[2023-06-27 05:57:52,405] [INFO] DFAST_QC pipeline started.
[2023-06-27 05:57:52,419] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 05:57:52,420] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0874f88-d42f-4d30-8869-87f86602ea65/dqc_reference
[2023-06-27 05:57:53,644] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 05:57:53,645] [INFO] Task started: Prodigal
[2023-06-27 05:57:53,645] [INFO] Running command: gunzip -c /var/lib/cwl/stgad8364ae-8eaf-4bb2-b222-a5bdb9ec2d0d/GCA_026391945.1_ASM2639194v1_genomic.fna.gz | prodigal -d GCA_026391945.1_ASM2639194v1_genomic.fna/cds.fna -a GCA_026391945.1_ASM2639194v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 05:58:09,707] [INFO] Task succeeded: Prodigal
[2023-06-27 05:58:09,708] [INFO] Task started: HMMsearch
[2023-06-27 05:58:09,708] [INFO] Running command: hmmsearch --tblout GCA_026391945.1_ASM2639194v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0874f88-d42f-4d30-8869-87f86602ea65/dqc_reference/reference_markers.hmm GCA_026391945.1_ASM2639194v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 05:58:09,990] [INFO] Task succeeded: HMMsearch
[2023-06-27 05:58:09,992] [INFO] Found 6/6 markers.
[2023-06-27 05:58:10,035] [INFO] Query marker FASTA was written to GCA_026391945.1_ASM2639194v1_genomic.fna/markers.fasta
[2023-06-27 05:58:10,035] [INFO] Task started: Blastn
[2023-06-27 05:58:10,035] [INFO] Running command: blastn -query GCA_026391945.1_ASM2639194v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0874f88-d42f-4d30-8869-87f86602ea65/dqc_reference/reference_markers.fasta -out GCA_026391945.1_ASM2639194v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:58:10,720] [INFO] Task succeeded: Blastn
[2023-06-27 05:58:10,741] [INFO] Selected 24 target genomes.
[2023-06-27 05:58:10,742] [INFO] Target genome list was writen to GCA_026391945.1_ASM2639194v1_genomic.fna/target_genomes.txt
[2023-06-27 05:58:10,745] [INFO] Task started: fastANI
[2023-06-27 05:58:10,745] [INFO] Running command: fastANI --query /var/lib/cwl/stgad8364ae-8eaf-4bb2-b222-a5bdb9ec2d0d/GCA_026391945.1_ASM2639194v1_genomic.fna.gz --refList GCA_026391945.1_ASM2639194v1_genomic.fna/target_genomes.txt --output GCA_026391945.1_ASM2639194v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 05:58:26,598] [INFO] Task succeeded: fastANI
[2023-06-27 05:58:26,599] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0874f88-d42f-4d30-8869-87f86602ea65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 05:58:26,599] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0874f88-d42f-4d30-8869-87f86602ea65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 05:58:26,601] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 05:58:26,601] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 05:58:26,601] [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
--------------------------------------------------------------------------------
[2023-06-27 05:58:26,604] [INFO] DFAST Taxonomy check result was written to GCA_026391945.1_ASM2639194v1_genomic.fna/tc_result.tsv
[2023-06-27 05:58:26,604] [INFO] ===== Taxonomy check completed =====
[2023-06-27 05:58:26,605] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 05:58:26,605] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0874f88-d42f-4d30-8869-87f86602ea65/dqc_reference/checkm_data
[2023-06-27 05:58:26,608] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 05:58:26,646] [INFO] Task started: CheckM
[2023-06-27 05:58:26,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026391945.1_ASM2639194v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026391945.1_ASM2639194v1_genomic.fna/checkm_input GCA_026391945.1_ASM2639194v1_genomic.fna/checkm_result
[2023-06-27 05:59:17,707] [INFO] Task succeeded: CheckM
[2023-06-27 05:59:17,708] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 05:59:17,728] [INFO] ===== Completeness check finished =====
[2023-06-27 05:59:17,729] [INFO] ===== Start GTDB Search =====
[2023-06-27 05:59:17,729] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026391945.1_ASM2639194v1_genomic.fna/markers.fasta)
[2023-06-27 05:59:17,729] [INFO] Task started: Blastn
[2023-06-27 05:59:17,729] [INFO] Running command: blastn -query GCA_026391945.1_ASM2639194v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0874f88-d42f-4d30-8869-87f86602ea65/dqc_reference/reference_markers_gtdb.fasta -out GCA_026391945.1_ASM2639194v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:59:18,795] [INFO] Task succeeded: Blastn
[2023-06-27 05:59:18,800] [INFO] Selected 29 target genomes.
[2023-06-27 05:59:18,801] [INFO] Target genome list was writen to GCA_026391945.1_ASM2639194v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 05:59:18,816] [INFO] Task started: fastANI
[2023-06-27 05:59:18,816] [INFO] Running command: fastANI --query /var/lib/cwl/stgad8364ae-8eaf-4bb2-b222-a5bdb9ec2d0d/GCA_026391945.1_ASM2639194v1_genomic.fna.gz --refList GCA_026391945.1_ASM2639194v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026391945.1_ASM2639194v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 05:59:36,080] [INFO] Task succeeded: fastANI
[2023-06-27 05:59:36,090] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 05:59:36,090] [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_016720655.1	s__JADKJP01 sp016720655	76.23	70	975	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767-A;f__2013-40CM-41-45;g__JADKJP01	95.0	98.44	98.22	0.95	0.93	7	-
GCA_003151745.1	s__PALSA-967 sp003151745	76.0688	58	975	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767-A;f__2013-40CM-41-45;g__PALSA-967	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720935.1	s__JADKJP01 sp016720935	75.9822	88	975	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767-A;f__2013-40CM-41-45;g__JADKJP01	95.0	99.14	99.10	0.95	0.94	3	-
--------------------------------------------------------------------------------
[2023-06-27 05:59:36,092] [INFO] GTDB search result was written to GCA_026391945.1_ASM2639194v1_genomic.fna/result_gtdb.tsv
[2023-06-27 05:59:36,093] [INFO] ===== GTDB Search completed =====
[2023-06-27 05:59:36,113] [INFO] DFAST_QC result json was written to GCA_026391945.1_ASM2639194v1_genomic.fna/dqc_result.json
[2023-06-27 05:59:36,114] [INFO] DFAST_QC completed!
[2023-06-27 05:59:36,114] [INFO] Total running time: 0h1m44s