[2023-06-28 19:29:21,244] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:29:21,247] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:29:21,247] [INFO] DQC Reference Directory: /var/lib/cwl/stg0520319b-7346-46c6-9ed0-59796c1a7830/dqc_reference
[2023-06-28 19:29:22,554] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:29:22,555] [INFO] Task started: Prodigal
[2023-06-28 19:29:22,556] [INFO] Running command: gunzip -c /var/lib/cwl/stg76ccb4aa-bed0-47a0-91f9-e9afc3e9e2fe/GCA_015261435.1_ASM1526143v1_genomic.fna.gz | prodigal -d GCA_015261435.1_ASM1526143v1_genomic.fna/cds.fna -a GCA_015261435.1_ASM1526143v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:29:30,634] [INFO] Task succeeded: Prodigal
[2023-06-28 19:29:30,635] [INFO] Task started: HMMsearch
[2023-06-28 19:29:30,635] [INFO] Running command: hmmsearch --tblout GCA_015261435.1_ASM1526143v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0520319b-7346-46c6-9ed0-59796c1a7830/dqc_reference/reference_markers.hmm GCA_015261435.1_ASM1526143v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:29:30,885] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:29:30,886] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg76ccb4aa-bed0-47a0-91f9-e9afc3e9e2fe/GCA_015261435.1_ASM1526143v1_genomic.fna.gz]
[2023-06-28 19:29:30,908] [INFO] Query marker FASTA was written to GCA_015261435.1_ASM1526143v1_genomic.fna/markers.fasta
[2023-06-28 19:29:30,908] [INFO] Task started: Blastn
[2023-06-28 19:29:30,908] [INFO] Running command: blastn -query GCA_015261435.1_ASM1526143v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0520319b-7346-46c6-9ed0-59796c1a7830/dqc_reference/reference_markers.fasta -out GCA_015261435.1_ASM1526143v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:29:31,500] [INFO] Task succeeded: Blastn
[2023-06-28 19:29:31,505] [INFO] Selected 9 target genomes.
[2023-06-28 19:29:31,505] [INFO] Target genome list was writen to GCA_015261435.1_ASM1526143v1_genomic.fna/target_genomes.txt
[2023-06-28 19:29:31,508] [INFO] Task started: fastANI
[2023-06-28 19:29:31,509] [INFO] Running command: fastANI --query /var/lib/cwl/stg76ccb4aa-bed0-47a0-91f9-e9afc3e9e2fe/GCA_015261435.1_ASM1526143v1_genomic.fna.gz --refList GCA_015261435.1_ASM1526143v1_genomic.fna/target_genomes.txt --output GCA_015261435.1_ASM1526143v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:29:36,291] [INFO] Task succeeded: fastANI
[2023-06-28 19:29:36,292] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0520319b-7346-46c6-9ed0-59796c1a7830/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:29:36,292] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0520319b-7346-46c6-9ed0-59796c1a7830/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:29:36,300] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2023-06-28 19:29:36,301] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 19:29:36,301] [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 pallens	strain=DSM 18710	GCA_003269195.1	60133	60133	type	True	98.326	612	662	95	conclusive
Prevotella pallens	strain=ATCC 700821	GCA_000220255.1	60133	60133	type	True	98.2367	626	662	95	conclusive
Prevotella intermedia	strain=ATCC 25611	GCA_000519165.1	28131	28131	type	True	80.9611	357	662	95	below_threshold
Prevotella intermedia	strain=DSM 20706	GCA_000439065.1	28131	28131	type	True	80.9513	359	662	95	below_threshold
Prevotella intermedia	strain=ATCC 25611	GCA_001953955.1	28131	28131	type	True	80.8364	373	662	95	below_threshold
Prevotella vespertina	strain=A2879	GCA_009728485.1	2608404	2608404	type	True	79.2828	68	662	95	below_threshold
Prevotella veroralis	strain=DSM 19559	GCA_000377625.1	28137	28137	type	True	78.5791	69	662	95	below_threshold
Prevotella veroralis	strain=JCM 6290	GCA_000613325.1	28137	28137	type	True	78.5192	64	662	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 19:29:36,303] [INFO] DFAST Taxonomy check result was written to GCA_015261435.1_ASM1526143v1_genomic.fna/tc_result.tsv
[2023-06-28 19:29:36,304] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:29:36,304] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:29:36,304] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0520319b-7346-46c6-9ed0-59796c1a7830/dqc_reference/checkm_data
[2023-06-28 19:29:36,305] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:29:36,333] [INFO] Task started: CheckM
[2023-06-28 19:29:36,333] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015261435.1_ASM1526143v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015261435.1_ASM1526143v1_genomic.fna/checkm_input GCA_015261435.1_ASM1526143v1_genomic.fna/checkm_result
[2023-06-28 19:30:05,404] [INFO] Task succeeded: CheckM
[2023-06-28 19:30:05,406] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:30:05,426] [INFO] ===== Completeness check finished =====
[2023-06-28 19:30:05,426] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:30:05,426] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015261435.1_ASM1526143v1_genomic.fna/markers.fasta)
[2023-06-28 19:30:05,427] [INFO] Task started: Blastn
[2023-06-28 19:30:05,427] [INFO] Running command: blastn -query GCA_015261435.1_ASM1526143v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0520319b-7346-46c6-9ed0-59796c1a7830/dqc_reference/reference_markers_gtdb.fasta -out GCA_015261435.1_ASM1526143v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:30:06,137] [INFO] Task succeeded: Blastn
[2023-06-28 19:30:06,142] [INFO] Selected 14 target genomes.
[2023-06-28 19:30:06,142] [INFO] Target genome list was writen to GCA_015261435.1_ASM1526143v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:30:06,151] [INFO] Task started: fastANI
[2023-06-28 19:30:06,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg76ccb4aa-bed0-47a0-91f9-e9afc3e9e2fe/GCA_015261435.1_ASM1526143v1_genomic.fna.gz --refList GCA_015261435.1_ASM1526143v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015261435.1_ASM1526143v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:30:13,109] [INFO] Task succeeded: fastANI
[2023-06-28 19:30:13,124] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 19:30:13,124] [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_000220255.1	s__Prevotella pallens	98.2367	626	662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.33	96.89	0.94	0.88	40	conclusive
GCF_000220235.1	s__Prevotella nigrescens	84.3279	474	662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.14	97.70	0.92	0.78	13	-
GCF_000614025.1	s__Prevotella aurantiaca	82.4659	395	662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.47	98.39	0.93	0.91	4	-
GCF_001953955.1	s__Prevotella intermedia	80.8597	371	662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.61	96.13	0.88	0.83	34	-
GCF_000613945.1	s__Prevotella falsenii	80.0404	330	662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000257925.1	s__Prevotella sp000257925	78.7785	81	662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.40	96.99	0.92	0.83	10	-
GCF_000377625.1	s__Prevotella veroralis	78.6223	70	662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.76	96.65	0.91	0.86	4	-
GCF_018127965.1	s__Prevotella melaninogenica_B	78.349	83	662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.77	95.72	0.91	0.89	4	-
GCF_000262545.1	s__Prevotella bivia	77.9115	77	662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.82	98.45	0.91	0.86	8	-
GCF_018128065.1	s__Prevotella sp000467895	77.7393	96	662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.71	96.42	0.91	0.83	4	-
GCF_000430525.1	s__Prevotella corporis	77.5804	79	662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.63	97.78	0.92	0.87	4	-
--------------------------------------------------------------------------------
[2023-06-28 19:30:13,126] [INFO] GTDB search result was written to GCA_015261435.1_ASM1526143v1_genomic.fna/result_gtdb.tsv
[2023-06-28 19:30:13,127] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:30:13,131] [INFO] DFAST_QC result json was written to GCA_015261435.1_ASM1526143v1_genomic.fna/dqc_result.json
[2023-06-28 19:30:13,131] [INFO] DFAST_QC completed!
[2023-06-28 19:30:13,131] [INFO] Total running time: 0h0m52s