[2023-06-28 20:40:49,616] [INFO] DFAST_QC pipeline started.
[2023-06-28 20:40:49,619] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 20:40:49,619] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2ed0cbe-437b-478d-bccb-bfe5a0a99d6d/dqc_reference
[2023-06-28 20:40:51,560] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 20:40:51,561] [INFO] Task started: Prodigal
[2023-06-28 20:40:51,561] [INFO] Running command: gunzip -c /var/lib/cwl/stg6809b7e5-376a-4a2b-bed0-9a0b447a5318/GCA_027456945.1_ASM2745694v1_genomic.fna.gz | prodigal -d GCA_027456945.1_ASM2745694v1_genomic.fna/cds.fna -a GCA_027456945.1_ASM2745694v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 20:40:57,465] [INFO] Task succeeded: Prodigal
[2023-06-28 20:40:57,466] [INFO] Task started: HMMsearch
[2023-06-28 20:40:57,466] [INFO] Running command: hmmsearch --tblout GCA_027456945.1_ASM2745694v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2ed0cbe-437b-478d-bccb-bfe5a0a99d6d/dqc_reference/reference_markers.hmm GCA_027456945.1_ASM2745694v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 20:40:57,691] [INFO] Task succeeded: HMMsearch
[2023-06-28 20:40:57,693] [INFO] Found 6/6 markers.
[2023-06-28 20:40:57,721] [INFO] Query marker FASTA was written to GCA_027456945.1_ASM2745694v1_genomic.fna/markers.fasta
[2023-06-28 20:40:57,721] [INFO] Task started: Blastn
[2023-06-28 20:40:57,721] [INFO] Running command: blastn -query GCA_027456945.1_ASM2745694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2ed0cbe-437b-478d-bccb-bfe5a0a99d6d/dqc_reference/reference_markers.fasta -out GCA_027456945.1_ASM2745694v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:40:58,668] [INFO] Task succeeded: Blastn
[2023-06-28 20:40:58,674] [INFO] Selected 14 target genomes.
[2023-06-28 20:40:58,675] [INFO] Target genome list was writen to GCA_027456945.1_ASM2745694v1_genomic.fna/target_genomes.txt
[2023-06-28 20:40:58,679] [INFO] Task started: fastANI
[2023-06-28 20:40:58,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg6809b7e5-376a-4a2b-bed0-9a0b447a5318/GCA_027456945.1_ASM2745694v1_genomic.fna.gz --refList GCA_027456945.1_ASM2745694v1_genomic.fna/target_genomes.txt --output GCA_027456945.1_ASM2745694v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 20:41:08,499] [INFO] Task succeeded: fastANI
[2023-06-28 20:41:08,500] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2ed0cbe-437b-478d-bccb-bfe5a0a99d6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 20:41:08,500] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2ed0cbe-437b-478d-bccb-bfe5a0a99d6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 20:41:08,509] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 20:41:08,509] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 20:41:08,509] [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
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	74.729	87	691	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	74.7077	87	691	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	74.6928	92	691	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 20:41:08,511] [INFO] DFAST Taxonomy check result was written to GCA_027456945.1_ASM2745694v1_genomic.fna/tc_result.tsv
[2023-06-28 20:41:08,512] [INFO] ===== Taxonomy check completed =====
[2023-06-28 20:41:08,512] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 20:41:08,512] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2ed0cbe-437b-478d-bccb-bfe5a0a99d6d/dqc_reference/checkm_data
[2023-06-28 20:41:08,513] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 20:41:08,548] [INFO] Task started: CheckM
[2023-06-28 20:41:08,548] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027456945.1_ASM2745694v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027456945.1_ASM2745694v1_genomic.fna/checkm_input GCA_027456945.1_ASM2745694v1_genomic.fna/checkm_result
[2023-06-28 20:41:31,484] [INFO] Task succeeded: CheckM
[2023-06-28 20:41:31,486] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 20:41:31,508] [INFO] ===== Completeness check finished =====
[2023-06-28 20:41:31,508] [INFO] ===== Start GTDB Search =====
[2023-06-28 20:41:31,509] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027456945.1_ASM2745694v1_genomic.fna/markers.fasta)
[2023-06-28 20:41:31,509] [INFO] Task started: Blastn
[2023-06-28 20:41:31,509] [INFO] Running command: blastn -query GCA_027456945.1_ASM2745694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2ed0cbe-437b-478d-bccb-bfe5a0a99d6d/dqc_reference/reference_markers_gtdb.fasta -out GCA_027456945.1_ASM2745694v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:41:32,451] [INFO] Task succeeded: Blastn
[2023-06-28 20:41:32,456] [INFO] Selected 14 target genomes.
[2023-06-28 20:41:32,456] [INFO] Target genome list was writen to GCA_027456945.1_ASM2745694v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 20:41:32,465] [INFO] Task started: fastANI
[2023-06-28 20:41:32,465] [INFO] Running command: fastANI --query /var/lib/cwl/stg6809b7e5-376a-4a2b-bed0-9a0b447a5318/GCA_027456945.1_ASM2745694v1_genomic.fna.gz --refList GCA_027456945.1_ASM2745694v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027456945.1_ASM2745694v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 20:41:38,640] [INFO] Task succeeded: fastANI
[2023-06-28 20:41:38,654] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 20:41:38,654] [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_003133745.1	s__Tyrphobacter aquilonaris	78.5892	336	691	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Tyrphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003155175.1	s__Hemerobacter limicola	76.7327	123	691	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Hemerobacter	95.0	99.36	99.32	0.90	0.89	6	-
GCA_019235995.1	s__Cybelea sp019235995	76.6906	137	691	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Cybelea	95.0	99.60	99.60	0.91	0.91	2	-
GCA_019240755.1	s__Cybelea sp019240755	76.6869	113	691	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Cybelea	95.0	99.35	99.34	0.91	0.89	3	-
GCA_019237435.1	s__Cybelea sp019237435	76.5101	74	691	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Cybelea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003140835.1	s__Tumulicola scandinaviensis	76.5026	118	691	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Tumulicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003167155.1	s__Cybelea tumulisoli	76.4552	116	691	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Cybelea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019232905.1	s__Aquilonibacter sp019232905	76.3666	128	691	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Aquilonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013044185.1	s__JABEUX01 sp013044185	76.3413	69	691	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__JABEUX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019236975.1	s__JAFAHZ01 sp019236975	76.3318	136	691	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__JAFAHZ01	95.0	98.54	98.14	0.85	0.83	4	-
GCA_003243975.1	s__Meridianibacter frigidus	75.8821	53	691	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Meridianibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003158195.1	s__Palsibacter borealis	75.8355	84	691	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Palsibacter	95.0	99.15	99.15	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-28 20:41:38,657] [INFO] GTDB search result was written to GCA_027456945.1_ASM2745694v1_genomic.fna/result_gtdb.tsv
[2023-06-28 20:41:38,657] [INFO] ===== GTDB Search completed =====
[2023-06-28 20:41:38,661] [INFO] DFAST_QC result json was written to GCA_027456945.1_ASM2745694v1_genomic.fna/dqc_result.json
[2023-06-28 20:41:38,661] [INFO] DFAST_QC completed!
[2023-06-28 20:41:38,661] [INFO] Total running time: 0h0m49s