[2024-01-24 14:47:55,928] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:55,933] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:55,933] [INFO] DQC Reference Directory: /var/lib/cwl/stgd32d63c8-7359-4052-84fe-0c7ca4ae59d0/dqc_reference
[2024-01-24 14:47:58,527] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:58,528] [INFO] Task started: Prodigal
[2024-01-24 14:47:58,529] [INFO] Running command: gunzip -c /var/lib/cwl/stg3da701fe-f501-4dbe-b92f-c7bdbc29f286/GCF_028548455.1_ASM2854845v1_genomic.fna.gz | prodigal -d GCF_028548455.1_ASM2854845v1_genomic.fna/cds.fna -a GCF_028548455.1_ASM2854845v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:48:11,890] [INFO] Task succeeded: Prodigal
[2024-01-24 14:48:11,890] [INFO] Task started: HMMsearch
[2024-01-24 14:48:11,890] [INFO] Running command: hmmsearch --tblout GCF_028548455.1_ASM2854845v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd32d63c8-7359-4052-84fe-0c7ca4ae59d0/dqc_reference/reference_markers.hmm GCF_028548455.1_ASM2854845v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:48:12,178] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:48:12,179] [INFO] Found 6/6 markers.
[2024-01-24 14:48:12,213] [INFO] Query marker FASTA was written to GCF_028548455.1_ASM2854845v1_genomic.fna/markers.fasta
[2024-01-24 14:48:12,213] [INFO] Task started: Blastn
[2024-01-24 14:48:12,213] [INFO] Running command: blastn -query GCF_028548455.1_ASM2854845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd32d63c8-7359-4052-84fe-0c7ca4ae59d0/dqc_reference/reference_markers.fasta -out GCF_028548455.1_ASM2854845v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:13,129] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:13,133] [INFO] Selected 16 target genomes.
[2024-01-24 14:48:13,133] [INFO] Target genome list was writen to GCF_028548455.1_ASM2854845v1_genomic.fna/target_genomes.txt
[2024-01-24 14:48:13,148] [INFO] Task started: fastANI
[2024-01-24 14:48:13,149] [INFO] Running command: fastANI --query /var/lib/cwl/stg3da701fe-f501-4dbe-b92f-c7bdbc29f286/GCF_028548455.1_ASM2854845v1_genomic.fna.gz --refList GCF_028548455.1_ASM2854845v1_genomic.fna/target_genomes.txt --output GCF_028548455.1_ASM2854845v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:27,343] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:27,344] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd32d63c8-7359-4052-84fe-0c7ca4ae59d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:27,344] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd32d63c8-7359-4052-84fe-0c7ca4ae59d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:27,360] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:48:27,360] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:48:27,360] [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
Vogesella mureinivorans	strain=389	GCA_007644035.2	657276	657276	type	True	90.6178	1022	1263	95	below_threshold
Vogesella urethralis	strain=YM-1	GCA_007644045.2	2592656	2592656	type	True	88.5691	1024	1263	95	below_threshold
Vogesella alkaliphila	strain=KCTC 32041	GCA_014652475.1	1193621	1193621	type	True	82.793	727	1263	95	below_threshold
Vogesella fluminis	strain=KCTC 23713	GCA_014652335.1	1069161	1069161	type	True	82.3437	685	1263	95	below_threshold
Vogesella indigofera	strain=DSM 3303	GCA_003633895.1	45465	45465	type	True	82.2988	737	1263	95	below_threshold
Aquitalea aquatilis	strain=THG-DN7.12	GCA_005155025.1	1537400	1537400	type	True	79.9938	548	1263	95	below_threshold
Chromobacterium paludis	strain=IIBBL 257-1	GCA_008275125.1	2605945	2605945	type	True	79.8424	525	1263	95	below_threshold
Chromobacterium phragmitis	strain=IIBBL 112-1	GCA_003325475.1	2202141	2202141	type	True	79.7345	523	1263	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	79.7255	499	1263	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	79.6862	504	1263	95	below_threshold
Chromobacterium alkanivorans	strain=IITR-71	GCA_016937655.1	1071719	1071719	type	True	79.6854	537	1263	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	79.5875	508	1263	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	79.3919	510	1263	95	below_threshold
Chromobacterium haemolyticum	strain=DSM 19808	GCA_000711885.1	394935	394935	type	True	79.054	469	1263	95	below_threshold
Rivicola pingtungensis	strain=DSM 29661	GCA_003201855.1	1054498	1054498	type	True	78.569	400	1263	95	below_threshold
Kingella potus	strain=NCTC13336	GCA_900451175.1	265175	265175	type	True	76.8469	82	1263	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:27,362] [INFO] DFAST Taxonomy check result was written to GCF_028548455.1_ASM2854845v1_genomic.fna/tc_result.tsv
[2024-01-24 14:48:27,362] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:27,363] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:27,363] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd32d63c8-7359-4052-84fe-0c7ca4ae59d0/dqc_reference/checkm_data
[2024-01-24 14:48:27,364] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:27,404] [INFO] Task started: CheckM
[2024-01-24 14:48:27,404] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028548455.1_ASM2854845v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028548455.1_ASM2854845v1_genomic.fna/checkm_input GCF_028548455.1_ASM2854845v1_genomic.fna/checkm_result
[2024-01-24 14:49:06,119] [INFO] Task succeeded: CheckM
[2024-01-24 14:49:06,121] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:49:06,140] [INFO] ===== Completeness check finished =====
[2024-01-24 14:49:06,141] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:49:06,141] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028548455.1_ASM2854845v1_genomic.fna/markers.fasta)
[2024-01-24 14:49:06,141] [INFO] Task started: Blastn
[2024-01-24 14:49:06,141] [INFO] Running command: blastn -query GCF_028548455.1_ASM2854845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd32d63c8-7359-4052-84fe-0c7ca4ae59d0/dqc_reference/reference_markers_gtdb.fasta -out GCF_028548455.1_ASM2854845v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:49:07,773] [INFO] Task succeeded: Blastn
[2024-01-24 14:49:07,784] [INFO] Selected 9 target genomes.
[2024-01-24 14:49:07,784] [INFO] Target genome list was writen to GCF_028548455.1_ASM2854845v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:49:07,798] [INFO] Task started: fastANI
[2024-01-24 14:49:07,798] [INFO] Running command: fastANI --query /var/lib/cwl/stg3da701fe-f501-4dbe-b92f-c7bdbc29f286/GCF_028548455.1_ASM2854845v1_genomic.fna.gz --refList GCF_028548455.1_ASM2854845v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028548455.1_ASM2854845v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:15,866] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:15,876] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:49:15,877] [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_000335715.1	s__Vogesella sp000335715	93.3593	1042	1263	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017998615.1	s__Vogesella sp017998615	92.9506	697	1263	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007644045.2	s__Vogesella urethralis	88.5828	1023	1263	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090205.1	s__Vogesella sp900090205	82.957	783	1263	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652475.1	s__Vogesella alkaliphila	82.7488	731	1263	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902829295.1	s__Vogesella oryzae	82.4283	695	1263	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652335.1	s__Vogesella fluminis	82.3625	683	1263	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003633895.1	s__Vogesella indigofera	82.3489	732	1263	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	97.25	97.21	0.95	0.93	3	-
GCF_016428945.1	s__Chromobacterium sp016428945	79.6983	497	1263	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.99	97.99	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:49:15,878] [INFO] GTDB search result was written to GCF_028548455.1_ASM2854845v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:15,879] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:15,885] [INFO] DFAST_QC result json was written to GCF_028548455.1_ASM2854845v1_genomic.fna/dqc_result.json
[2024-01-24 14:49:15,885] [INFO] DFAST_QC completed!
[2024-01-24 14:49:15,885] [INFO] Total running time: 0h1m20s