[2024-01-25 19:44:50,836] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:44:50,838] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:44:50,839] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e970f2f-2e2a-474a-aa0e-7f1c093d1464/dqc_reference
[2024-01-25 19:44:51,938] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:44:51,938] [INFO] Task started: Prodigal
[2024-01-25 19:44:51,939] [INFO] Running command: gunzip -c /var/lib/cwl/stg132353d9-5d97-4578-ae64-7f05da10ed76/GCF_019565575.1_ASM1956557v1_genomic.fna.gz | prodigal -d GCF_019565575.1_ASM1956557v1_genomic.fna/cds.fna -a GCF_019565575.1_ASM1956557v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:45:00,098] [INFO] Task succeeded: Prodigal
[2024-01-25 19:45:00,098] [INFO] Task started: HMMsearch
[2024-01-25 19:45:00,098] [INFO] Running command: hmmsearch --tblout GCF_019565575.1_ASM1956557v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e970f2f-2e2a-474a-aa0e-7f1c093d1464/dqc_reference/reference_markers.hmm GCF_019565575.1_ASM1956557v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:45:00,306] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:45:00,307] [INFO] Found 6/6 markers.
[2024-01-25 19:45:00,335] [INFO] Query marker FASTA was written to GCF_019565575.1_ASM1956557v1_genomic.fna/markers.fasta
[2024-01-25 19:45:00,335] [INFO] Task started: Blastn
[2024-01-25 19:45:00,336] [INFO] Running command: blastn -query GCF_019565575.1_ASM1956557v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e970f2f-2e2a-474a-aa0e-7f1c093d1464/dqc_reference/reference_markers.fasta -out GCF_019565575.1_ASM1956557v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:00,955] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:00,957] [INFO] Selected 15 target genomes.
[2024-01-25 19:45:00,958] [INFO] Target genome list was writen to GCF_019565575.1_ASM1956557v1_genomic.fna/target_genomes.txt
[2024-01-25 19:45:00,968] [INFO] Task started: fastANI
[2024-01-25 19:45:00,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg132353d9-5d97-4578-ae64-7f05da10ed76/GCF_019565575.1_ASM1956557v1_genomic.fna.gz --refList GCF_019565575.1_ASM1956557v1_genomic.fna/target_genomes.txt --output GCF_019565575.1_ASM1956557v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:45:10,886] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:10,887] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e970f2f-2e2a-474a-aa0e-7f1c093d1464/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:45:10,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e970f2f-2e2a-474a-aa0e-7f1c093d1464/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:45:10,896] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:45:10,896] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:45:10,897] [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
Flavobacterium columnare	strain=ATCC 23463	GCA_002530675.1	996	996	type	True	91.1745	841	1133	95	below_threshold
Flavobacterium columnare	strain=NBRC 100251	GCA_007990835.1	996	996	type	True	91.061	834	1133	95	below_threshold
Flavobacterium davisii	strain=90-106	GCA_019565505.1	2906077	2906077	type	True	85.3402	865	1133	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	83.7061	813	1133	95	below_threshold
Flavobacterium terrae	strain=DSM 18829	GCA_900142035.1	415425	415425	type	True	78.4601	309	1133	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	78.2871	186	1133	95	below_threshold
Flavobacterium amnicola	strain=LLJ-11	GCA_004122165.1	2506422	2506422	type	True	78.0263	250	1133	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.7644	215	1133	95	below_threshold
Flavobacterium haoranii	strain=DSM 22807	GCA_900142055.1	683124	683124	type	True	77.7412	198	1133	95	below_threshold
Flavobacterium aquaticum	strain=CGMCC 1.12398	GCA_003259835.1	1236486	1236486	type	True	77.712	170	1133	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.6433	233	1133	95	below_threshold
Flavobacterium supellecticarium	strain=CC-CTC003	GCA_004801375.1	2565924	2565924	type	True	77.5017	96	1133	95	below_threshold
Flavobacterium filum	strain=DSM 17961	GCA_000425465.1	370974	370974	type	True	77.3437	141	1133	95	below_threshold
Flavobacterium agrisoli	strain=SE-1-e	GCA_016522065.1	2793066	2793066	type	True	77.1997	133	1133	95	below_threshold
Flavobacterium branchiophilum	strain=ATCC 35035	GCA_002217205.1	55197	55197	type	True	76.6353	129	1133	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:45:10,898] [INFO] DFAST Taxonomy check result was written to GCF_019565575.1_ASM1956557v1_genomic.fna/tc_result.tsv
[2024-01-25 19:45:10,898] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:45:10,898] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:45:10,899] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e970f2f-2e2a-474a-aa0e-7f1c093d1464/dqc_reference/checkm_data
[2024-01-25 19:45:10,899] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:45:10,934] [INFO] Task started: CheckM
[2024-01-25 19:45:10,934] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019565575.1_ASM1956557v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019565575.1_ASM1956557v1_genomic.fna/checkm_input GCF_019565575.1_ASM1956557v1_genomic.fna/checkm_result
[2024-01-25 19:45:38,450] [INFO] Task succeeded: CheckM
[2024-01-25 19:45:38,451] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.10%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:45:38,469] [INFO] ===== Completeness check finished =====
[2024-01-25 19:45:38,469] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:45:38,470] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019565575.1_ASM1956557v1_genomic.fna/markers.fasta)
[2024-01-25 19:45:38,470] [INFO] Task started: Blastn
[2024-01-25 19:45:38,470] [INFO] Running command: blastn -query GCF_019565575.1_ASM1956557v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e970f2f-2e2a-474a-aa0e-7f1c093d1464/dqc_reference/reference_markers_gtdb.fasta -out GCF_019565575.1_ASM1956557v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:39,312] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:39,315] [INFO] Selected 10 target genomes.
[2024-01-25 19:45:39,315] [INFO] Target genome list was writen to GCF_019565575.1_ASM1956557v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:45:39,327] [INFO] Task started: fastANI
[2024-01-25 19:45:39,327] [INFO] Running command: fastANI --query /var/lib/cwl/stg132353d9-5d97-4578-ae64-7f05da10ed76/GCF_019565575.1_ASM1956557v1_genomic.fna.gz --refList GCF_019565575.1_ASM1956557v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019565575.1_ASM1956557v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:45:46,363] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:46,371] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:45:46,371] [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_002217245.1	s__Flavobacterium columnare_A	98.7419	875	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.08	98.79	0.92	0.89	11	conclusive
GCF_002530675.1	s__Flavobacterium columnare	91.2234	838	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.33	99.02	0.96	0.93	39	-
GCF_900290975.1	s__Flavobacterium columnare_D	85.1299	820	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.86	98.55	0.90	0.88	3	-
GCF_002204895.1	s__Flavobacterium columnare_C	83.7739	774	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.67	99.21	0.94	0.90	7	-
GCF_004959765.1	s__Flavobacterium sp004959765	78.4846	321	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142035.1	s__Flavobacterium terrae	78.4457	310	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259835.1	s__Flavobacterium aquaticum	77.761	167	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801375.1	s__Flavobacterium sp004801375	77.4575	98	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903838055.1	s__Flavobacterium sp903838055	77.1589	158	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.97	99.95	0.98	0.97	3	-
GCA_017988155.1	s__Flavobacterium sp017988155	76.3251	99	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:45:46,372] [INFO] GTDB search result was written to GCF_019565575.1_ASM1956557v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:45:46,373] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:45:46,376] [INFO] DFAST_QC result json was written to GCF_019565575.1_ASM1956557v1_genomic.fna/dqc_result.json
[2024-01-25 19:45:46,377] [INFO] DFAST_QC completed!
[2024-01-25 19:45:46,377] [INFO] Total running time: 0h0m56s