[2024-01-25 17:39:05,666] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:39:05,668] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:39:05,668] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d22b857-74ff-47d5-913e-6c62d81b185e/dqc_reference
[2024-01-25 17:39:06,856] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:39:06,857] [INFO] Task started: Prodigal
[2024-01-25 17:39:06,857] [INFO] Running command: gunzip -c /var/lib/cwl/stgdae29140-aa03-4ef6-90cc-15da17f33680/GCF_000177315.1_ASM17731v1_genomic.fna.gz | prodigal -d GCF_000177315.1_ASM17731v1_genomic.fna/cds.fna -a GCF_000177315.1_ASM17731v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:39:15,442] [INFO] Task succeeded: Prodigal
[2024-01-25 17:39:15,442] [INFO] Task started: HMMsearch
[2024-01-25 17:39:15,442] [INFO] Running command: hmmsearch --tblout GCF_000177315.1_ASM17731v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d22b857-74ff-47d5-913e-6c62d81b185e/dqc_reference/reference_markers.hmm GCF_000177315.1_ASM17731v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:39:15,662] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:39:15,663] [INFO] Found 6/6 markers.
[2024-01-25 17:39:15,684] [INFO] Query marker FASTA was written to GCF_000177315.1_ASM17731v1_genomic.fna/markers.fasta
[2024-01-25 17:39:15,684] [INFO] Task started: Blastn
[2024-01-25 17:39:15,684] [INFO] Running command: blastn -query GCF_000177315.1_ASM17731v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d22b857-74ff-47d5-913e-6c62d81b185e/dqc_reference/reference_markers.fasta -out GCF_000177315.1_ASM17731v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:16,246] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:16,249] [INFO] Selected 13 target genomes.
[2024-01-25 17:39:16,249] [INFO] Target genome list was writen to GCF_000177315.1_ASM17731v1_genomic.fna/target_genomes.txt
[2024-01-25 17:39:16,276] [INFO] Task started: fastANI
[2024-01-25 17:39:16,276] [INFO] Running command: fastANI --query /var/lib/cwl/stgdae29140-aa03-4ef6-90cc-15da17f33680/GCF_000177315.1_ASM17731v1_genomic.fna.gz --refList GCF_000177315.1_ASM17731v1_genomic.fna/target_genomes.txt --output GCF_000177315.1_ASM17731v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:39:23,480] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:23,481] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d22b857-74ff-47d5-913e-6c62d81b185e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:39:23,481] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d22b857-74ff-47d5-913e-6c62d81b185e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:39:23,490] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:39:23,490] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:39:23,490] [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 bivia	strain=JCVIHMP010	GCA_000177315.1	28125	28125	type	True	100.0	747	753	95	conclusive
Prevotella bivia	strain=DSM 20514	GCA_000262545.1	28125	28125	type	True	99.9989	753	753	95	conclusive
Prevotella ihumii	strain=Marseille-P3385	GCA_900155655.1	1917878	1917878	type	True	83.2583	188	753	95	below_threshold
Prevotella disiens	strain=ATCC 29426	GCA_000467875.1	28130	28130	type	True	81.7183	143	753	95	below_threshold
Prevotella amnii	strain=DSM 23384	GCA_000378745.1	419005	419005	type	True	81.3816	312	753	95	below_threshold
Prevotella amnii	strain=JCM 14753	GCA_000613765.1	419005	419005	type	True	81.0238	290	753	95	below_threshold
Prevotella vespertina	strain=A2879	GCA_009728485.1	2608404	2608404	type	True	80.1738	142	753	95	below_threshold
Prevotella scopos	strain=W2052	GCA_001683355.1	589437	589437	type	True	79.4522	171	753	95	below_threshold
Prevotella scopos	strain=W2052	GCA_018127785.1	589437	589437	type	True	79.4514	172	753	95	below_threshold
Prevotella melaninogenica	strain=FDAARGOS_1566	GCA_020735785.1	28132	28132	suspected-type	True	79.2072	151	753	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	77.6026	65	753	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	77.5686	65	753	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	77.3369	64	753	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:39:23,492] [INFO] DFAST Taxonomy check result was written to GCF_000177315.1_ASM17731v1_genomic.fna/tc_result.tsv
[2024-01-25 17:39:23,492] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:39:23,492] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:39:23,493] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d22b857-74ff-47d5-913e-6c62d81b185e/dqc_reference/checkm_data
[2024-01-25 17:39:23,493] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:39:23,520] [INFO] Task started: CheckM
[2024-01-25 17:39:23,520] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000177315.1_ASM17731v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000177315.1_ASM17731v1_genomic.fna/checkm_input GCF_000177315.1_ASM17731v1_genomic.fna/checkm_result
[2024-01-25 17:39:52,253] [INFO] Task succeeded: CheckM
[2024-01-25 17:39:52,254] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:39:52,272] [INFO] ===== Completeness check finished =====
[2024-01-25 17:39:52,272] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:39:52,272] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000177315.1_ASM17731v1_genomic.fna/markers.fasta)
[2024-01-25 17:39:52,273] [INFO] Task started: Blastn
[2024-01-25 17:39:52,273] [INFO] Running command: blastn -query GCF_000177315.1_ASM17731v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d22b857-74ff-47d5-913e-6c62d81b185e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000177315.1_ASM17731v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:53,155] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:53,158] [INFO] Selected 17 target genomes.
[2024-01-25 17:39:53,159] [INFO] Target genome list was writen to GCF_000177315.1_ASM17731v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:39:53,179] [INFO] Task started: fastANI
[2024-01-25 17:39:53,179] [INFO] Running command: fastANI --query /var/lib/cwl/stgdae29140-aa03-4ef6-90cc-15da17f33680/GCF_000177315.1_ASM17731v1_genomic.fna.gz --refList GCF_000177315.1_ASM17731v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000177315.1_ASM17731v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:03,142] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:03,154] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:40:03,154] [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_000262545.1	s__Prevotella bivia	99.9989	753	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.82	98.45	0.91	0.86	8	conclusive
GCF_900155655.1	s__Prevotella ihumii	83.353	186	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613345.1	s__Prevotella disiens	82.5874	167	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.74	97.99	0.90	0.82	7	-
GCF_000378745.1	s__Prevotella amnii	81.4309	311	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.70	98.21	0.90	0.86	5	-
GCF_018127925.1	s__Prevotella melaninogenica_C	80.3317	167	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018128065.1	s__Prevotella sp000467895	80.2595	169	753	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	79.6061	130	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.40	96.99	0.92	0.83	10	-
GCF_018127785.1	s__Prevotella scopos	79.4535	171	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.97	1.00	1.00	4	-
GCF_000144405.1	s__Prevotella melaninogenica	79.0309	144	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.46	95.36	0.87	0.78	36	-
GCF_000688375.1	s__Prevotella sp000688375	78.4922	108	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019127135.1	s__Prevotella sp900551275	78.4617	62	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0063	98.12	96.96	0.86	0.77	7	-
GCF_003609775.1	s__Prevotella melaninogenica_A	78.0633	145	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015074785.1	s__Prevotella sp015074785	77.9513	58	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.50	95.88	0.80	0.71	45	-
GCF_000157935.1	s__Prevotella copri	77.6203	66	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.34	95.85	0.75	0.69	97	-
--------------------------------------------------------------------------------
[2024-01-25 17:40:03,155] [INFO] GTDB search result was written to GCF_000177315.1_ASM17731v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:03,156] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:03,159] [INFO] DFAST_QC result json was written to GCF_000177315.1_ASM17731v1_genomic.fna/dqc_result.json
[2024-01-25 17:40:03,159] [INFO] DFAST_QC completed!
[2024-01-25 17:40:03,159] [INFO] Total running time: 0h0m57s