[2023-06-29 21:18:35,243] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:18:35,245] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:18:35,245] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb11279f-749c-4fff-9cb2-2dfb92047a07/dqc_reference
[2023-06-29 21:18:36,581] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:18:36,582] [INFO] Task started: Prodigal
[2023-06-29 21:18:36,583] [INFO] Running command: gunzip -c /var/lib/cwl/stg716ffe3e-de2c-4f89-82b0-7aa6c0e435db/GCA_016283415.1_ASM1628341v1_genomic.fna.gz | prodigal -d GCA_016283415.1_ASM1628341v1_genomic.fna/cds.fna -a GCA_016283415.1_ASM1628341v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:19:05,699] [INFO] Task succeeded: Prodigal
[2023-06-29 21:19:05,700] [INFO] Task started: HMMsearch
[2023-06-29 21:19:05,700] [INFO] Running command: hmmsearch --tblout GCA_016283415.1_ASM1628341v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb11279f-749c-4fff-9cb2-2dfb92047a07/dqc_reference/reference_markers.hmm GCA_016283415.1_ASM1628341v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:19:06,007] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:19:06,009] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg716ffe3e-de2c-4f89-82b0-7aa6c0e435db/GCA_016283415.1_ASM1628341v1_genomic.fna.gz]
[2023-06-29 21:19:06,053] [INFO] Query marker FASTA was written to GCA_016283415.1_ASM1628341v1_genomic.fna/markers.fasta
[2023-06-29 21:19:06,054] [INFO] Task started: Blastn
[2023-06-29 21:19:06,054] [INFO] Running command: blastn -query GCA_016283415.1_ASM1628341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb11279f-749c-4fff-9cb2-2dfb92047a07/dqc_reference/reference_markers.fasta -out GCA_016283415.1_ASM1628341v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:19:06,640] [INFO] Task succeeded: Blastn
[2023-06-29 21:19:06,645] [INFO] Selected 32 target genomes.
[2023-06-29 21:19:06,645] [INFO] Target genome list was writen to GCA_016283415.1_ASM1628341v1_genomic.fna/target_genomes.txt
[2023-06-29 21:19:06,647] [INFO] Task started: fastANI
[2023-06-29 21:19:06,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg716ffe3e-de2c-4f89-82b0-7aa6c0e435db/GCA_016283415.1_ASM1628341v1_genomic.fna.gz --refList GCA_016283415.1_ASM1628341v1_genomic.fna/target_genomes.txt --output GCA_016283415.1_ASM1628341v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:19:23,772] [INFO] Task succeeded: fastANI
[2023-06-29 21:19:23,773] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb11279f-749c-4fff-9cb2-2dfb92047a07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:19:23,773] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb11279f-749c-4fff-9cb2-2dfb92047a07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:19:23,788] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:19:23,788] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 21:19:23,788] [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
Prevotella koreensis	strain=KCOM 3155	GCA_003977605.1	2490854	2490854	type	True	76.6987	50	1457	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.4957	59	1457	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.4063	82	1457	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	76.3924	99	1457	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	76.376	66	1457	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	76.3154	67	1457	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	76.3026	57	1457	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.2893	64	1457	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	76.2393	57	1457	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.2333	64	1457	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.0248	87	1457	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	75.9903	73	1457	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	75.9651	106	1457	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	75.7018	73	1457	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 21:19:23,791] [INFO] DFAST Taxonomy check result was written to GCA_016283415.1_ASM1628341v1_genomic.fna/tc_result.tsv
[2023-06-29 21:19:23,791] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:19:23,792] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:19:23,792] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb11279f-749c-4fff-9cb2-2dfb92047a07/dqc_reference/checkm_data
[2023-06-29 21:19:23,793] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:19:23,841] [INFO] Task started: CheckM
[2023-06-29 21:19:23,841] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016283415.1_ASM1628341v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016283415.1_ASM1628341v1_genomic.fna/checkm_input GCA_016283415.1_ASM1628341v1_genomic.fna/checkm_result
[2023-06-29 21:20:46,194] [INFO] Task succeeded: CheckM
[2023-06-29 21:20:46,195] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 21:20:46,240] [INFO] ===== Completeness check finished =====
[2023-06-29 21:20:46,240] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:20:46,240] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016283415.1_ASM1628341v1_genomic.fna/markers.fasta)
[2023-06-29 21:20:46,240] [INFO] Task started: Blastn
[2023-06-29 21:20:46,241] [INFO] Running command: blastn -query GCA_016283415.1_ASM1628341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb11279f-749c-4fff-9cb2-2dfb92047a07/dqc_reference/reference_markers_gtdb.fasta -out GCA_016283415.1_ASM1628341v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:20:47,197] [INFO] Task succeeded: Blastn
[2023-06-29 21:20:47,202] [INFO] Selected 17 target genomes.
[2023-06-29 21:20:47,203] [INFO] Target genome list was writen to GCA_016283415.1_ASM1628341v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:20:47,209] [INFO] Task started: fastANI
[2023-06-29 21:20:47,209] [INFO] Running command: fastANI --query /var/lib/cwl/stg716ffe3e-de2c-4f89-82b0-7aa6c0e435db/GCA_016283415.1_ASM1628341v1_genomic.fna.gz --refList GCA_016283415.1_ASM1628341v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016283415.1_ASM1628341v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:21:00,306] [INFO] Task succeeded: fastANI
[2023-06-29 21:21:00,326] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 21:21:00,327] [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_902803455.1	s__Prevotella sp902803455	98.4032	738	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.80	98.80	0.94	0.94	2	conclusive
GCA_902776475.1	s__Prevotella sp902776475	79.2727	474	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.89	97.89	0.91	0.91	2	-
GCA_902767775.1	s__Prevotella sp902767775	79.0765	483	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.97	97.97	0.86	0.86	2	-
GCA_016281815.1	s__Prevotella sp016281815	78.9367	442	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317305.1	s__Prevotella sp900317305	78.7893	416	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.38	97.82	0.87	0.83	11	-
GCA_902780635.1	s__Prevotella sp902780635	78.706	364	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.41	97.41	0.85	0.85	2	-
GCA_902786665.1	s__Prevotella sp902786665	78.6634	450	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.72	98.72	0.89	0.89	2	-
GCA_900315745.1	s__Prevotella sp900315745	78.5986	344	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.44	97.86	0.88	0.79	6	-
GCA_900320585.1	s__Prevotella sp900320585	78.5911	367	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.77	98.44	0.87	0.81	6	-
GCA_017961115.1	s__Prevotella sp017961115	78.5434	394	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017524385.1	s__Prevotella sp017524385	78.3961	398	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902795605.1	s__Prevotella sp902795605	78.1442	405	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017619755.1	s__Prevotella sp017619755	78.1224	305	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315075.1	s__Prevotella sp900315075	78.1156	269	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.96	98.41	0.92	0.87	4	-
GCA_017548385.1	s__Prevotella sp017548385	76.9344	194	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002395135.1	s__Prevotella sp002395135	76.0407	94	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.98	98.98	0.83	0.83	2	-
GCA_905198745.1	s__Prevotella sp905198745	75.7956	65	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 21:21:00,329] [INFO] GTDB search result was written to GCA_016283415.1_ASM1628341v1_genomic.fna/result_gtdb.tsv
[2023-06-29 21:21:00,330] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:21:00,334] [INFO] DFAST_QC result json was written to GCA_016283415.1_ASM1628341v1_genomic.fna/dqc_result.json
[2023-06-29 21:21:00,335] [INFO] DFAST_QC completed!
[2023-06-29 21:21:00,335] [INFO] Total running time: 0h2m25s