[2024-01-24 13:17:26,949] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:26,951] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:26,951] [INFO] DQC Reference Directory: /var/lib/cwl/stg1122e51e-51ee-48e8-8874-19a3379298e9/dqc_reference
[2024-01-24 13:17:28,213] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:28,214] [INFO] Task started: Prodigal
[2024-01-24 13:17:28,214] [INFO] Running command: gunzip -c /var/lib/cwl/stga7c1df71-4597-467f-a57f-aef88bf26a24/GCF_000025925.1_ASM2592v1_genomic.fna.gz | prodigal -d GCF_000025925.1_ASM2592v1_genomic.fna/cds.fna -a GCF_000025925.1_ASM2592v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:47,082] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:47,083] [INFO] Task started: HMMsearch
[2024-01-24 13:17:47,083] [INFO] Running command: hmmsearch --tblout GCF_000025925.1_ASM2592v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1122e51e-51ee-48e8-8874-19a3379298e9/dqc_reference/reference_markers.hmm GCF_000025925.1_ASM2592v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:47,351] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:47,353] [INFO] Found 6/6 markers.
[2024-01-24 13:17:47,387] [INFO] Query marker FASTA was written to GCF_000025925.1_ASM2592v1_genomic.fna/markers.fasta
[2024-01-24 13:17:47,388] [INFO] Task started: Blastn
[2024-01-24 13:17:47,388] [INFO] Running command: blastn -query GCF_000025925.1_ASM2592v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1122e51e-51ee-48e8-8874-19a3379298e9/dqc_reference/reference_markers.fasta -out GCF_000025925.1_ASM2592v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:47,984] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:47,989] [INFO] Selected 19 target genomes.
[2024-01-24 13:17:47,990] [INFO] Target genome list was writen to GCF_000025925.1_ASM2592v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:48,000] [INFO] Task started: fastANI
[2024-01-24 13:17:48,001] [INFO] Running command: fastANI --query /var/lib/cwl/stga7c1df71-4597-467f-a57f-aef88bf26a24/GCF_000025925.1_ASM2592v1_genomic.fna.gz --refList GCF_000025925.1_ASM2592v1_genomic.fna/target_genomes.txt --output GCF_000025925.1_ASM2592v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:58,244] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:58,244] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1122e51e-51ee-48e8-8874-19a3379298e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:58,244] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1122e51e-51ee-48e8-8874-19a3379298e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:58,256] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:17:58,256] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:58,257] [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 ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	100.0	1206	1206	95	conclusive
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	99.9812	1177	1206	95	conclusive
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	79.2366	258	1206	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	78.089	149	1206	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	77.9771	82	1206	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	77.8994	141	1206	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	77.8607	80	1206	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	77.5991	138	1206	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	77.4518	68	1206	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	77.3482	68	1206	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.2572	75	1206	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	77.2475	92	1206	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.9923	58	1206	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.9066	54	1206	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:58,258] [INFO] DFAST Taxonomy check result was written to GCF_000025925.1_ASM2592v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:58,259] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:58,259] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:58,259] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1122e51e-51ee-48e8-8874-19a3379298e9/dqc_reference/checkm_data
[2024-01-24 13:17:58,260] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:58,299] [INFO] Task started: CheckM
[2024-01-24 13:17:58,299] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000025925.1_ASM2592v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000025925.1_ASM2592v1_genomic.fna/checkm_input GCF_000025925.1_ASM2592v1_genomic.fna/checkm_result
[2024-01-24 13:18:55,560] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:55,561] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:55,581] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:55,582] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:55,582] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000025925.1_ASM2592v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:55,583] [INFO] Task started: Blastn
[2024-01-24 13:18:55,583] [INFO] Running command: blastn -query GCF_000025925.1_ASM2592v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1122e51e-51ee-48e8-8874-19a3379298e9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000025925.1_ASM2592v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:56,671] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:56,681] [INFO] Selected 7 target genomes.
[2024-01-24 13:18:56,681] [INFO] Target genome list was writen to GCF_000025925.1_ASM2592v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:56,689] [INFO] Task started: fastANI
[2024-01-24 13:18:56,690] [INFO] Running command: fastANI --query /var/lib/cwl/stga7c1df71-4597-467f-a57f-aef88bf26a24/GCF_000025925.1_ASM2592v1_genomic.fna.gz --refList GCF_000025925.1_ASM2592v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000025925.1_ASM2592v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:03,388] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:03,400] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:03,400] [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_000025925.1	s__Prevotella ruminicola	100.0	1206	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.74	96.82	0.88	0.80	15	conclusive
GCF_900107775.1	s__Prevotella ruminicola_C	94.4437	945	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.61	97.61	0.89	0.89	3	-
GCF_000687715.1	s__Prevotella ruminicola_B	94.299	925	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902789415.1	s__Prevotella sp902789415	90.2788	745	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015060625.1	s__Prevotella ruminicola_D	89.3239	866	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000619825.1	s__Prevotella sp000619825	85.6395	785	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702825.1	s__Prevotella sp000702825	84.8089	728	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.44	98.44	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:03,402] [INFO] GTDB search result was written to GCF_000025925.1_ASM2592v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:03,402] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:03,405] [INFO] DFAST_QC result json was written to GCF_000025925.1_ASM2592v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:03,406] [INFO] DFAST_QC completed!
[2024-01-24 13:19:03,406] [INFO] Total running time: 0h1m36s