[2024-01-25 17:43:35,424] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:43:35,425] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:43:35,425] [INFO] DQC Reference Directory: /var/lib/cwl/stgaaea41b4-e589-4d04-9c1b-9d7e1e508aec/dqc_reference
[2024-01-25 17:43:36,562] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:43:36,563] [INFO] Task started: Prodigal
[2024-01-25 17:43:36,563] [INFO] Running command: gunzip -c /var/lib/cwl/stg86605064-bff0-4cc9-bfc1-879346fb413e/GCF_025457485.1_ASM2545748v1_genomic.fna.gz | prodigal -d GCF_025457485.1_ASM2545748v1_genomic.fna/cds.fna -a GCF_025457485.1_ASM2545748v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:43:54,048] [INFO] Task succeeded: Prodigal
[2024-01-25 17:43:54,048] [INFO] Task started: HMMsearch
[2024-01-25 17:43:54,048] [INFO] Running command: hmmsearch --tblout GCF_025457485.1_ASM2545748v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaaea41b4-e589-4d04-9c1b-9d7e1e508aec/dqc_reference/reference_markers.hmm GCF_025457485.1_ASM2545748v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:43:54,266] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:43:54,267] [INFO] Found 6/6 markers.
[2024-01-25 17:43:54,295] [INFO] Query marker FASTA was written to GCF_025457485.1_ASM2545748v1_genomic.fna/markers.fasta
[2024-01-25 17:43:54,295] [INFO] Task started: Blastn
[2024-01-25 17:43:54,295] [INFO] Running command: blastn -query GCF_025457485.1_ASM2545748v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaaea41b4-e589-4d04-9c1b-9d7e1e508aec/dqc_reference/reference_markers.fasta -out GCF_025457485.1_ASM2545748v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:54,872] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:54,875] [INFO] Selected 16 target genomes.
[2024-01-25 17:43:54,875] [INFO] Target genome list was writen to GCF_025457485.1_ASM2545748v1_genomic.fna/target_genomes.txt
[2024-01-25 17:43:54,905] [INFO] Task started: fastANI
[2024-01-25 17:43:54,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg86605064-bff0-4cc9-bfc1-879346fb413e/GCF_025457485.1_ASM2545748v1_genomic.fna.gz --refList GCF_025457485.1_ASM2545748v1_genomic.fna/target_genomes.txt --output GCF_025457485.1_ASM2545748v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:44:04,208] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:04,208] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaaea41b4-e589-4d04-9c1b-9d7e1e508aec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:44:04,208] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaaea41b4-e589-4d04-9c1b-9d7e1e508aec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:44:04,217] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:44:04,218] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:44:04,218] [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 mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	93.3651	926	1150	95	below_threshold
Prevotella multisaccharivorax	strain=DSM 17128	GCA_000218235.1	310514	310514	type	True	78.8189	199	1150	95	below_threshold
Prevotella multisaccharivorax	strain=JCM 12954	GCA_019973315.1	310514	310514	type	True	78.727	196	1150	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	78.2754	200	1150	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	77.3549	238	1150	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	77.3182	231	1150	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	77.2964	230	1150	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	77.1682	120	1150	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	77.0014	117	1150	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	76.8157	120	1150	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	76.802	119	1150	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.6817	150	1150	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.5549	87	1150	95	below_threshold
Palleniella intestinalis	strain=PINT	GCA_013166595.1	2736291	2736291	type	True	76.434	67	1150	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:44:04,219] [INFO] DFAST Taxonomy check result was written to GCF_025457485.1_ASM2545748v1_genomic.fna/tc_result.tsv
[2024-01-25 17:44:04,220] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:44:04,220] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:44:04,220] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaaea41b4-e589-4d04-9c1b-9d7e1e508aec/dqc_reference/checkm_data
[2024-01-25 17:44:04,221] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:44:04,258] [INFO] Task started: CheckM
[2024-01-25 17:44:04,258] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025457485.1_ASM2545748v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025457485.1_ASM2545748v1_genomic.fna/checkm_input GCF_025457485.1_ASM2545748v1_genomic.fna/checkm_result
[2024-01-25 17:44:54,370] [INFO] Task succeeded: CheckM
[2024-01-25 17:44:54,371] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:44:54,388] [INFO] ===== Completeness check finished =====
[2024-01-25 17:44:54,388] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:44:54,388] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025457485.1_ASM2545748v1_genomic.fna/markers.fasta)
[2024-01-25 17:44:54,389] [INFO] Task started: Blastn
[2024-01-25 17:44:54,389] [INFO] Running command: blastn -query GCF_025457485.1_ASM2545748v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaaea41b4-e589-4d04-9c1b-9d7e1e508aec/dqc_reference/reference_markers_gtdb.fasta -out GCF_025457485.1_ASM2545748v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:55,336] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:55,342] [INFO] Selected 6 target genomes.
[2024-01-25 17:44:55,342] [INFO] Target genome list was writen to GCF_025457485.1_ASM2545748v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:44:55,356] [INFO] Task started: fastANI
[2024-01-25 17:44:55,356] [INFO] Running command: fastANI --query /var/lib/cwl/stg86605064-bff0-4cc9-bfc1-879346fb413e/GCF_025457485.1_ASM2545748v1_genomic.fna.gz --refList GCF_025457485.1_ASM2545748v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025457485.1_ASM2545748v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:45:00,315] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:00,320] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:45:00,320] [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_002481295.1	s__Prevotella sp002481295	96.687	794	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.83	96.70	0.87	0.78	4	conclusive
GCF_009695775.1	s__Prevotella mizrahii	93.4298	922	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.15	96.87	0.87	0.84	6	-
GCA_900317685.1	s__Prevotella sp900317685	90.3228	763	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.13	96.10	0.84	0.76	12	-
GCA_900540375.1	s__Prevotella sp900540375	89.0815	787	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.83	98.80	0.92	0.91	3	-
GCA_900546345.1	s__Prevotella sp900546345	85.2705	705	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902801375.1	s__Prevotella sp902801375	76.6119	97	1150	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.75	97.75	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:45:00,322] [INFO] GTDB search result was written to GCF_025457485.1_ASM2545748v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:45:00,323] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:45:00,326] [INFO] DFAST_QC result json was written to GCF_025457485.1_ASM2545748v1_genomic.fna/dqc_result.json
[2024-01-25 17:45:00,326] [INFO] DFAST_QC completed!
[2024-01-25 17:45:00,326] [INFO] Total running time: 0h1m25s