[2024-01-24 12:53:57,098] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:57,101] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:57,101] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9471cf2-2de2-4ce5-a6f1-64eb20f841b5/dqc_reference
[2024-01-24 12:53:58,546] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:58,547] [INFO] Task started: Prodigal
[2024-01-24 12:53:58,547] [INFO] Running command: gunzip -c /var/lib/cwl/stge68a986b-c394-4699-a030-00e07a2a0069/GCF_000262545.1_ASM26254v1_genomic.fna.gz | prodigal -d GCF_000262545.1_ASM26254v1_genomic.fna/cds.fna -a GCF_000262545.1_ASM26254v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:09,939] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:09,939] [INFO] Task started: HMMsearch
[2024-01-24 12:54:09,939] [INFO] Running command: hmmsearch --tblout GCF_000262545.1_ASM26254v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9471cf2-2de2-4ce5-a6f1-64eb20f841b5/dqc_reference/reference_markers.hmm GCF_000262545.1_ASM26254v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:10,216] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:10,217] [INFO] Found 6/6 markers.
[2024-01-24 12:54:10,238] [INFO] Query marker FASTA was written to GCF_000262545.1_ASM26254v1_genomic.fna/markers.fasta
[2024-01-24 12:54:10,239] [INFO] Task started: Blastn
[2024-01-24 12:54:10,239] [INFO] Running command: blastn -query GCF_000262545.1_ASM26254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9471cf2-2de2-4ce5-a6f1-64eb20f841b5/dqc_reference/reference_markers.fasta -out GCF_000262545.1_ASM26254v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:10,863] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:10,866] [INFO] Selected 13 target genomes.
[2024-01-24 12:54:10,866] [INFO] Target genome list was writen to GCF_000262545.1_ASM26254v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:10,933] [INFO] Task started: fastANI
[2024-01-24 12:54:10,934] [INFO] Running command: fastANI --query /var/lib/cwl/stge68a986b-c394-4699-a030-00e07a2a0069/GCF_000262545.1_ASM26254v1_genomic.fna.gz --refList GCF_000262545.1_ASM26254v1_genomic.fna/target_genomes.txt --output GCF_000262545.1_ASM26254v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:18,318] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:18,318] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9471cf2-2de2-4ce5-a6f1-64eb20f841b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:18,318] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9471cf2-2de2-4ce5-a6f1-64eb20f841b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:18,330] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:54:18,330] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:18,330] [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=DSM 20514	GCA_000262545.1	28125	28125	type	True	100.0	838	839	95	conclusive
Prevotella bivia	strain=JCVIHMP010	GCA_000177315.1	28125	28125	type	True	99.895	752	839	95	conclusive
Prevotella ihumii	strain=Marseille-P3385	GCA_900155655.1	1917878	1917878	type	True	83.8998	217	839	95	below_threshold
Prevotella disiens	strain=ATCC 29426	GCA_000467875.1	28130	28130	type	True	81.8265	156	839	95	below_threshold
Prevotella amnii	strain=DSM 23384	GCA_000378745.1	419005	419005	type	True	81.1522	334	839	95	below_threshold
Prevotella amnii	strain=JCM 14753	GCA_000613765.1	419005	419005	type	True	81.0012	303	839	95	below_threshold
Prevotella scopos	strain=W2052	GCA_001683355.1	589437	589437	type	True	80.4714	182	839	95	below_threshold
Prevotella vespertina	strain=A2879	GCA_009728485.1	2608404	2608404	type	True	80.202	161	839	95	below_threshold
Prevotella scopos	strain=W2052	GCA_018127785.1	589437	589437	type	True	80.1564	173	839	95	below_threshold
Prevotella melaninogenica	strain=FDAARGOS_1566	GCA_020735785.1	28132	28132	suspected-type	True	79.3645	174	839	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	79.3548	72	839	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	79.1748	68	839	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	77.8308	64	839	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:18,334] [INFO] DFAST Taxonomy check result was written to GCF_000262545.1_ASM26254v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:18,335] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:18,335] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:18,335] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9471cf2-2de2-4ce5-a6f1-64eb20f841b5/dqc_reference/checkm_data
[2024-01-24 12:54:18,337] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:18,374] [INFO] Task started: CheckM
[2024-01-24 12:54:18,374] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000262545.1_ASM26254v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000262545.1_ASM26254v1_genomic.fna/checkm_input GCF_000262545.1_ASM26254v1_genomic.fna/checkm_result
[2024-01-24 12:54:53,962] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:53,963] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:53,983] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:53,983] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:53,983] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000262545.1_ASM26254v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:53,984] [INFO] Task started: Blastn
[2024-01-24 12:54:53,984] [INFO] Running command: blastn -query GCF_000262545.1_ASM26254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9471cf2-2de2-4ce5-a6f1-64eb20f841b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000262545.1_ASM26254v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:54,720] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:54,723] [INFO] Selected 17 target genomes.
[2024-01-24 12:54:54,723] [INFO] Target genome list was writen to GCF_000262545.1_ASM26254v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:54,756] [INFO] Task started: fastANI
[2024-01-24 12:54:54,756] [INFO] Running command: fastANI --query /var/lib/cwl/stge68a986b-c394-4699-a030-00e07a2a0069/GCF_000262545.1_ASM26254v1_genomic.fna.gz --refList GCF_000262545.1_ASM26254v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000262545.1_ASM26254v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:03,877] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:03,889] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:03,889] [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	100.0	838	839	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	84.0838	215	839	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	82.9971	178	839	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	81.1884	336	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.70	98.21	0.90	0.86	5	-
GCF_018128065.1	s__Prevotella sp000467895	80.9499	178	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.71	96.42	0.91	0.83	4	-
GCF_018127925.1	s__Prevotella melaninogenica_C	80.6998	183	839	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	80.2673	172	839	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	79.5145	172	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.46	95.36	0.87	0.78	36	-
GCF_000257925.1	s__Prevotella sp000257925	79.4728	147	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.40	96.99	0.92	0.83	10	-
GCF_015074785.1	s__Prevotella sp015074785	79.3355	66	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.50	95.88	0.80	0.71	45	-
GCF_000688375.1	s__Prevotella sp000688375	79.2736	130	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000157935.1	s__Prevotella copri	78.9906	68	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.34	95.85	0.75	0.69	97	-
GCF_003609775.1	s__Prevotella melaninogenica_A	78.8766	160	839	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	78.8564	68	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0063	98.12	96.96	0.86	0.77	7	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:03,891] [INFO] GTDB search result was written to GCF_000262545.1_ASM26254v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:03,891] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:03,895] [INFO] DFAST_QC result json was written to GCF_000262545.1_ASM26254v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:03,896] [INFO] DFAST_QC completed!
[2024-01-24 12:55:03,896] [INFO] Total running time: 0h1m7s