[2024-01-25 18:48:05,708] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:48:05,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:48:05,710] [INFO] DQC Reference Directory: /var/lib/cwl/stg58178c10-4c1b-411f-bf5d-54e1d692542c/dqc_reference
[2024-01-25 18:48:06,842] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:48:06,851] [INFO] Task started: Prodigal
[2024-01-25 18:48:06,851] [INFO] Running command: gunzip -c /var/lib/cwl/stg5575caa2-9b88-4b30-8717-1ebc793c09dc/GCF_025151385.1_ASM2515138v1_genomic.fna.gz | prodigal -d GCF_025151385.1_ASM2515138v1_genomic.fna/cds.fna -a GCF_025151385.1_ASM2515138v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:48:23,670] [INFO] Task succeeded: Prodigal
[2024-01-25 18:48:23,670] [INFO] Task started: HMMsearch
[2024-01-25 18:48:23,670] [INFO] Running command: hmmsearch --tblout GCF_025151385.1_ASM2515138v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58178c10-4c1b-411f-bf5d-54e1d692542c/dqc_reference/reference_markers.hmm GCF_025151385.1_ASM2515138v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:48:23,891] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:48:23,892] [INFO] Found 6/6 markers.
[2024-01-25 18:48:23,919] [INFO] Query marker FASTA was written to GCF_025151385.1_ASM2515138v1_genomic.fna/markers.fasta
[2024-01-25 18:48:23,919] [INFO] Task started: Blastn
[2024-01-25 18:48:23,919] [INFO] Running command: blastn -query GCF_025151385.1_ASM2515138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58178c10-4c1b-411f-bf5d-54e1d692542c/dqc_reference/reference_markers.fasta -out GCF_025151385.1_ASM2515138v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:24,469] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:24,472] [INFO] Selected 26 target genomes.
[2024-01-25 18:48:24,472] [INFO] Target genome list was writen to GCF_025151385.1_ASM2515138v1_genomic.fna/target_genomes.txt
[2024-01-25 18:48:24,493] [INFO] Task started: fastANI
[2024-01-25 18:48:24,493] [INFO] Running command: fastANI --query /var/lib/cwl/stg5575caa2-9b88-4b30-8717-1ebc793c09dc/GCF_025151385.1_ASM2515138v1_genomic.fna.gz --refList GCF_025151385.1_ASM2515138v1_genomic.fna/target_genomes.txt --output GCF_025151385.1_ASM2515138v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:48:37,111] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:37,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58178c10-4c1b-411f-bf5d-54e1d692542c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:48:37,112] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58178c10-4c1b-411f-bf5d-54e1d692542c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:48:37,138] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:48:37,138] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:48:37,139] [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 timonensis	strain=4401737	GCA_000455445.1	386414	386414	type	True	85.9561	432	1102	95	below_threshold
Prevotella timonensis	strain=DSM 22865	GCA_000430565.1	386414	386414	suspected-type	True	85.8896	409	1102	95	below_threshold
Prevotella timonensis	strain=JCM 15640	GCA_000614005.1	386414	386414	type	True	85.8707	413	1102	95	below_threshold
Prevotella koreensis	strain=KCOM 3155	GCA_003977605.1	2490854	2490854	type	True	81.2773	104	1102	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	81.135	122	1102	95	below_threshold
Xylanibacter muris	strain=PMUR	GCA_013166605.1	2736290	2736290	type	True	80.2733	52	1102	95	below_threshold
Prevotella oris	strain=NCTC13071	GCA_900637655.1	28135	28135	type	True	80.2053	118	1102	95	below_threshold
Prevotella enoeca	strain=JCM 12259	GCA_000613405.1	76123	76123	type	True	79.863	117	1102	95	below_threshold
Prevotella multisaccharivorax	strain=DSM 17128	GCA_000218235.1	310514	310514	type	True	79.8066	63	1102	95	below_threshold
Prevotella shahii	strain=DSM 15611	GCA_003201715.1	228603	228603	type	True	79.7901	76	1102	95	below_threshold
Prevotella maculosa	strain=DSM 19339	GCA_000382385.1	439703	439703	type	True	79.6467	110	1102	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	79.6226	119	1102	95	below_threshold
Prevotella oris	strain=DSM 18711	GCA_000377685.1	28135	28135	type	True	79.6099	112	1102	95	below_threshold
Prevotella multisaccharivorax	strain=JCM 12954	GCA_019973315.1	310514	310514	type	True	79.46	60	1102	95	below_threshold
Prevotella oris	strain=JCM 12252	GCA_000613505.1	28135	28135	type	True	79.453	114	1102	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	79.4455	112	1102	95	below_threshold
Prevotella maculosa	strain=JCM 15638	GCA_000613965.1	439703	439703	type	True	79.2056	105	1102	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	79.1218	120	1102	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	78.7597	135	1102	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	78.7191	106	1102	95	below_threshold
Prevotella loescheii	strain=DSM 19665	GCA_000378085.1	840	840	type	True	78.6668	103	1102	95	below_threshold
Prevotella herbatica	strain=WR041	GCA_017347605.1	2801997	2801997	type	True	78.148	51	1102	95	below_threshold
Prevotella phocaeensis	strain=SN19	GCA_900065875.1	1776388	1776388	type	True	78.0281	103	1102	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:48:37,140] [INFO] DFAST Taxonomy check result was written to GCF_025151385.1_ASM2515138v1_genomic.fna/tc_result.tsv
[2024-01-25 18:48:37,141] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:48:37,141] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:48:37,141] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58178c10-4c1b-411f-bf5d-54e1d692542c/dqc_reference/checkm_data
[2024-01-25 18:48:37,143] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:48:37,189] [INFO] Task started: CheckM
[2024-01-25 18:48:37,189] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025151385.1_ASM2515138v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025151385.1_ASM2515138v1_genomic.fna/checkm_input GCF_025151385.1_ASM2515138v1_genomic.fna/checkm_result
[2024-01-25 18:49:26,834] [INFO] Task succeeded: CheckM
[2024-01-25 18:49:26,836] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:49:26,855] [INFO] ===== Completeness check finished =====
[2024-01-25 18:49:26,855] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:49:26,856] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025151385.1_ASM2515138v1_genomic.fna/markers.fasta)
[2024-01-25 18:49:26,856] [INFO] Task started: Blastn
[2024-01-25 18:49:26,856] [INFO] Running command: blastn -query GCF_025151385.1_ASM2515138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58178c10-4c1b-411f-bf5d-54e1d692542c/dqc_reference/reference_markers_gtdb.fasta -out GCF_025151385.1_ASM2515138v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:27,679] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:27,683] [INFO] Selected 16 target genomes.
[2024-01-25 18:49:27,683] [INFO] Target genome list was writen to GCF_025151385.1_ASM2515138v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:49:27,708] [INFO] Task started: fastANI
[2024-01-25 18:49:27,708] [INFO] Running command: fastANI --query /var/lib/cwl/stg5575caa2-9b88-4b30-8717-1ebc793c09dc/GCF_025151385.1_ASM2515138v1_genomic.fna.gz --refList GCF_025151385.1_ASM2515138v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025151385.1_ASM2515138v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:49:36,288] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:36,297] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:49:36,298] [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_000177075.1	s__Prevotella buccalis	95.3893	837	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.19	95.19	0.85	0.85	2	conclusive
GCA_900547085.1	s__Prevotella sp900547085	94.3682	526	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000479005.1	s__Prevotella sp000479005	93.1994	759	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.86	96.42	0.92	0.87	3	-
GCF_000455445.1	s__Prevotella timonensis	85.9564	434	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0025	97.81	95.47	0.90	0.82	5	-
GCF_000762405.1	s__Prevotella timonensis_A	84.9381	393	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0025	96.56	96.39	0.83	0.81	3	-
GCF_001553265.1	s__Prevotella sp001553265	84.7037	146	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.33	99.33	0.90	0.90	2	-
GCF_000758925.1	s__Prevotella sp000758925	83.8713	145	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003043925.1	s__Prevotella sp003043925	80.6185	115	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.98	0.98	0.98	2	-
GCF_900637655.1	s__Prevotella oris	80.1466	118	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.96	97.06	0.90	0.82	10	-
GCF_000613405.1	s__Prevotella enoeca	79.8814	115	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.97	99.97	1.00	1.00	2	-
GCF_000426585.1	s__Prevotella baroniae	79.7306	116	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.79	98.01	0.95	0.92	4	-
GCF_000184945.1	s__Prevotella buccae	78.7731	136	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.38	98.24	0.91	0.87	7	-
GCF_002251385.1	s__Prevotella sp002251385	78.68	79	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.22	97.07	0.92	0.88	8	-
GCA_905202125.1	s__Prevotella sp900556275	76.4333	65	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:49:36,299] [INFO] GTDB search result was written to GCF_025151385.1_ASM2515138v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:49:36,300] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:49:36,304] [INFO] DFAST_QC result json was written to GCF_025151385.1_ASM2515138v1_genomic.fna/dqc_result.json
[2024-01-25 18:49:36,304] [INFO] DFAST_QC completed!
[2024-01-25 18:49:36,304] [INFO] Total running time: 0h1m31s