib/cwl/stg53ba74ca-1b05-4c41-90db-5677857aa88b/GCA_016875975.1_JGI_2017-08-21_genomic.fna.gz | prodigal -d GCA_016875975.1_JGI_2017-08-21_genomic.fna/cds.fna -a GCA_016875975.1_JGI_2017-08-21_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 04:49:35,520] [INFO] Task succeeded: Prodigal
[2023-06-30 04:49:35,520] [INFO] Task started: HMMsearch
[2023-06-30 04:49:35,520] [INFO] Running command: hmmsearch --tblout GCA_016875975.1_JGI_2017-08-21_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd52d294-d9b4-4b9a-b1fe-02be28d9054d/dqc_reference/reference_markers.hmm GCA_016875975.1_JGI_2017-08-21_genomic.fna/protein.faa > /dev/null
[2023-06-30 04:49:35,717] [INFO] Task succeeded: HMMsearch
[2023-06-30 04:49:35,719] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg53ba74ca-1b05-4c41-90db-5677857aa88b/GCA_016875975.1_JGI_2017-08-21_genomic.fna.gz]
[2023-06-30 04:49:35,742] [INFO] Query marker FASTA was written to GCA_016875975.1_JGI_2017-08-21_genomic.fna/markers.fasta
[2023-06-30 04:49:35,742] [INFO] Task started: Blastn
[2023-06-30 04:49:35,742] [INFO] Running command: blastn -query GCA_016875975.1_JGI_2017-08-21_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd52d294-d9b4-4b9a-b1fe-02be28d9054d/dqc_reference/reference_markers.fasta -out GCA_016875975.1_JGI_2017-08-21_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:49:36,287] [INFO] Task succeeded: Blastn
[2023-06-30 04:49:36,292] [INFO] Selected 18 target genomes.
[2023-06-30 04:49:36,292] [INFO] Target genome list was writen to GCA_016875975.1_JGI_2017-08-21_genomic.fna/target_genomes.txt
[2023-06-30 04:49:36,296] [INFO] Task started: fastANI
[2023-06-30 04:49:36,297] [INFO] Running command: fastANI --query /var/lib/cwl/stg53ba74ca-1b05-4c41-90db-5677857aa88b/GCA_016875975.1_JGI_2017-08-21_genomic.fna.gz --refList GCA_016875975.1_JGI_2017-08-21_genomic.fna/target_genomes.txt --output GCA_016875975.1_JGI_2017-08-21_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 04:49:45,142] [INFO] Task succeeded: fastANI
[2023-06-30 04:49:45,142] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd52d294-d9b4-4b9a-b1fe-02be28d9054d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 04:49:45,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd52d294-d9b4-4b9a-b1fe-02be28d9054d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 04:49:45,146] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 04:49:45,146] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 04:49:45,146] [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
--------------------------------------------------------------------------------
[2023-06-30 04:49:45,148] [INFO] DFAST Taxonomy check result was written to GCA_016875975.1_JGI_2017-08-21_genomic.fna/tc_result.tsv
[2023-06-30 04:49:45,149] [INFO] ===== Taxonomy check completed =====
[2023-06-30 04:49:45,149] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 04:49:45,150] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd52d294-d9b4-4b9a-b1fe-02be28d9054d/dqc_reference/checkm_data
[2023-06-30 04:49:45,153] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 04:49:45,179] [INFO] Task started: CheckM
[2023-06-30 04:49:45,179] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016875975.1_JGI_2017-08-21_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016875975.1_JGI_2017-08-21_genomic.fna/checkm_input GCA_016875975.1_JGI_2017-08-21_genomic.fna/checkm_result
[2023-06-30 04:50:03,654] [INFO] Task succeeded: CheckM
[2023-06-30 04:50:03,656] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 04:50:03,677] [INFO] ===== Completeness check finished =====
[2023-06-30 04:50:03,677] [INFO] ===== Start GTDB Search =====
[2023-06-30 04:50:03,678] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016875975.1_JGI_2017-08-21_genomic.fna/markers.fasta)
[2023-06-30 04:50:03,678] [INFO] Task started: Blastn
[2023-06-30 04:50:03,678] [INFO] Running command: blastn -query GCA_016875975.1_JGI_2017-08-21_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd52d294-d9b4-4b9a-b1fe-02be28d9054d/dqc_reference/reference_markers_gtdb.fasta -out GCA_016875975.1_JGI_2017-08-21_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:50:04,387] [INFO] Task succeeded: Blastn
[2023-06-30 04:50:04,393] [INFO] Selected 18 target genomes.
[2023-06-30 04:50:04,393] [INFO] Target genome list was writen to GCA_016875975.1_JGI_2017-08-21_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 04:50:04,407] [INFO] Task started: fastANI
[2023-06-30 04:50:04,408] [INFO] Running command: fastANI --query /var/lib/cwl/stg53ba74ca-1b05-4c41-90db-5677857aa88b/GCA_016875975.1_JGI_2017-08-21_genomic.fna.gz --refList GCA_016875975.1_JGI_2017-08-21_genomic.fna/target_genomes_gtdb.txt --output GCA_016875975.1_JGI_2017-08-21_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 04:50:10,957] [INFO] Task succeeded: fastANI
[2023-06-30 04:50:10,963] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 04:50:10,963] [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_016875975.1	s__VGOF01 sp016875975	99.9999	405	412	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__GIF9;f__UBA5620;g__VGOF01	95.0	97.92	97.92	0.67	0.67	2	conclusive
GCA_016875925.1	s__VGOF01 sp016875925	87.8945	260	412	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__GIF9;f__UBA5620;g__VGOF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 04:50:10,966] [INFO] GTDB search result was written to GCA_016875975.1_JGI_2017-08-21_genomic.fna/result_gtdb.tsv
[2023-06-30 04:50:10,967] [INFO] ===== GTDB Search completed =====
[2023-06-30 04:50:10,969] [INFO] DFAST_QC result json was written to GCA_016875975.1_JGI_2017-08-21_genomic.fna/dqc_result.json
[2023-06-30 04:50:10,969] [INFO] DFAST_QC completed!
[2023-06-30 04:50:10,969] [INFO] Total running time: 0h0m41s