[2024-01-25 20:05:50,596] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:05:50,597] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:05:50,597] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f620e9f-5838-4b7d-8a0d-a92527504be4/dqc_reference
[2024-01-25 20:05:51,723] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:05:51,724] [INFO] Task started: Prodigal
[2024-01-25 20:05:51,724] [INFO] Running command: gunzip -c /var/lib/cwl/stg85d8c350-7e01-4906-9d37-edaf667e667a/GCF_900065875.1_PRJEB126981_genomic.fna.gz | prodigal -d GCF_900065875.1_PRJEB126981_genomic.fna/cds.fna -a GCF_900065875.1_PRJEB126981_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:06:04,525] [INFO] Task succeeded: Prodigal
[2024-01-25 20:06:04,525] [INFO] Task started: HMMsearch
[2024-01-25 20:06:04,525] [INFO] Running command: hmmsearch --tblout GCF_900065875.1_PRJEB126981_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f620e9f-5838-4b7d-8a0d-a92527504be4/dqc_reference/reference_markers.hmm GCF_900065875.1_PRJEB126981_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:06:04,745] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:06:04,746] [INFO] Found 6/6 markers.
[2024-01-25 20:06:04,778] [INFO] Query marker FASTA was written to GCF_900065875.1_PRJEB126981_genomic.fna/markers.fasta
[2024-01-25 20:06:04,779] [INFO] Task started: Blastn
[2024-01-25 20:06:04,779] [INFO] Running command: blastn -query GCF_900065875.1_PRJEB126981_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f620e9f-5838-4b7d-8a0d-a92527504be4/dqc_reference/reference_markers.fasta -out GCF_900065875.1_PRJEB126981_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:05,358] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:05,361] [INFO] Selected 16 target genomes.
[2024-01-25 20:06:05,361] [INFO] Target genome list was writen to GCF_900065875.1_PRJEB126981_genomic.fna/target_genomes.txt
[2024-01-25 20:06:05,377] [INFO] Task started: fastANI
[2024-01-25 20:06:05,377] [INFO] Running command: fastANI --query /var/lib/cwl/stg85d8c350-7e01-4906-9d37-edaf667e667a/GCF_900065875.1_PRJEB126981_genomic.fna.gz --refList GCF_900065875.1_PRJEB126981_genomic.fna/target_genomes.txt --output GCF_900065875.1_PRJEB126981_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:06:14,079] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:14,080] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f620e9f-5838-4b7d-8a0d-a92527504be4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:06:14,080] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f620e9f-5838-4b7d-8a0d-a92527504be4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:06:14,088] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:06:14,088] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 20:06:14,088] [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 phocaeensis	strain=SN19	GCA_900065875.1	1776388	1776388	type	True	100.0	969	969	95	inconclusive
Prevotella oralis	strain=DSM 20702	GCA_900129435.1	28134	28134	type	True	97.1633	866	969	95	inconclusive
Prevotella oralis	strain=ATCC 33269	GCA_000185145.2	28134	28134	type	True	97.1592	869	969	95	inconclusive
Prevotella oris	strain=NCTC13071	GCA_900637655.1	28135	28135	type	True	79.2439	101	969	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	79.0557	91	969	95	below_threshold
Prevotella timonensis	strain=4401737	GCA_000455445.1	386414	386414	type	True	78.539	83	969	95	below_threshold
Prevotella oris	strain=DSM 18711	GCA_000377685.1	28135	28135	type	True	78.4929	96	969	95	below_threshold
Prevotella timonensis	strain=DSM 22865	GCA_000430565.1	386414	386414	suspected-type	True	78.3297	79	969	95	below_threshold
Prevotella pleuritidis	strain=JCM 14110	GCA_000613725.1	407975	407975	type	True	78.0368	88	969	95	below_threshold
Prevotella shahii	strain=DSM 15611	GCA_003201715.1	228603	228603	type	True	76.9441	53	969	95	below_threshold
Prevotella loescheii	strain=DSM 19665	GCA_000378085.1	840	840	type	True	76.9423	57	969	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:06:14,089] [INFO] DFAST Taxonomy check result was written to GCF_900065875.1_PRJEB126981_genomic.fna/tc_result.tsv
[2024-01-25 20:06:14,089] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:06:14,090] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:06:14,090] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f620e9f-5838-4b7d-8a0d-a92527504be4/dqc_reference/checkm_data
[2024-01-25 20:06:14,090] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:06:14,120] [INFO] Task started: CheckM
[2024-01-25 20:06:14,120] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900065875.1_PRJEB126981_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900065875.1_PRJEB126981_genomic.fna/checkm_input GCF_900065875.1_PRJEB126981_genomic.fna/checkm_result
[2024-01-25 20:06:51,797] [INFO] Task succeeded: CheckM
[2024-01-25 20:06:51,798] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:06:51,813] [INFO] ===== Completeness check finished =====
[2024-01-25 20:06:51,814] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:06:51,814] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900065875.1_PRJEB126981_genomic.fna/markers.fasta)
[2024-01-25 20:06:51,814] [INFO] Task started: Blastn
[2024-01-25 20:06:51,814] [INFO] Running command: blastn -query GCF_900065875.1_PRJEB126981_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f620e9f-5838-4b7d-8a0d-a92527504be4/dqc_reference/reference_markers_gtdb.fasta -out GCF_900065875.1_PRJEB126981_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:52,666] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:52,669] [INFO] Selected 28 target genomes.
[2024-01-25 20:06:52,669] [INFO] Target genome list was writen to GCF_900065875.1_PRJEB126981_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:06:52,729] [INFO] Task started: fastANI
[2024-01-25 20:06:52,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg85d8c350-7e01-4906-9d37-edaf667e667a/GCF_900065875.1_PRJEB126981_genomic.fna.gz --refList GCF_900065875.1_PRJEB126981_genomic.fna/target_genomes_gtdb.txt --output GCF_900065875.1_PRJEB126981_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:07:06,434] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:06,445] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:07:06,445] [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_000185145.2	s__Prevotella oralis	97.1853	868	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.83	97.13	0.96	0.92	6	conclusive
GCF_003043925.1	s__Prevotella sp003043925	79.9463	91	969	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	79.3654	99	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.96	97.06	0.90	0.82	10	-
GCF_000455445.1	s__Prevotella timonensis	78.5161	81	969	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	78.3508	80	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0025	96.56	96.39	0.83	0.81	3	-
GCF_000613725.1	s__Prevotella pleuritidis	78.0901	86	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.72	98.65	0.96	0.96	4	-
GCF_000191065.1	s__Prevotella multiformis	77.8997	67	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.87	97.87	0.89	0.89	2	-
GCF_000479005.1	s__Prevotella sp000479005	77.8489	80	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.86	96.42	0.92	0.87	3	-
GCF_001553265.1	s__Prevotella sp001553265	77.5458	80	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.33	99.33	0.90	0.90	2	-
GCF_000177075.1	s__Prevotella buccalis	77.4902	91	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.19	95.19	0.85	0.85	2	-
GCF_000373185.1	s__Prevotella paludivivens	77.1074	59	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000834015.1	s__Prevotella pectinovora	77.0983	51	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.37	97.34	0.86	0.79	12	-
GCF_001275135.1	s__Prevotella rara	76.9856	65	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.17	97.70	0.90	0.86	7	-
GCA_900554695.1	s__Prevotella sp900554695	76.7721	54	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.93	97.88	0.84	0.83	3	-
GCF_019052365.1	s__Prevotella sp000434975	76.7217	52	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.59	0.82	0.74	11	-
GCA_902769705.1	s__Prevotella sp902769705	76.4313	50	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.61	96.53	0.84	0.80	3	-
GCA_905373605.1	s__Prevotella sp905373605	76.2489	51	969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:07:06,447] [INFO] GTDB search result was written to GCF_900065875.1_PRJEB126981_genomic.fna/result_gtdb.tsv
[2024-01-25 20:07:06,447] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:07:06,450] [INFO] DFAST_QC result json was written to GCF_900065875.1_PRJEB126981_genomic.fna/dqc_result.json
[2024-01-25 20:07:06,450] [INFO] DFAST_QC completed!
[2024-01-25 20:07:06,450] [INFO] Total running time: 0h1m16s