[2023-06-13 15:57:56,178] [INFO] DFAST_QC pipeline started.
[2023-06-13 15:57:56,180] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 15:57:56,181] [INFO] DQC Reference Directory: /var/lib/cwl/stg85c50271-fd69-4456-82af-1d222bd2b38e/dqc_reference
[2023-06-13 15:57:57,862] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 15:57:57,863] [INFO] Task started: Prodigal
[2023-06-13 15:57:57,863] [INFO] Running command: gunzip -c /var/lib/cwl/stgc9bc473f-1020-4e12-b5f5-bfa0c25ca027/GCA_022778905.1_ASM2277890v1_genomic.fna.gz | prodigal -d GCA_022778905.1_ASM2277890v1_genomic.fna/cds.fna -a GCA_022778905.1_ASM2277890v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 15:58:16,505] [INFO] Task succeeded: Prodigal
[2023-06-13 15:58:16,505] [INFO] Task started: HMMsearch
[2023-06-13 15:58:16,505] [INFO] Running command: hmmsearch --tblout GCA_022778905.1_ASM2277890v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85c50271-fd69-4456-82af-1d222bd2b38e/dqc_reference/reference_markers.hmm GCA_022778905.1_ASM2277890v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 15:58:16,804] [INFO] Task succeeded: HMMsearch
[2023-06-13 15:58:16,805] [INFO] Found 6/6 markers.
[2023-06-13 15:58:16,846] [INFO] Query marker FASTA was written to GCA_022778905.1_ASM2277890v1_genomic.fna/markers.fasta
[2023-06-13 15:58:16,847] [INFO] Task started: Blastn
[2023-06-13 15:58:16,847] [INFO] Running command: blastn -query GCA_022778905.1_ASM2277890v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85c50271-fd69-4456-82af-1d222bd2b38e/dqc_reference/reference_markers.fasta -out GCA_022778905.1_ASM2277890v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:58:17,623] [INFO] Task succeeded: Blastn
[2023-06-13 15:58:17,627] [INFO] Selected 29 target genomes.
[2023-06-13 15:58:17,627] [INFO] Target genome list was writen to GCA_022778905.1_ASM2277890v1_genomic.fna/target_genomes.txt
[2023-06-13 15:58:17,631] [INFO] Task started: fastANI
[2023-06-13 15:58:17,631] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9bc473f-1020-4e12-b5f5-bfa0c25ca027/GCA_022778905.1_ASM2277890v1_genomic.fna.gz --refList GCA_022778905.1_ASM2277890v1_genomic.fna/target_genomes.txt --output GCA_022778905.1_ASM2277890v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 15:58:36,783] [INFO] Task succeeded: fastANI
[2023-06-13 15:58:36,784] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85c50271-fd69-4456-82af-1d222bd2b38e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 15:58:36,784] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85c50271-fd69-4456-82af-1d222bd2b38e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 15:58:36,797] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 15:58:36,797] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 15:58:36,797] [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	77.0396	77	977	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.8357	87	977	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	76.8048	104	977	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.7766	93	977	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	76.764	100	977	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.7437	92	977	95	below_threshold
Prevotella dentasini	strain=JCM 15908	GCA_000614065.1	589537	589537	type	True	76.6837	58	977	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	76.6753	60	977	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.6596	104	977	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.5845	54	977	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.5781	105	977	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.538	56	977	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.5307	106	977	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.5039	60	977	95	below_threshold
Prevotella multisaccharivorax	strain=JCM 12954	GCA_019973315.1	310514	310514	type	True	76.4805	50	977	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 15:58:36,801] [INFO] DFAST Taxonomy check result was written to GCA_022778905.1_ASM2277890v1_genomic.fna/tc_result.tsv
[2023-06-13 15:58:36,801] [INFO] ===== Taxonomy check completed =====
[2023-06-13 15:58:36,802] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 15:58:36,802] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85c50271-fd69-4456-82af-1d222bd2b38e/dqc_reference/checkm_data
[2023-06-13 15:58:36,803] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 15:58:36,869] [INFO] Task started: CheckM
[2023-06-13 15:58:36,870] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022778905.1_ASM2277890v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022778905.1_ASM2277890v1_genomic.fna/checkm_input GCA_022778905.1_ASM2277890v1_genomic.fna/checkm_result
[2023-06-13 15:59:33,306] [INFO] Task succeeded: CheckM
[2023-06-13 15:59:33,310] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.88%
Contamintation: 6.11%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-13 15:59:33,346] [INFO] ===== Completeness check finished =====
[2023-06-13 15:59:33,346] [INFO] ===== Start GTDB Search =====
[2023-06-13 15:59:33,347] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022778905.1_ASM2277890v1_genomic.fna/markers.fasta)
[2023-06-13 15:59:33,347] [INFO] Task started: Blastn
[2023-06-13 15:59:33,347] [INFO] Running command: blastn -query GCA_022778905.1_ASM2277890v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85c50271-fd69-4456-82af-1d222bd2b38e/dqc_reference/reference_markers_gtdb.fasta -out GCA_022778905.1_ASM2277890v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:59:34,499] [INFO] Task succeeded: Blastn
[2023-06-13 15:59:34,504] [INFO] Selected 28 target genomes.
[2023-06-13 15:59:34,505] [INFO] Target genome list was writen to GCA_022778905.1_ASM2277890v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 15:59:34,517] [INFO] Task started: fastANI
[2023-06-13 15:59:34,517] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9bc473f-1020-4e12-b5f5-bfa0c25ca027/GCA_022778905.1_ASM2277890v1_genomic.fna.gz --refList GCA_022778905.1_ASM2277890v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022778905.1_ASM2277890v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:59:50,700] [INFO] Task succeeded: fastANI
[2023-06-13 15:59:50,730] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 15:59:50,730] [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_900317545.1	s__Prevotella sp900317545	92.8369	712	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.65	99.65	0.96	0.96	2	-
GCA_002481295.1	s__Prevotella sp002481295	76.8537	83	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.83	96.70	0.87	0.78	4	-
GCF_009695775.1	s__Prevotella mizrahii	76.8357	87	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.15	96.87	0.87	0.84	6	-
GCA_002317385.1	s__Prevotella sp002317385	76.7991	98	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540375.1	s__Prevotella sp900540375	76.7278	83	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.83	98.80	0.92	0.91	3	-
GCF_002251365.1	s__Prevotella sp002251365	76.5456	55	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.20	97.97	0.85	0.80	5	-
GCA_905196835.1	s__Prevotella stercoripullorum	76.5169	59	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.53	95.99	0.92	0.86	5	-
GCA_900762125.1	s__Prevotella sp900762125	76.4977	105	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000431975.1	s__Prevotella sp000431975	76.4921	76	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.89	99.89	0.92	0.91	3	-
GCA_900318855.1	s__Prevotella sp900318855	76.4912	68	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.94	98.64	0.80	0.74	4	-
GCA_002353825.1	s__Prevotella sp002353825	76.3726	56	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.40	98.85	0.91	0.85	4	-
GCF_003043925.1	s__Prevotella sp003043925	76.2755	65	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.98	0.98	0.98	2	-
GCA_017847725.1	s__Prevotella sp017847725	76.1963	57	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905198745.1	s__Prevotella sp905198745	76.0572	58	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902801375.1	s__Prevotella sp902801375	76.0072	65	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.75	97.75	0.82	0.82	2	-
GCA_900315835.1	s__Prevotella sp900315835	75.9887	107	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.59	98.19	0.88	0.85	9	-
GCA_900319905.1	s__Prevotella sp900319905	75.9794	78	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.87	98.44	0.89	0.87	7	-
GCA_017508965.1	s__Prevotella sp017508965	75.9453	60	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.39	95.39	0.73	0.73	2	-
GCA_017458195.1	s__Prevotella sp017458195	75.8991	77	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016285055.1	s__Prevotella sp016285055	75.7639	73	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 15:59:50,733] [INFO] GTDB search result was written to GCA_022778905.1_ASM2277890v1_genomic.fna/result_gtdb.tsv
[2023-06-13 15:59:50,734] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:59:50,739] [INFO] DFAST_QC result json was written to GCA_022778905.1_ASM2277890v1_genomic.fna/dqc_result.json
[2023-06-13 15:59:50,740] [INFO] DFAST_QC completed!
[2023-06-13 15:59:50,740] [INFO] Total running time: 0h1m55s