[2024-01-24 13:10:04,043] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:04,045] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:04,045] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ce21378-122a-4192-904c-78c39912ebec/dqc_reference
[2024-01-24 13:10:05,384] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:05,384] [INFO] Task started: Prodigal
[2024-01-24 13:10:05,385] [INFO] Running command: gunzip -c /var/lib/cwl/stg83dbfa32-b8f8-4383-ab2e-8664bb5cbf50/GCF_001262015.1_ASM126201v1_genomic.fna.gz | prodigal -d GCF_001262015.1_ASM126201v1_genomic.fna/cds.fna -a GCF_001262015.1_ASM126201v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:21,810] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:21,811] [INFO] Task started: HMMsearch
[2024-01-24 13:10:21,811] [INFO] Running command: hmmsearch --tblout GCF_001262015.1_ASM126201v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ce21378-122a-4192-904c-78c39912ebec/dqc_reference/reference_markers.hmm GCF_001262015.1_ASM126201v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:22,141] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:22,142] [INFO] Found 6/6 markers.
[2024-01-24 13:10:22,170] [INFO] Query marker FASTA was written to GCF_001262015.1_ASM126201v1_genomic.fna/markers.fasta
[2024-01-24 13:10:22,170] [INFO] Task started: Blastn
[2024-01-24 13:10:22,170] [INFO] Running command: blastn -query GCF_001262015.1_ASM126201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ce21378-122a-4192-904c-78c39912ebec/dqc_reference/reference_markers.fasta -out GCF_001262015.1_ASM126201v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:22,779] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:22,783] [INFO] Selected 14 target genomes.
[2024-01-24 13:10:22,784] [INFO] Target genome list was writen to GCF_001262015.1_ASM126201v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:22,790] [INFO] Task started: fastANI
[2024-01-24 13:10:22,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg83dbfa32-b8f8-4383-ab2e-8664bb5cbf50/GCF_001262015.1_ASM126201v1_genomic.fna.gz --refList GCF_001262015.1_ASM126201v1_genomic.fna/target_genomes.txt --output GCF_001262015.1_ASM126201v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:37,159] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:37,160] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ce21378-122a-4192-904c-78c39912ebec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:37,161] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ce21378-122a-4192-904c-78c39912ebec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:37,176] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:10:37,176] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:37,177] [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 fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	100.0	1086	1086	95	conclusive
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	99.9831	1084	1086	95	conclusive
Prevotella fusca	strain=JCM 17724	GCA_000614245.1	589436	589436	type	True	99.89	999	1086	95	conclusive
Prevotella melaninogenica	strain=ATCC 25845	GCA_000144405.1	28132	28132	suspected-type	True	83.3871	684	1086	95	below_threshold
Prevotella melaninogenica	strain=FDAARGOS_1566	GCA_020735785.1	28132	28132	suspected-type	True	83.377	682	1086	95	below_threshold
Prevotella scopos	strain=W2052	GCA_001683355.1	589437	589437	type	True	82.8416	648	1086	95	below_threshold
Prevotella jejuni	strain=DSM 26989	GCA_900187995.1	1177574	1177574	type	True	81.873	601	1086	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	81.2771	534	1086	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	81.1065	528	1086	95	below_threshold
Prevotella veroralis	strain=DSM 19559	GCA_000377625.1	28137	28137	type	True	80.2543	352	1086	95	below_threshold
Prevotella veroralis	strain=JCM 6290	GCA_000613325.1	28137	28137	type	True	79.8676	363	1086	95	below_threshold
Prevotella falsenii	strain=JCM 15124	GCA_000613945.1	515414	515414	type	True	79.3253	119	1086	95	below_threshold
Palleniella intestinalis	strain=PINT	GCA_013166595.1	2736291	2736291	type	True	77.5765	54	1086	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:37,179] [INFO] DFAST Taxonomy check result was written to GCF_001262015.1_ASM126201v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:37,179] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:37,179] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:37,180] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ce21378-122a-4192-904c-78c39912ebec/dqc_reference/checkm_data
[2024-01-24 13:10:37,181] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:37,213] [INFO] Task started: CheckM
[2024-01-24 13:10:37,213] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001262015.1_ASM126201v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001262015.1_ASM126201v1_genomic.fna/checkm_input GCF_001262015.1_ASM126201v1_genomic.fna/checkm_result
[2024-01-24 13:11:27,313] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:27,315] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:27,335] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:27,335] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:27,335] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001262015.1_ASM126201v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:27,336] [INFO] Task started: Blastn
[2024-01-24 13:11:27,336] [INFO] Running command: blastn -query GCF_001262015.1_ASM126201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ce21378-122a-4192-904c-78c39912ebec/dqc_reference/reference_markers_gtdb.fasta -out GCF_001262015.1_ASM126201v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:28,133] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:28,137] [INFO] Selected 13 target genomes.
[2024-01-24 13:11:28,137] [INFO] Target genome list was writen to GCF_001262015.1_ASM126201v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:28,147] [INFO] Task started: fastANI
[2024-01-24 13:11:28,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg83dbfa32-b8f8-4383-ab2e-8664bb5cbf50/GCF_001262015.1_ASM126201v1_genomic.fna.gz --refList GCF_001262015.1_ASM126201v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001262015.1_ASM126201v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:39,828] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:39,846] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:39,846] [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_001262015.1	s__Prevotella fusca	100.0	1086	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.97	1.00	1.00	3	conclusive
GCF_018128065.1	s__Prevotella sp000467895	83.986	696	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.71	96.42	0.91	0.83	4	-
GCF_018127965.1	s__Prevotella melaninogenica_B	83.5144	674	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.77	95.72	0.91	0.89	4	-
GCF_018127925.1	s__Prevotella melaninogenica_C	83.4334	672	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000144405.1	s__Prevotella melaninogenica	83.4144	683	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.46	95.36	0.87	0.78	36	-
GCF_003609775.1	s__Prevotella melaninogenica_A	83.368	666	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018127785.1	s__Prevotella scopos	82.9025	639	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.97	1.00	1.00	4	-
GCF_900187995.1	s__Prevotella jejuni	81.8758	600	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.57	0.92	0.88	7	-
GCF_900454835.1	s__Prevotella denticola	81.2032	535	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.27	97.69	0.92	0.88	14	-
GCF_000191065.1	s__Prevotella multiformis	80.7903	488	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.87	97.87	0.89	0.89	2	-
GCF_000257925.1	s__Prevotella sp000257925	80.5992	338	1086	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	80.238	353	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.76	96.65	0.91	0.86	4	-
GCF_000613945.1	s__Prevotella falsenii	79.3109	119	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:39,848] [INFO] GTDB search result was written to GCF_001262015.1_ASM126201v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:39,848] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:39,852] [INFO] DFAST_QC result json was written to GCF_001262015.1_ASM126201v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:39,852] [INFO] DFAST_QC completed!
[2024-01-24 13:11:39,852] [INFO] Total running time: 0h1m36s