[2023-06-28 05:08:51,997] [INFO] DFAST_QC pipeline started.
[2023-06-28 05:08:52,006] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 05:08:52,006] [INFO] DQC Reference Directory: /var/lib/cwl/stgc59c24e3-41ed-4052-ac45-ee7590d881f0/dqc_reference
[2023-06-28 05:08:53,705] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 05:08:53,715] [INFO] Task started: Prodigal
[2023-06-28 05:08:53,715] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2575902-41f8-4404-92e3-734ab48bc5a2/GCA_944391455.1_E02_bin279_genomic.fna.gz | prodigal -d GCA_944391455.1_E02_bin279_genomic.fna/cds.fna -a GCA_944391455.1_E02_bin279_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 05:08:57,687] [INFO] Task succeeded: Prodigal
[2023-06-28 05:08:57,687] [INFO] Task started: HMMsearch
[2023-06-28 05:08:57,687] [INFO] Running command: hmmsearch --tblout GCA_944391455.1_E02_bin279_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc59c24e3-41ed-4052-ac45-ee7590d881f0/dqc_reference/reference_markers.hmm GCA_944391455.1_E02_bin279_genomic.fna/protein.faa > /dev/null
[2023-06-28 05:08:57,921] [INFO] Task succeeded: HMMsearch
[2023-06-28 05:08:57,922] [INFO] Found 6/6 markers.
[2023-06-28 05:08:57,943] [INFO] Query marker FASTA was written to GCA_944391455.1_E02_bin279_genomic.fna/markers.fasta
[2023-06-28 05:08:57,943] [INFO] Task started: Blastn
[2023-06-28 05:08:57,943] [INFO] Running command: blastn -query GCA_944391455.1_E02_bin279_genomic.fna/markers.fasta -db /var/lib/cwl/stgc59c24e3-41ed-4052-ac45-ee7590d881f0/dqc_reference/reference_markers.fasta -out GCA_944391455.1_E02_bin279_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:08:58,646] [INFO] Task succeeded: Blastn
[2023-06-28 05:08:58,651] [INFO] Selected 31 target genomes.
[2023-06-28 05:08:58,652] [INFO] Target genome list was writen to GCA_944391455.1_E02_bin279_genomic.fna/target_genomes.txt
[2023-06-28 05:08:58,657] [INFO] Task started: fastANI
[2023-06-28 05:08:58,657] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2575902-41f8-4404-92e3-734ab48bc5a2/GCA_944391455.1_E02_bin279_genomic.fna.gz --refList GCA_944391455.1_E02_bin279_genomic.fna/target_genomes.txt --output GCA_944391455.1_E02_bin279_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 05:09:20,369] [INFO] Task succeeded: fastANI
[2023-06-28 05:09:20,370] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc59c24e3-41ed-4052-ac45-ee7590d881f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 05:09:20,370] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc59c24e3-41ed-4052-ac45-ee7590d881f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 05:09:20,372] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 05:09:20,373] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 05:09:20,373] [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 05:09:20,375] [INFO] DFAST Taxonomy check result was written to GCA_944391455.1_E02_bin279_genomic.fna/tc_result.tsv
[2023-06-28 05:09:20,388] [INFO] ===== Taxonomy check completed =====
[2023-06-28 05:09:20,388] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 05:09:20,389] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc59c24e3-41ed-4052-ac45-ee7590d881f0/dqc_reference/checkm_data
[2023-06-28 05:09:20,393] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 05:09:20,419] [INFO] Task started: CheckM
[2023-06-28 05:09:20,419] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944391455.1_E02_bin279_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944391455.1_E02_bin279_genomic.fna/checkm_input GCA_944391455.1_E02_bin279_genomic.fna/checkm_result
[2023-06-28 05:09:39,464] [INFO] Task succeeded: CheckM
[2023-06-28 05:09:39,466] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 05:09:39,498] [INFO] ===== Completeness check finished =====
[2023-06-28 05:09:39,498] [INFO] ===== Start GTDB Search =====
[2023-06-28 05:09:39,499] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944391455.1_E02_bin279_genomic.fna/markers.fasta)
[2023-06-28 05:09:39,499] [INFO] Task started: Blastn
[2023-06-28 05:09:39,499] [INFO] Running command: blastn -query GCA_944391455.1_E02_bin279_genomic.fna/markers.fasta -db /var/lib/cwl/stgc59c24e3-41ed-4052-ac45-ee7590d881f0/dqc_reference/reference_markers_gtdb.fasta -out GCA_944391455.1_E02_bin279_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:09:40,646] [INFO] Task succeeded: Blastn
[2023-06-28 05:09:40,649] [INFO] Selected 16 target genomes.
[2023-06-28 05:09:40,650] [INFO] Target genome list was writen to GCA_944391455.1_E02_bin279_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 05:09:40,656] [INFO] Task started: fastANI
[2023-06-28 05:09:40,656] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2575902-41f8-4404-92e3-734ab48bc5a2/GCA_944391455.1_E02_bin279_genomic.fna.gz --refList GCA_944391455.1_E02_bin279_genomic.fna/target_genomes_gtdb.txt --output GCA_944391455.1_E02_bin279_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 05:09:45,804] [INFO] Task succeeded: fastANI
[2023-06-28 05:09:45,827] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 05:09:45,828] [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_900538765.1	s__HGM16780 sp900538765	98.8508	481	519	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__HGM16780	95.0	98.94	98.77	0.94	0.91	4	conclusive
GCA_900762585.1	s__HGM16780 sp900762585	78.7118	198	519	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__HGM16780	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001917125.1	s__Scatocola faecipullorum	77.6987	130	519	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__Scatocola	95.0	98.98	98.59	0.91	0.85	10	-
GCA_017626035.1	s__JAGAJR01 sp017626035	77.3902	115	519	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__JAGAJR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000436375.1	s__Scatacola_A faecigallinarum	77.3053	117	519	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__Scatacola_A	95.0	97.40	96.59	0.91	0.88	10	-
GCA_910585375.1	s__MGBC133411 sp910585375	77.2997	108	519	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__MGBC133411	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577205.1	s__Scatocola sp910577205	77.1186	113	519	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__Scatocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551585.1	s__CAJLXD01 sp900551585	77.1171	83	519	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAJLXD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017935485.1	s__MGBC133411 sp017935485	77.071	110	519	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__MGBC133411	95.0	98.32	98.32	0.87	0.87	2	-
GCA_910587405.1	s__51-20 sp910587405	76.673	51	519	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__51-20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017480995.1	s__CAZU01 sp017480995	76.4653	66	519	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAZU01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 05:09:45,851] [INFO] GTDB search result was written to GCA_944391455.1_E02_bin279_genomic.fna/result_gtdb.tsv
[2023-06-28 05:09:45,852] [INFO] ===== GTDB Search completed =====
[2023-06-28 05:09:45,855] [INFO] DFAST_QC result json was written to GCA_944391455.1_E02_bin279_genomic.fna/dqc_result.json
[2023-06-28 05:09:45,856] [INFO] DFAST_QC completed!
[2023-06-28 05:09:45,856] [INFO] Total running time: 0h0m54s