[2024-01-24 10:57:06,793] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:06,811] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:06,811] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9b1d75c-cc61-41c6-ae98-220be97c872b/dqc_reference
[2024-01-24 10:57:08,075] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:08,076] [INFO] Task started: Prodigal
[2024-01-24 10:57:08,076] [INFO] Running command: gunzip -c /var/lib/cwl/stg43cc0fde-da3d-46f1-b8ab-d0c2d763dff2/GCF_016766875.1_ASM1676687v1_genomic.fna.gz | prodigal -d GCF_016766875.1_ASM1676687v1_genomic.fna/cds.fna -a GCF_016766875.1_ASM1676687v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:29,210] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:29,210] [INFO] Task started: HMMsearch
[2024-01-24 10:57:29,210] [INFO] Running command: hmmsearch --tblout GCF_016766875.1_ASM1676687v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9b1d75c-cc61-41c6-ae98-220be97c872b/dqc_reference/reference_markers.hmm GCF_016766875.1_ASM1676687v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:29,530] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:29,531] [INFO] Found 6/6 markers.
[2024-01-24 10:57:29,582] [INFO] Query marker FASTA was written to GCF_016766875.1_ASM1676687v1_genomic.fna/markers.fasta
[2024-01-24 10:57:29,583] [INFO] Task started: Blastn
[2024-01-24 10:57:29,583] [INFO] Running command: blastn -query GCF_016766875.1_ASM1676687v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9b1d75c-cc61-41c6-ae98-220be97c872b/dqc_reference/reference_markers.fasta -out GCF_016766875.1_ASM1676687v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:30,257] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:30,263] [INFO] Selected 15 target genomes.
[2024-01-24 10:57:30,264] [INFO] Target genome list was writen to GCF_016766875.1_ASM1676687v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:30,272] [INFO] Task started: fastANI
[2024-01-24 10:57:30,272] [INFO] Running command: fastANI --query /var/lib/cwl/stg43cc0fde-da3d-46f1-b8ab-d0c2d763dff2/GCF_016766875.1_ASM1676687v1_genomic.fna.gz --refList GCF_016766875.1_ASM1676687v1_genomic.fna/target_genomes.txt --output GCF_016766875.1_ASM1676687v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:47,315] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:47,316] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9b1d75c-cc61-41c6-ae98-220be97c872b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:47,316] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9b1d75c-cc61-41c6-ae98-220be97c872b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:47,335] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 10:57:47,335] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:47,335] [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
Chryseobacterium gleum	strain=FDAARGOS_1103	GCA_016766875.1	250	250	type	True	100.0	1875	1881	95	conclusive
Chryseobacterium gleum	strain=NCTC11432	GCA_900636535.1	250	250	type	True	99.9955	1867	1881	95	conclusive
Chryseobacterium gleum	strain=ATCC 35910	GCA_000143785.1	250	250	type	True	99.9952	1853	1881	95	conclusive
Chryseobacterium cucumeris	strain=GSE06	GCA_001593385.1	1813611	1813611	type	True	87.4704	1348	1881	95	below_threshold
Chryseobacterium candidae	strain=JC507	GCA_004916905.1	1978493	1978493	type	True	87.1826	1188	1881	95	below_threshold
Chryseobacterium sediminis	strain=IMT-174	GCA_008386505.1	1679494	1679494	type	True	86.536	1295	1881	95	below_threshold
Chryseobacterium aureum	strain=17S1E7	GCA_003971235.1	2497456	2497456	type	True	85.9035	1278	1881	95	below_threshold
Chryseobacterium viscerum	strain=687B-08	GCA_002899945.2	1037377	1037377	type	True	85.6788	1281	1881	95	below_threshold
Chryseobacterium contaminans	strain=C-26	GCA_001684955.1	1423959	1423959	type	True	83.3543	957	1881	95	below_threshold
Chryseobacterium contaminans	strain=DSM 27621	GCA_900142615.1	1423959	1423959	type	True	83.2817	1058	1881	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.4926	686	1881	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.4027	742	1881	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.2682	772	1881	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	79.816	537	1881	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	79.2472	584	1881	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:47,337] [INFO] DFAST Taxonomy check result was written to GCF_016766875.1_ASM1676687v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:47,337] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:47,338] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:47,338] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9b1d75c-cc61-41c6-ae98-220be97c872b/dqc_reference/checkm_data
[2024-01-24 10:57:47,339] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:47,391] [INFO] Task started: CheckM
[2024-01-24 10:57:47,392] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016766875.1_ASM1676687v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016766875.1_ASM1676687v1_genomic.fna/checkm_input GCF_016766875.1_ASM1676687v1_genomic.fna/checkm_result
[2024-01-24 10:58:48,650] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:48,652] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:48,672] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:48,672] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:48,672] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016766875.1_ASM1676687v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:48,673] [INFO] Task started: Blastn
[2024-01-24 10:58:48,673] [INFO] Running command: blastn -query GCF_016766875.1_ASM1676687v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9b1d75c-cc61-41c6-ae98-220be97c872b/dqc_reference/reference_markers_gtdb.fasta -out GCF_016766875.1_ASM1676687v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:49,524] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:49,528] [INFO] Selected 13 target genomes.
[2024-01-24 10:58:49,528] [INFO] Target genome list was writen to GCF_016766875.1_ASM1676687v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:49,539] [INFO] Task started: fastANI
[2024-01-24 10:58:49,539] [INFO] Running command: fastANI --query /var/lib/cwl/stg43cc0fde-da3d-46f1-b8ab-d0c2d763dff2/GCF_016766875.1_ASM1676687v1_genomic.fna.gz --refList GCF_016766875.1_ASM1676687v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016766875.1_ASM1676687v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:05,555] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:05,578] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:05,578] [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_900636535.1	s__Chryseobacterium gleum	99.9955	1867	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.52	97.29	0.95	0.89	6	conclusive
GCF_006829085.1	s__Chryseobacterium sp006829085	88.981	1378	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.29	97.29	0.93	0.93	2	-
GCF_016775705.1	s__Chryseobacterium sp003182335	88.2034	1317	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.03	95.49	0.90	0.89	5	-
GCF_001593385.1	s__Chryseobacterium cucumeris	87.4711	1349	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.67	98.29	0.93	0.90	5	-
GCF_000745535.1	s__Chryseobacterium sp000745535	87.427	1293	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003347605.1	s__Chryseobacterium sp003347605	87.4237	1286	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002025665.1	s__Chryseobacterium indologenes_F	87.3652	1307	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004916905.1	s__Chryseobacterium candidae	87.169	1190	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.64	98.56	0.91	0.91	3	-
GCF_002979755.1	s__Chryseobacterium culicis_A	86.9873	1283	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.05	96.10	0.96	0.92	3	-
GCF_004119445.1	s__Chryseobacterium sp004119445	86.4615	1194	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003971235.1	s__Chryseobacterium aureum	85.8921	1280	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815975.1	s__Chryseobacterium bernardetii_A	84.3176	1162	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.62	98.62	0.90	0.90	2	-
GCF_011752975.1	s__Chryseobacterium sp011752975	84.3129	1097	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:05,580] [INFO] GTDB search result was written to GCF_016766875.1_ASM1676687v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:05,581] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:05,587] [INFO] DFAST_QC result json was written to GCF_016766875.1_ASM1676687v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:05,587] [INFO] DFAST_QC completed!
[2024-01-24 10:59:05,587] [INFO] Total running time: 0h1m59s