[2023-06-13 05:12:50,557] [INFO] DFAST_QC pipeline started.
[2023-06-13 05:12:50,560] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 05:12:50,560] [INFO] DQC Reference Directory: /var/lib/cwl/stg502c3089-12cd-4931-bd74-164d0d723b7d/dqc_reference
[2023-06-13 05:12:51,836] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 05:12:51,840] [INFO] Task started: Prodigal
[2023-06-13 05:12:51,840] [INFO] Running command: gunzip -c /var/lib/cwl/stgc32ef061-22cf-45ff-8e59-b8a06777d02e/GCA_022775405.1_ASM2277540v1_genomic.fna.gz | prodigal -d GCA_022775405.1_ASM2277540v1_genomic.fna/cds.fna -a GCA_022775405.1_ASM2277540v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 05:13:03,827] [INFO] Task succeeded: Prodigal
[2023-06-13 05:13:03,828] [INFO] Task started: HMMsearch
[2023-06-13 05:13:03,828] [INFO] Running command: hmmsearch --tblout GCA_022775405.1_ASM2277540v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg502c3089-12cd-4931-bd74-164d0d723b7d/dqc_reference/reference_markers.hmm GCA_022775405.1_ASM2277540v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 05:13:04,046] [INFO] Task succeeded: HMMsearch
[2023-06-13 05:13:04,047] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc32ef061-22cf-45ff-8e59-b8a06777d02e/GCA_022775405.1_ASM2277540v1_genomic.fna.gz]
[2023-06-13 05:13:04,070] [INFO] Query marker FASTA was written to GCA_022775405.1_ASM2277540v1_genomic.fna/markers.fasta
[2023-06-13 05:13:04,070] [INFO] Task started: Blastn
[2023-06-13 05:13:04,070] [INFO] Running command: blastn -query GCA_022775405.1_ASM2277540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg502c3089-12cd-4931-bd74-164d0d723b7d/dqc_reference/reference_markers.fasta -out GCA_022775405.1_ASM2277540v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:13:04,681] [INFO] Task succeeded: Blastn
[2023-06-13 05:13:04,685] [INFO] Selected 19 target genomes.
[2023-06-13 05:13:04,686] [INFO] Target genome list was writen to GCA_022775405.1_ASM2277540v1_genomic.fna/target_genomes.txt
[2023-06-13 05:13:04,693] [INFO] Task started: fastANI
[2023-06-13 05:13:04,693] [INFO] Running command: fastANI --query /var/lib/cwl/stgc32ef061-22cf-45ff-8e59-b8a06777d02e/GCA_022775405.1_ASM2277540v1_genomic.fna.gz --refList GCA_022775405.1_ASM2277540v1_genomic.fna/target_genomes.txt --output GCA_022775405.1_ASM2277540v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 05:13:14,685] [INFO] Task succeeded: fastANI
[2023-06-13 05:13:14,685] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg502c3089-12cd-4931-bd74-164d0d723b7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 05:13:14,686] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg502c3089-12cd-4931-bd74-164d0d723b7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 05:13:14,698] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 05:13:14,698] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 05:13:14,699] [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 stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	89.0091	515	634	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	78.5903	160	634	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	78.0685	103	634	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.6038	149	634	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	77.5048	126	634	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	77.3986	117	634	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.8593	88	634	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.6889	62	634	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.5628	105	634	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.5505	108	634	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	76.5413	85	634	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	76.5388	85	634	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.4643	113	634	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 05:13:14,701] [INFO] DFAST Taxonomy check result was written to GCA_022775405.1_ASM2277540v1_genomic.fna/tc_result.tsv
[2023-06-13 05:13:14,702] [INFO] ===== Taxonomy check completed =====
[2023-06-13 05:13:14,702] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 05:13:14,702] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg502c3089-12cd-4931-bd74-164d0d723b7d/dqc_reference/checkm_data
[2023-06-13 05:13:14,704] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 05:13:14,737] [INFO] Task started: CheckM
[2023-06-13 05:13:14,738] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022775405.1_ASM2277540v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022775405.1_ASM2277540v1_genomic.fna/checkm_input GCA_022775405.1_ASM2277540v1_genomic.fna/checkm_result
[2023-06-13 05:13:52,720] [INFO] Task succeeded: CheckM
[2023-06-13 05:13:52,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.69%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 05:13:52,740] [INFO] ===== Completeness check finished =====
[2023-06-13 05:13:52,741] [INFO] ===== Start GTDB Search =====
[2023-06-13 05:13:52,741] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022775405.1_ASM2277540v1_genomic.fna/markers.fasta)
[2023-06-13 05:13:52,741] [INFO] Task started: Blastn
[2023-06-13 05:13:52,741] [INFO] Running command: blastn -query GCA_022775405.1_ASM2277540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg502c3089-12cd-4931-bd74-164d0d723b7d/dqc_reference/reference_markers_gtdb.fasta -out GCA_022775405.1_ASM2277540v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:13:53,640] [INFO] Task succeeded: Blastn
[2023-06-13 05:13:53,645] [INFO] Selected 9 target genomes.
[2023-06-13 05:13:53,645] [INFO] Target genome list was writen to GCA_022775405.1_ASM2277540v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 05:13:53,649] [INFO] Task started: fastANI
[2023-06-13 05:13:53,650] [INFO] Running command: fastANI --query /var/lib/cwl/stgc32ef061-22cf-45ff-8e59-b8a06777d02e/GCA_022775405.1_ASM2277540v1_genomic.fna.gz --refList GCA_022775405.1_ASM2277540v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022775405.1_ASM2277540v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 05:13:58,995] [INFO] Task succeeded: fastANI
[2023-06-13 05:13:59,012] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 05:13:59,013] [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_019052365.1	s__Prevotella sp000434975	97.0001	536	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.59	0.82	0.74	11	conclusive
GCF_000235885.1	s__Prevotella stercorea	89.0604	513	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.02	96.84	0.81	0.69	8	-
GCA_900552515.1	s__Prevotella sp900552515	80.7718	245	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.61	97.50	0.85	0.85	3	-
GCA_900550035.1	s__Prevotella sp900550035	80.6814	322	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.97	99.93	0.97	0.97	3	-
GCF_002265625.1	s__Prevotella sp002265625	80.6504	358	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.90	96.80	0.88	0.86	4	-
GCA_002490315.1	s__Prevotella sp002490315	80.6187	258	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544495.1	s__Prevotella sp900544495	80.5562	299	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.45	98.42	0.86	0.82	3	-
GCA_900546575.1	s__Prevotella sp900546575	80.0895	317	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.21	95.49	0.86	0.86	4	-
GCA_900553155.1	s__Prevotella sp900553155	79.9115	213	634	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.04	96.93	0.80	0.75	3	-
--------------------------------------------------------------------------------
[2023-06-13 05:13:59,015] [INFO] GTDB search result was written to GCA_022775405.1_ASM2277540v1_genomic.fna/result_gtdb.tsv
[2023-06-13 05:13:59,016] [INFO] ===== GTDB Search completed =====
[2023-06-13 05:13:59,021] [INFO] DFAST_QC result json was written to GCA_022775405.1_ASM2277540v1_genomic.fna/dqc_result.json
[2023-06-13 05:13:59,021] [INFO] DFAST_QC completed!
[2023-06-13 05:13:59,021] [INFO] Total running time: 0h1m8s