[2023-06-04 20:37:26,480] [INFO] DFAST_QC pipeline started.
[2023-06-04 20:37:26,485] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 20:37:26,485] [INFO] DQC Reference Directory: /var/lib/cwl/stg5aa33491-be8d-4aa4-9443-43d27601ef41/dqc_reference
[2023-06-04 20:37:27,842] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 20:37:27,843] [INFO] Task started: Prodigal
[2023-06-04 20:37:27,843] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f1d675f-57c8-4807-874d-868e44f4e6c2/GCA_934087065.1_ERR7738596_bin.96_genomic.fna.gz | prodigal -d GCA_934087065.1_ERR7738596_bin.96_genomic.fna/cds.fna -a GCA_934087065.1_ERR7738596_bin.96_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 20:37:29,464] [INFO] Task succeeded: Prodigal
[2023-06-04 20:37:29,464] [INFO] Task started: HMMsearch
[2023-06-04 20:37:29,464] [INFO] Running command: hmmsearch --tblout GCA_934087065.1_ERR7738596_bin.96_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5aa33491-be8d-4aa4-9443-43d27601ef41/dqc_reference/reference_markers.hmm GCA_934087065.1_ERR7738596_bin.96_genomic.fna/protein.faa > /dev/null
[2023-06-04 20:37:29,668] [INFO] Task succeeded: HMMsearch
[2023-06-04 20:37:29,670] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5f1d675f-57c8-4807-874d-868e44f4e6c2/GCA_934087065.1_ERR7738596_bin.96_genomic.fna.gz]
[2023-06-04 20:37:29,689] [INFO] Query marker FASTA was written to GCA_934087065.1_ERR7738596_bin.96_genomic.fna/markers.fasta
[2023-06-04 20:37:29,689] [INFO] Task started: Blastn
[2023-06-04 20:37:29,690] [INFO] Running command: blastn -query GCA_934087065.1_ERR7738596_bin.96_genomic.fna/markers.fasta -db /var/lib/cwl/stg5aa33491-be8d-4aa4-9443-43d27601ef41/dqc_reference/reference_markers.fasta -out GCA_934087065.1_ERR7738596_bin.96_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:37:30,950] [INFO] Task succeeded: Blastn
[2023-06-04 20:37:30,955] [INFO] Selected 21 target genomes.
[2023-06-04 20:37:30,956] [INFO] Target genome list was writen to GCA_934087065.1_ERR7738596_bin.96_genomic.fna/target_genomes.txt
[2023-06-04 20:37:30,982] [INFO] Task started: fastANI
[2023-06-04 20:37:30,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f1d675f-57c8-4807-874d-868e44f4e6c2/GCA_934087065.1_ERR7738596_bin.96_genomic.fna.gz --refList GCA_934087065.1_ERR7738596_bin.96_genomic.fna/target_genomes.txt --output GCA_934087065.1_ERR7738596_bin.96_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 20:37:38,517] [INFO] Task succeeded: fastANI
[2023-06-04 20:37:38,518] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5aa33491-be8d-4aa4-9443-43d27601ef41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 20:37:38,518] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5aa33491-be8d-4aa4-9443-43d27601ef41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 20:37:38,520] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 20:37:38,520] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 20:37:38,520] [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
--------------------------------------------------------------------------------
[2023-06-04 20:37:38,523] [INFO] DFAST Taxonomy check result was written to GCA_934087065.1_ERR7738596_bin.96_genomic.fna/tc_result.tsv
[2023-06-04 20:37:38,523] [INFO] ===== Taxonomy check completed =====
[2023-06-04 20:37:38,523] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 20:37:38,524] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5aa33491-be8d-4aa4-9443-43d27601ef41/dqc_reference/checkm_data
[2023-06-04 20:37:38,526] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 20:37:38,544] [INFO] Task started: CheckM
[2023-06-04 20:37:38,544] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934087065.1_ERR7738596_bin.96_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934087065.1_ERR7738596_bin.96_genomic.fna/checkm_input GCA_934087065.1_ERR7738596_bin.96_genomic.fna/checkm_result
[2023-06-04 20:37:52,883] [INFO] Task succeeded: CheckM
[2023-06-04 20:37:52,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 20:37:52,909] [INFO] ===== Completeness check finished =====
[2023-06-04 20:37:52,909] [INFO] ===== Start GTDB Search =====
[2023-06-04 20:37:52,909] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934087065.1_ERR7738596_bin.96_genomic.fna/markers.fasta)
[2023-06-04 20:37:52,910] [INFO] Task started: Blastn
[2023-06-04 20:37:52,910] [INFO] Running command: blastn -query GCA_934087065.1_ERR7738596_bin.96_genomic.fna/markers.fasta -db /var/lib/cwl/stg5aa33491-be8d-4aa4-9443-43d27601ef41/dqc_reference/reference_markers_gtdb.fasta -out GCA_934087065.1_ERR7738596_bin.96_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:37:53,722] [INFO] Task succeeded: Blastn
[2023-06-04 20:37:53,727] [INFO] Selected 17 target genomes.
[2023-06-04 20:37:53,728] [INFO] Target genome list was writen to GCA_934087065.1_ERR7738596_bin.96_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 20:37:53,791] [INFO] Task started: fastANI
[2023-06-04 20:37:53,792] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f1d675f-57c8-4807-874d-868e44f4e6c2/GCA_934087065.1_ERR7738596_bin.96_genomic.fna.gz --refList GCA_934087065.1_ERR7738596_bin.96_genomic.fna/target_genomes_gtdb.txt --output GCA_934087065.1_ERR7738596_bin.96_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 20:37:58,201] [INFO] Task succeeded: fastANI
[2023-06-04 20:37:58,211] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-04 20:37:58,211] [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_003524085.1	s__CAG-628 sp003524085	94.6215	285	334	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-628	95.0	98.02	97.61	0.90	0.89	5	-
GCA_000438415.1	s__CAG-628 sp000438415	84.3807	204	334	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-628	95.0	97.86	97.71	0.86	0.83	4	-
GCA_900553835.1	s__CAG-628 sp900553835	78.9113	121	334	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-628	95.0	99.81	99.81	0.82	0.82	2	-
GCA_910586295.1	s__MGBC139354 sp910586295	77.9302	70	334	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__MGBC139354	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900321795.1	s__RUG727 sp900321795	77.7093	59	334	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG727	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902797005.1	s__RUG727 sp902797005	77.3776	62	334	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG727	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016292035.1	s__RUG727 sp016292035	77.2362	59	334	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG727	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 20:37:58,213] [INFO] GTDB search result was written to GCA_934087065.1_ERR7738596_bin.96_genomic.fna/result_gtdb.tsv
[2023-06-04 20:37:58,214] [INFO] ===== GTDB Search completed =====
[2023-06-04 20:37:58,217] [INFO] DFAST_QC result json was written to GCA_934087065.1_ERR7738596_bin.96_genomic.fna/dqc_result.json
[2023-06-04 20:37:58,217] [INFO] DFAST_QC completed!
[2023-06-04 20:37:58,217] [INFO] Total running time: 0h0m32s