[2023-06-27 09:44:40,540] [INFO] DFAST_QC pipeline started.
[2023-06-27 09:44:40,553] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 09:44:40,554] [INFO] DQC Reference Directory: /var/lib/cwl/stgf25fca0b-fa4a-4209-b708-8e4a79b5d51b/dqc_reference
[2023-06-27 09:44:41,807] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 09:44:41,807] [INFO] Task started: Prodigal
[2023-06-27 09:44:41,808] [INFO] Running command: gunzip -c /var/lib/cwl/stg2aa18121-14cd-4696-99c6-44eab8e57620/GCA_027402945.1_ASM2740294v1_genomic.fna.gz | prodigal -d GCA_027402945.1_ASM2740294v1_genomic.fna/cds.fna -a GCA_027402945.1_ASM2740294v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 09:44:49,433] [INFO] Task succeeded: Prodigal
[2023-06-27 09:44:49,433] [INFO] Task started: HMMsearch
[2023-06-27 09:44:49,434] [INFO] Running command: hmmsearch --tblout GCA_027402945.1_ASM2740294v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf25fca0b-fa4a-4209-b708-8e4a79b5d51b/dqc_reference/reference_markers.hmm GCA_027402945.1_ASM2740294v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 09:44:49,685] [INFO] Task succeeded: HMMsearch
[2023-06-27 09:44:49,687] [INFO] Found 6/6 markers.
[2023-06-27 09:44:49,726] [INFO] Query marker FASTA was written to GCA_027402945.1_ASM2740294v1_genomic.fna/markers.fasta
[2023-06-27 09:44:49,727] [INFO] Task started: Blastn
[2023-06-27 09:44:49,727] [INFO] Running command: blastn -query GCA_027402945.1_ASM2740294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf25fca0b-fa4a-4209-b708-8e4a79b5d51b/dqc_reference/reference_markers.fasta -out GCA_027402945.1_ASM2740294v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 09:44:50,451] [INFO] Task succeeded: Blastn
[2023-06-27 09:44:50,455] [INFO] Selected 25 target genomes.
[2023-06-27 09:44:50,455] [INFO] Target genome list was writen to GCA_027402945.1_ASM2740294v1_genomic.fna/target_genomes.txt
[2023-06-27 09:44:50,459] [INFO] Task started: fastANI
[2023-06-27 09:44:50,459] [INFO] Running command: fastANI --query /var/lib/cwl/stg2aa18121-14cd-4696-99c6-44eab8e57620/GCA_027402945.1_ASM2740294v1_genomic.fna.gz --refList GCA_027402945.1_ASM2740294v1_genomic.fna/target_genomes.txt --output GCA_027402945.1_ASM2740294v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 09:45:06,503] [INFO] Task succeeded: fastANI
[2023-06-27 09:45:06,503] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf25fca0b-fa4a-4209-b708-8e4a79b5d51b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 09:45:06,504] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf25fca0b-fa4a-4209-b708-8e4a79b5d51b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 09:45:06,518] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 09:45:06,518] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 09:45:06,518] [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 weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	75.2059	63	917	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	75.061	68	917	95	below_threshold
Roseomonas mucosa	strain=ATCC BAA-692	GCA_000622225.1	207340	207340	type	True	75.0007	55	917	95	below_threshold
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	74.9911	82	917	95	below_threshold
Roseomonas mucosa	strain=NCTC13291	GCA_900455935.1	207340	207340	type	True	74.9901	56	917	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	74.9563	63	917	95	below_threshold
Alsobacter soli	strain=SH9	GCA_003004785.1	2109933	2109933	type	True	74.9186	59	917	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=NCTC13290	GCA_900455865.1	243956	257708	type	True	74.902	51	917	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=ATCC BAA-691	GCA_000518625.1	243956	257708	type	True	74.8805	53	917	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	74.812	72	917	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	74.6753	113	917	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	74.6535	113	917	95	below_threshold
Actinomycetospora cinnamomea	strain=DSM 45771	GCA_003096675.1	663609	663609	type	True	74.5994	75	917	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 09:45:06,526] [INFO] DFAST Taxonomy check result was written to GCA_027402945.1_ASM2740294v1_genomic.fna/tc_result.tsv
[2023-06-27 09:45:06,527] [INFO] ===== Taxonomy check completed =====
[2023-06-27 09:45:06,528] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 09:45:06,528] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf25fca0b-fa4a-4209-b708-8e4a79b5d51b/dqc_reference/checkm_data
[2023-06-27 09:45:06,531] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 09:45:06,566] [INFO] Task started: CheckM
[2023-06-27 09:45:06,567] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027402945.1_ASM2740294v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027402945.1_ASM2740294v1_genomic.fna/checkm_input GCA_027402945.1_ASM2740294v1_genomic.fna/checkm_result
[2023-06-27 09:45:33,290] [INFO] Task succeeded: CheckM
[2023-06-27 09:45:33,291] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 09:45:33,319] [INFO] ===== Completeness check finished =====
[2023-06-27 09:45:33,319] [INFO] ===== Start GTDB Search =====
[2023-06-27 09:45:33,320] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027402945.1_ASM2740294v1_genomic.fna/markers.fasta)
[2023-06-27 09:45:33,320] [INFO] Task started: Blastn
[2023-06-27 09:45:33,320] [INFO] Running command: blastn -query GCA_027402945.1_ASM2740294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf25fca0b-fa4a-4209-b708-8e4a79b5d51b/dqc_reference/reference_markers_gtdb.fasta -out GCA_027402945.1_ASM2740294v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 09:45:34,371] [INFO] Task succeeded: Blastn
[2023-06-27 09:45:34,378] [INFO] Selected 17 target genomes.
[2023-06-27 09:45:34,379] [INFO] Target genome list was writen to GCA_027402945.1_ASM2740294v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 09:45:34,390] [INFO] Task started: fastANI
[2023-06-27 09:45:34,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg2aa18121-14cd-4696-99c6-44eab8e57620/GCA_027402945.1_ASM2740294v1_genomic.fna.gz --refList GCA_027402945.1_ASM2740294v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027402945.1_ASM2740294v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 09:45:43,444] [INFO] Task succeeded: fastANI
[2023-06-27 09:45:43,456] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 09:45:43,457] [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_011334465.1	s__DTIX01 sp011334465	76.8365	121	917	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__Binatales;f__Binataceae;g__DTIX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003135855.1	s__Binatus sp003135855	76.5241	60	917	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__Binatales;f__Binataceae;g__Binatus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014896235.1	s__JADMIL01 sp014896235	76.5218	122	917	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__Binatales;f__Binataceae;g__JADMIL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003161515.1	s__Binatus sp003161515	76.4672	63	917	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__Binatales;f__Binataceae;g__Binatus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015478645.1	s__JADMIL01 sp015478645	76.4154	148	917	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__Binatales;f__Binataceae;g__JADMIL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019237115.1	s__JAFAHS01 sp019237115	76.3706	77	917	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__Binatales;f__Binataceae;g__JAFAHS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003135135.1	s__Binatus sp003135135	76.3406	105	917	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__Binatales;f__Binataceae;g__Binatus	95.0	99.92	99.78	0.98	0.97	5	-
GCA_002479255.1	s__Binatus soli	76.3139	100	917	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__Binatales;f__Binataceae;g__Binatus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003416885.1	s__Luteimonas_B sp003416885	75.1659	67	917	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 09:45:43,472] [INFO] GTDB search result was written to GCA_027402945.1_ASM2740294v1_genomic.fna/result_gtdb.tsv
[2023-06-27 09:45:43,472] [INFO] ===== GTDB Search completed =====
[2023-06-27 09:45:43,478] [INFO] DFAST_QC result json was written to GCA_027402945.1_ASM2740294v1_genomic.fna/dqc_result.json
[2023-06-27 09:45:43,478] [INFO] DFAST_QC completed!
[2023-06-27 09:45:43,478] [INFO] Total running time: 0h1m3s