[2024-01-25 17:42:05,636] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:42:05,637] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:42:05,637] [INFO] DQC Reference Directory: /var/lib/cwl/stg2db50594-328a-4a2a-87fc-57b72b621216/dqc_reference
[2024-01-25 17:42:06,743] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:42:06,744] [INFO] Task started: Prodigal
[2024-01-25 17:42:06,744] [INFO] Running command: gunzip -c /var/lib/cwl/stg377912dc-d229-4b7e-b0fd-0ac2f8e4c10f/GCF_000191065.1_ASM19106v1_genomic.fna.gz | prodigal -d GCF_000191065.1_ASM19106v1_genomic.fna/cds.fna -a GCF_000191065.1_ASM19106v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:42:20,517] [INFO] Task succeeded: Prodigal
[2024-01-25 17:42:20,517] [INFO] Task started: HMMsearch
[2024-01-25 17:42:20,518] [INFO] Running command: hmmsearch --tblout GCF_000191065.1_ASM19106v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2db50594-328a-4a2a-87fc-57b72b621216/dqc_reference/reference_markers.hmm GCF_000191065.1_ASM19106v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:42:20,746] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:42:20,748] [INFO] Found 6/6 markers.
[2024-01-25 17:42:20,772] [INFO] Query marker FASTA was written to GCF_000191065.1_ASM19106v1_genomic.fna/markers.fasta
[2024-01-25 17:42:20,772] [INFO] Task started: Blastn
[2024-01-25 17:42:20,772] [INFO] Running command: blastn -query GCF_000191065.1_ASM19106v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2db50594-328a-4a2a-87fc-57b72b621216/dqc_reference/reference_markers.fasta -out GCF_000191065.1_ASM19106v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:21,361] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:21,364] [INFO] Selected 10 target genomes.
[2024-01-25 17:42:21,364] [INFO] Target genome list was writen to GCF_000191065.1_ASM19106v1_genomic.fna/target_genomes.txt
[2024-01-25 17:42:21,373] [INFO] Task started: fastANI
[2024-01-25 17:42:21,373] [INFO] Running command: fastANI --query /var/lib/cwl/stg377912dc-d229-4b7e-b0fd-0ac2f8e4c10f/GCF_000191065.1_ASM19106v1_genomic.fna.gz --refList GCF_000191065.1_ASM19106v1_genomic.fna/target_genomes.txt --output GCF_000191065.1_ASM19106v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:42:28,771] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:28,771] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2db50594-328a-4a2a-87fc-57b72b621216/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:42:28,772] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2db50594-328a-4a2a-87fc-57b72b621216/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:42:28,778] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:42:28,778] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:42:28,778] [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 multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	99.9962	1007	1010	95	conclusive
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	89.4736	725	1010	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	89.3496	744	1010	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	80.9366	488	1010	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	80.9273	488	1010	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	79.0179	108	1010	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	78.9385	92	1010	95	below_threshold
Palleniella intestinalis	strain=PINT	GCA_013166595.1	2736291	2736291	type	True	78.9155	66	1010	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	76.8393	117	1010	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:42:28,780] [INFO] DFAST Taxonomy check result was written to GCF_000191065.1_ASM19106v1_genomic.fna/tc_result.tsv
[2024-01-25 17:42:28,780] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:42:28,781] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:42:28,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2db50594-328a-4a2a-87fc-57b72b621216/dqc_reference/checkm_data
[2024-01-25 17:42:28,782] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:42:28,813] [INFO] Task started: CheckM
[2024-01-25 17:42:28,813] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000191065.1_ASM19106v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000191065.1_ASM19106v1_genomic.fna/checkm_input GCF_000191065.1_ASM19106v1_genomic.fna/checkm_result
[2024-01-25 17:43:09,763] [INFO] Task succeeded: CheckM
[2024-01-25 17:43:09,764] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:43:09,780] [INFO] ===== Completeness check finished =====
[2024-01-25 17:43:09,780] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:43:09,780] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000191065.1_ASM19106v1_genomic.fna/markers.fasta)
[2024-01-25 17:43:09,781] [INFO] Task started: Blastn
[2024-01-25 17:43:09,781] [INFO] Running command: blastn -query GCF_000191065.1_ASM19106v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2db50594-328a-4a2a-87fc-57b72b621216/dqc_reference/reference_markers_gtdb.fasta -out GCF_000191065.1_ASM19106v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:10,708] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:10,712] [INFO] Selected 14 target genomes.
[2024-01-25 17:43:10,712] [INFO] Target genome list was writen to GCF_000191065.1_ASM19106v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:43:10,725] [INFO] Task started: fastANI
[2024-01-25 17:43:10,725] [INFO] Running command: fastANI --query /var/lib/cwl/stg377912dc-d229-4b7e-b0fd-0ac2f8e4c10f/GCF_000191065.1_ASM19106v1_genomic.fna.gz --refList GCF_000191065.1_ASM19106v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000191065.1_ASM19106v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:43:20,033] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:20,042] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:43:20,042] [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_000191065.1	s__Prevotella multiformis	99.9962	1007	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.87	97.87	0.89	0.89	2	conclusive
GCF_900454835.1	s__Prevotella denticola	89.3394	744	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.27	97.69	0.92	0.88	14	-
GCF_001262015.1	s__Prevotella fusca	80.8318	496	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.97	1.00	1.00	3	-
GCF_018128065.1	s__Prevotella sp000467895	80.5092	342	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.71	96.42	0.91	0.83	4	-
GCF_000257925.1	s__Prevotella sp000257925	80.2561	202	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.40	96.99	0.92	0.83	10	-
GCF_000144405.1	s__Prevotella melaninogenica	79.865	290	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.46	95.36	0.87	0.78	36	-
GCF_018127965.1	s__Prevotella melaninogenica_B	79.785	308	1010	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	79.6281	316	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003609775.1	s__Prevotella melaninogenica_A	78.954	291	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000614065.1	s__Prevotella dentasini	77.8855	246	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113305.1	s__Prevotella sp900113305	77.7213	139	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770845.1	s__Prevotella sp900770845	77.141	131	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003447235.1	s__Prevotella sp003447235	77.0835	143	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.02	97.84	0.85	0.82	13	-
GCA_900762125.1	s__Prevotella sp900762125	76.9909	138	1010	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 17:43:20,044] [INFO] GTDB search result was written to GCF_000191065.1_ASM19106v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:43:20,044] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:43:20,047] [INFO] DFAST_QC result json was written to GCF_000191065.1_ASM19106v1_genomic.fna/dqc_result.json
[2024-01-25 17:43:20,047] [INFO] DFAST_QC completed!
[2024-01-25 17:43:20,047] [INFO] Total running time: 0h1m14s