[2023-06-19 02:16:56,287] [INFO] DFAST_QC pipeline started.
[2023-06-19 02:16:56,289] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 02:16:56,290] [INFO] DQC Reference Directory: /var/lib/cwl/stg33bb9218-881e-47c0-aa71-5011ee81af40/dqc_reference
[2023-06-19 02:16:59,551] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 02:16:59,551] [INFO] Task started: Prodigal
[2023-06-19 02:16:59,552] [INFO] Running command: gunzip -c /var/lib/cwl/stg42c062ad-e80f-469e-9fea-cb69d6074c45/GCA_018006255.1_ASM1800625v1_genomic.fna.gz | prodigal -d GCA_018006255.1_ASM1800625v1_genomic.fna/cds.fna -a GCA_018006255.1_ASM1800625v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 02:17:03,159] [INFO] Task succeeded: Prodigal
[2023-06-19 02:17:03,159] [INFO] Task started: HMMsearch
[2023-06-19 02:17:03,160] [INFO] Running command: hmmsearch --tblout GCA_018006255.1_ASM1800625v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33bb9218-881e-47c0-aa71-5011ee81af40/dqc_reference/reference_markers.hmm GCA_018006255.1_ASM1800625v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 02:17:03,400] [INFO] Task succeeded: HMMsearch
[2023-06-19 02:17:03,402] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg42c062ad-e80f-469e-9fea-cb69d6074c45/GCA_018006255.1_ASM1800625v1_genomic.fna.gz]
[2023-06-19 02:17:03,423] [INFO] Query marker FASTA was written to GCA_018006255.1_ASM1800625v1_genomic.fna/markers.fasta
[2023-06-19 02:17:03,424] [INFO] Task started: Blastn
[2023-06-19 02:17:03,424] [INFO] Running command: blastn -query GCA_018006255.1_ASM1800625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33bb9218-881e-47c0-aa71-5011ee81af40/dqc_reference/reference_markers.fasta -out GCA_018006255.1_ASM1800625v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:17:06,435] [INFO] Task succeeded: Blastn
[2023-06-19 02:17:06,440] [INFO] Selected 9 target genomes.
[2023-06-19 02:17:06,440] [INFO] Target genome list was writen to GCA_018006255.1_ASM1800625v1_genomic.fna/target_genomes.txt
[2023-06-19 02:17:06,443] [INFO] Task started: fastANI
[2023-06-19 02:17:06,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg42c062ad-e80f-469e-9fea-cb69d6074c45/GCA_018006255.1_ASM1800625v1_genomic.fna.gz --refList GCA_018006255.1_ASM1800625v1_genomic.fna/target_genomes.txt --output GCA_018006255.1_ASM1800625v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 02:17:11,721] [INFO] Task succeeded: fastANI
[2023-06-19 02:17:11,721] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33bb9218-881e-47c0-aa71-5011ee81af40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 02:17:11,722] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33bb9218-881e-47c0-aa71-5011ee81af40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 02:17:11,734] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 02:17:11,734] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 02:17:11,734] [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
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	78.2951	119	331	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	78.1539	143	331	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	78.0312	142	331	95	below_threshold
Lysobacter aestuarii	strain=JCM 31130	GCA_006546775.1	1706195	1706195	type	True	77.9592	103	331	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	77.7667	131	331	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	77.7278	132	331	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	77.7173	126	331	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	77.702	159	331	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	77.4325	138	331	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 02:17:11,736] [INFO] DFAST Taxonomy check result was written to GCA_018006255.1_ASM1800625v1_genomic.fna/tc_result.tsv
[2023-06-19 02:17:11,737] [INFO] ===== Taxonomy check completed =====
[2023-06-19 02:17:11,737] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 02:17:11,737] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33bb9218-881e-47c0-aa71-5011ee81af40/dqc_reference/checkm_data
[2023-06-19 02:17:11,738] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 02:17:11,757] [INFO] Task started: CheckM
[2023-06-19 02:17:11,758] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018006255.1_ASM1800625v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018006255.1_ASM1800625v1_genomic.fna/checkm_input GCA_018006255.1_ASM1800625v1_genomic.fna/checkm_result
[2023-06-19 02:17:28,901] [INFO] Task succeeded: CheckM
[2023-06-19 02:17:28,902] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 29.17%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 02:17:28,922] [INFO] ===== Completeness check finished =====
[2023-06-19 02:17:28,922] [INFO] ===== Start GTDB Search =====
[2023-06-19 02:17:28,922] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018006255.1_ASM1800625v1_genomic.fna/markers.fasta)
[2023-06-19 02:17:28,923] [INFO] Task started: Blastn
[2023-06-19 02:17:28,923] [INFO] Running command: blastn -query GCA_018006255.1_ASM1800625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33bb9218-881e-47c0-aa71-5011ee81af40/dqc_reference/reference_markers_gtdb.fasta -out GCA_018006255.1_ASM1800625v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:17:29,681] [INFO] Task succeeded: Blastn
[2023-06-19 02:17:29,686] [INFO] Selected 7 target genomes.
[2023-06-19 02:17:29,686] [INFO] Target genome list was writen to GCA_018006255.1_ASM1800625v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 02:17:29,691] [INFO] Task started: fastANI
[2023-06-19 02:17:29,692] [INFO] Running command: fastANI --query /var/lib/cwl/stg42c062ad-e80f-469e-9fea-cb69d6074c45/GCA_018006255.1_ASM1800625v1_genomic.fna.gz --refList GCA_018006255.1_ASM1800625v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018006255.1_ASM1800625v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 02:17:34,176] [INFO] Task succeeded: fastANI
[2023-06-19 02:17:34,188] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 02:17:34,189] [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_017997455.1	s__JAGOEZ01 sp017997455	98.184	261	331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__JAGOEZ01	95.0	98.60	98.27	0.77	0.77	3	conclusive
GCA_002405525.1	s__UBA4656 sp002405525	79.3205	153	331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__UBA4656	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016182785.1	s__JADKHK01 sp016182785	78.4184	124	331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__JADKHK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009996615.1	s__Dokdonella_A sp009996615	78.0683	150	331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002297645.1	s__Dokdonella_A sp002297645	77.9262	103	331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	99.81	99.81	0.89	0.89	2	-
GCA_017744955.1	s__Dokdonella_A sp017744955	77.7773	149	331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342425.1	s__Dokdonella_A fugitiva	77.7401	125	331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	99.45	99.45	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-06-19 02:17:34,191] [INFO] GTDB search result was written to GCA_018006255.1_ASM1800625v1_genomic.fna/result_gtdb.tsv
[2023-06-19 02:17:34,191] [INFO] ===== GTDB Search completed =====
[2023-06-19 02:17:34,194] [INFO] DFAST_QC result json was written to GCA_018006255.1_ASM1800625v1_genomic.fna/dqc_result.json
[2023-06-19 02:17:34,195] [INFO] DFAST_QC completed!
[2023-06-19 02:17:34,195] [INFO] Total running time: 0h0m38s