[2024-01-24 13:35:27,609] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:35:27,611] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:35:27,611] [INFO] DQC Reference Directory: /var/lib/cwl/stg80ccf753-f8f1-4016-bb5a-b07463400cef/dqc_reference
[2024-01-24 13:35:28,801] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:35:28,802] [INFO] Task started: Prodigal
[2024-01-24 13:35:28,802] [INFO] Running command: gunzip -c /var/lib/cwl/stgd271cc3e-b27c-4889-a164-2d7b9d063342/GCF_000153485.2_ASM15348v2_genomic.fna.gz | prodigal -d GCF_000153485.2_ASM15348v2_genomic.fna/cds.fna -a GCF_000153485.2_ASM15348v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:35:43,084] [INFO] Task succeeded: Prodigal
[2024-01-24 13:35:43,085] [INFO] Task started: HMMsearch
[2024-01-24 13:35:43,085] [INFO] Running command: hmmsearch --tblout GCF_000153485.2_ASM15348v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80ccf753-f8f1-4016-bb5a-b07463400cef/dqc_reference/reference_markers.hmm GCF_000153485.2_ASM15348v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:35:43,384] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:35:43,385] [INFO] Found 6/6 markers.
[2024-01-24 13:35:43,427] [INFO] Query marker FASTA was written to GCF_000153485.2_ASM15348v2_genomic.fna/markers.fasta
[2024-01-24 13:35:43,428] [INFO] Task started: Blastn
[2024-01-24 13:35:43,428] [INFO] Running command: blastn -query GCF_000153485.2_ASM15348v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg80ccf753-f8f1-4016-bb5a-b07463400cef/dqc_reference/reference_markers.fasta -out GCF_000153485.2_ASM15348v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:44,049] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:44,052] [INFO] Selected 19 target genomes.
[2024-01-24 13:35:44,053] [INFO] Target genome list was writen to GCF_000153485.2_ASM15348v2_genomic.fna/target_genomes.txt
[2024-01-24 13:35:44,712] [INFO] Task started: fastANI
[2024-01-24 13:35:44,713] [INFO] Running command: fastANI --query /var/lib/cwl/stgd271cc3e-b27c-4889-a164-2d7b9d063342/GCF_000153485.2_ASM15348v2_genomic.fna.gz --refList GCF_000153485.2_ASM15348v2_genomic.fna/target_genomes.txt --output GCF_000153485.2_ASM15348v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:35:57,895] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:57,896] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80ccf753-f8f1-4016-bb5a-b07463400cef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:35:57,896] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80ccf753-f8f1-4016-bb5a-b07463400cef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:35:57,924] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:35:57,924] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:35:57,924] [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
Psychroflexus torquis	strain=ATCC 700755	GCA_000153485.2	57029	57029	type	True	100.0	1440	1440	95	conclusive
Psychroflexus gondwanensis	strain=ACAM 44	GCA_000355905.1	251	251	type	True	90.4639	901	1440	95	below_threshold
Psychroflexus lacisalsi	strain=KACC 14089	GCA_020164495.1	503928	503928	type	True	79.4528	373	1440	95	below_threshold
Psychroflexus sediminis	strain=DSM 19803	GCA_900099815.1	470826	470826	type	True	77.8933	276	1440	95	below_threshold
Psychroflexus aurantiacus	strain=YR1-1	GCA_010820555.1	2709310	2709310	type	True	77.6441	255	1440	95	below_threshold
Psychroflexus tropicus	strain=DSM 15496	GCA_000378765.1	197345	197345	type	True	77.4672	262	1440	95	below_threshold
Aurantibacter crassamenti	strain=HG732	GCA_016811105.1	1837375	1837375	type	True	76.7387	52	1440	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	76.6498	58	1440	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	76.5082	70	1440	95	below_threshold
Algibacter mikhailovii	strain=KCTC 12710	GCA_014651495.1	425498	425498	type	True	76.2631	58	1440	95	below_threshold
Gillisia marina	strain=CBA3202	GCA_000258765.1	1167637	1167637	type	True	76.1791	65	1440	95	below_threshold
Tenacibaculum finnmarkense	strain=TNO010	GCA_900239495.1	2781243	2781243	type	True	76.1283	62	1440	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.06	61	1440	95	below_threshold
Mesonia phycicola	strain=DSM 21425	GCA_900141885.1	579105	579105	type	True	75.7834	85	1440	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:35:57,926] [INFO] DFAST Taxonomy check result was written to GCF_000153485.2_ASM15348v2_genomic.fna/tc_result.tsv
[2024-01-24 13:35:57,927] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:35:57,927] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:35:57,927] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80ccf753-f8f1-4016-bb5a-b07463400cef/dqc_reference/checkm_data
[2024-01-24 13:35:57,928] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:35:57,973] [INFO] Task started: CheckM
[2024-01-24 13:35:57,973] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000153485.2_ASM15348v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000153485.2_ASM15348v2_genomic.fna/checkm_input GCF_000153485.2_ASM15348v2_genomic.fna/checkm_result
[2024-01-24 13:36:41,884] [INFO] Task succeeded: CheckM
[2024-01-24 13:36:41,885] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:36:41,907] [INFO] ===== Completeness check finished =====
[2024-01-24 13:36:41,907] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:36:41,908] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000153485.2_ASM15348v2_genomic.fna/markers.fasta)
[2024-01-24 13:36:41,908] [INFO] Task started: Blastn
[2024-01-24 13:36:41,908] [INFO] Running command: blastn -query GCF_000153485.2_ASM15348v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg80ccf753-f8f1-4016-bb5a-b07463400cef/dqc_reference/reference_markers_gtdb.fasta -out GCF_000153485.2_ASM15348v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:42,690] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:42,695] [INFO] Selected 14 target genomes.
[2024-01-24 13:36:42,696] [INFO] Target genome list was writen to GCF_000153485.2_ASM15348v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:36:42,720] [INFO] Task started: fastANI
[2024-01-24 13:36:42,721] [INFO] Running command: fastANI --query /var/lib/cwl/stgd271cc3e-b27c-4889-a164-2d7b9d063342/GCF_000153485.2_ASM15348v2_genomic.fna.gz --refList GCF_000153485.2_ASM15348v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000153485.2_ASM15348v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:36:53,457] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:53,469] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:36:53,469] [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
GCF_000153485.2	s__Psychroflexus torquis	100.0	1440	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002836055.1	s__Psychroflexus sp002836055	94.2379	948	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000355905.1	s__Psychroflexus gondwanensis	90.4644	901	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	98.53	98.53	0.91	0.91	2	-
GCF_900099815.1	s__Psychroflexus sediminis	77.8777	278	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010820555.1	s__Psychroflexus sp010820555	77.6451	255	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378765.1	s__Psychroflexus tropicus	77.4672	262	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003565575.1	s__Psychroflexus sp003565575	77.2882	187	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004010055.1	s__Psychroflexus aestuariivivens	77.2414	208	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387355.1	s__Winogradskyella sediminis	76.9331	58	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
GCF_016811105.1	s__Aurantibacter_A crassamenti	76.6954	53	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aurantibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813425.1	s__Cellulophaga sp002813425	76.6585	74	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651495.1	s__Algibacter_E mikhailovii	76.2284	58	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141885.1	s__Mesonia phycicola	75.7831	85	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:36:53,471] [INFO] GTDB search result was written to GCF_000153485.2_ASM15348v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:36:53,472] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:36:53,475] [INFO] DFAST_QC result json was written to GCF_000153485.2_ASM15348v2_genomic.fna/dqc_result.json
[2024-01-24 13:36:53,476] [INFO] DFAST_QC completed!
[2024-01-24 13:36:53,476] [INFO] Total running time: 0h1m26s