[2023-06-29 10:06:32,384] [INFO] DFAST_QC pipeline started.
[2023-06-29 10:06:32,388] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 10:06:32,388] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e86fa54-2e3e-4029-98a2-21248cb860fa/dqc_reference
[2023-06-29 10:06:33,618] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 10:06:33,619] [INFO] Task started: Prodigal
[2023-06-29 10:06:33,619] [INFO] Running command: gunzip -c /var/lib/cwl/stg83f69794-9054-4a7a-96ae-9f8b212e8d7b/GCA_020859845.1_ASM2085984v1_genomic.fna.gz | prodigal -d GCA_020859845.1_ASM2085984v1_genomic.fna/cds.fna -a GCA_020859845.1_ASM2085984v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 10:06:50,145] [INFO] Task succeeded: Prodigal
[2023-06-29 10:06:50,145] [INFO] Task started: HMMsearch
[2023-06-29 10:06:50,145] [INFO] Running command: hmmsearch --tblout GCA_020859845.1_ASM2085984v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e86fa54-2e3e-4029-98a2-21248cb860fa/dqc_reference/reference_markers.hmm GCA_020859845.1_ASM2085984v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 10:06:50,403] [INFO] Task succeeded: HMMsearch
[2023-06-29 10:06:50,405] [INFO] Found 6/6 markers.
[2023-06-29 10:06:50,434] [INFO] Query marker FASTA was written to GCA_020859845.1_ASM2085984v1_genomic.fna/markers.fasta
[2023-06-29 10:06:50,434] [INFO] Task started: Blastn
[2023-06-29 10:06:50,434] [INFO] Running command: blastn -query GCA_020859845.1_ASM2085984v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e86fa54-2e3e-4029-98a2-21248cb860fa/dqc_reference/reference_markers.fasta -out GCA_020859845.1_ASM2085984v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 10:06:51,054] [INFO] Task succeeded: Blastn
[2023-06-29 10:06:51,062] [INFO] Selected 21 target genomes.
[2023-06-29 10:06:51,063] [INFO] Target genome list was writen to GCA_020859845.1_ASM2085984v1_genomic.fna/target_genomes.txt
[2023-06-29 10:06:51,068] [INFO] Task started: fastANI
[2023-06-29 10:06:51,069] [INFO] Running command: fastANI --query /var/lib/cwl/stg83f69794-9054-4a7a-96ae-9f8b212e8d7b/GCA_020859845.1_ASM2085984v1_genomic.fna.gz --refList GCA_020859845.1_ASM2085984v1_genomic.fna/target_genomes.txt --output GCA_020859845.1_ASM2085984v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 10:07:01,702] [INFO] Task succeeded: fastANI
[2023-06-29 10:07:01,703] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e86fa54-2e3e-4029-98a2-21248cb860fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 10:07:01,704] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e86fa54-2e3e-4029-98a2-21248cb860fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 10:07:01,711] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 10:07:01,711] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 10:07:01,711] [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
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	77.3403	77	919	95	below_threshold
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	77.2833	81	919	95	below_threshold
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	77.2	103	919	95	below_threshold
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	77.1428	96	919	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	76.864	91	919	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_002201515.1	1796646	1796646	type	True	76.8501	89	919	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_001688845.2	1796646	1796646	type	True	76.8399	92	919	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 10:07:01,713] [INFO] DFAST Taxonomy check result was written to GCA_020859845.1_ASM2085984v1_genomic.fna/tc_result.tsv
[2023-06-29 10:07:01,714] [INFO] ===== Taxonomy check completed =====
[2023-06-29 10:07:01,714] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 10:07:01,714] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e86fa54-2e3e-4029-98a2-21248cb860fa/dqc_reference/checkm_data
[2023-06-29 10:07:01,715] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 10:07:01,751] [INFO] Task started: CheckM
[2023-06-29 10:07:01,752] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020859845.1_ASM2085984v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020859845.1_ASM2085984v1_genomic.fna/checkm_input GCA_020859845.1_ASM2085984v1_genomic.fna/checkm_result
[2023-06-29 10:07:50,125] [INFO] Task succeeded: CheckM
[2023-06-29 10:07:50,127] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 10:07:50,155] [INFO] ===== Completeness check finished =====
[2023-06-29 10:07:50,156] [INFO] ===== Start GTDB Search =====
[2023-06-29 10:07:50,156] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020859845.1_ASM2085984v1_genomic.fna/markers.fasta)
[2023-06-29 10:07:50,156] [INFO] Task started: Blastn
[2023-06-29 10:07:50,156] [INFO] Running command: blastn -query GCA_020859845.1_ASM2085984v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e86fa54-2e3e-4029-98a2-21248cb860fa/dqc_reference/reference_markers_gtdb.fasta -out GCA_020859845.1_ASM2085984v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 10:07:51,008] [INFO] Task succeeded: Blastn
[2023-06-29 10:07:51,013] [INFO] Selected 30 target genomes.
[2023-06-29 10:07:51,013] [INFO] Target genome list was writen to GCA_020859845.1_ASM2085984v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 10:07:51,069] [INFO] Task started: fastANI
[2023-06-29 10:07:51,070] [INFO] Running command: fastANI --query /var/lib/cwl/stg83f69794-9054-4a7a-96ae-9f8b212e8d7b/GCA_020859845.1_ASM2085984v1_genomic.fna.gz --refList GCA_020859845.1_ASM2085984v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020859845.1_ASM2085984v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 10:08:04,509] [INFO] Task succeeded: fastANI
[2023-06-29 10:08:04,537] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 10:08:04,537] [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_900546365.1	s__Paramuribaculum sp900546365	77.4378	106	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001689535.1	s__Paramuribaculum sp001689535	77.3023	71	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	98.63	98.52	0.86	0.84	5	-
GCA_900539915.1	s__Amulumruptor sp900539915	77.2829	83	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Amulumruptor	95.0	97.54	97.54	0.92	0.92	2	-
GCA_905207535.1	s__UBA7173 sp905207535	77.2826	103	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584825.1	s__Duncaniella sp910584825	77.2738	133	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587185.1	s__Paramuribaculum sp910587185	77.2533	70	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	96.59	96.53	0.88	0.86	5	-
GCA_910579675.1	s__Paramuribaculum sp910579675	77.204	142	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024925.1	s__Paramuribaculum intestinale	77.2	103	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	99.05	97.83	0.86	0.82	16	-
GCA_910587925.1	s__CAG-873 sp910587925	77.1938	120	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588065.1	s__Paramuribaculum sp910588065	77.17	90	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001689495.1	s__Duncaniella sp001689495	77.1423	114	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	99.23	99.23	0.93	0.93	2	-
GCA_910589485.1	s__Duncaniella sp910589485	77.0999	98	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003762875.1	s__Duncaniella sp001689575	77.0907	112	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	97.25	96.19	0.92	0.80	7	-
GCA_910578835.1	s__Muribaculum sp910578835	77.0751	64	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575615.1	s__UBA7173 sp001689685	77.0631	100	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	99.70	99.58	0.97	0.94	9	-
GCA_014802105.1	s__Duncaniella sp014802105	77.012	87	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	98.28	98.28	0.74	0.74	2	-
GCA_905210435.1	s__UBA7173 sp905210435	76.9943	89	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587425.1	s__Paramuribaculum sp910587425	76.9637	107	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001689405.1	s__Muribaculum arabinoxylanisolvens	76.9623	69	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.46	99.01	0.94	0.92	3	-
GCA_009775605.1	s__Paramuribaculum sp009775605	76.9532	101	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	99.73	99.73	0.91	0.91	2	-
GCA_014802385.1	s__UBA7173 sp014802385	76.9344	81	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002493945.1	s__CAG-873 sp002493945	76.867	90	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.61	97.51	0.95	0.88	8	-
GCA_900551515.1	s__Paramuribaculum sp900551515	76.8073	88	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577255.1	s__Duncaniella sp910577255	76.7731	87	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900759915.1	s__Paramuribaculum sp900759915	76.6196	93	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	97.33	97.33	0.87	0.87	2	-
GCA_900759825.1	s__CAG-873 sp900759825	76.5988	69	919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 10:08:04,540] [INFO] GTDB search result was written to GCA_020859845.1_ASM2085984v1_genomic.fna/result_gtdb.tsv
[2023-06-29 10:08:04,540] [INFO] ===== GTDB Search completed =====
[2023-06-29 10:08:04,545] [INFO] DFAST_QC result json was written to GCA_020859845.1_ASM2085984v1_genomic.fna/dqc_result.json
[2023-06-29 10:08:04,545] [INFO] DFAST_QC completed!
[2023-06-29 10:08:04,545] [INFO] Total running time: 0h1m32s