[2023-06-08 05:14:40,092] [INFO] DFAST_QC pipeline started.
[2023-06-08 05:14:40,097] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 05:14:40,097] [INFO] DQC Reference Directory: /var/lib/cwl/stg5fef8e1f-b873-4b9a-abb3-d06b10278a57/dqc_reference
[2023-06-08 05:14:42,416] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 05:14:42,418] [INFO] Task started: Prodigal
[2023-06-08 05:14:42,418] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1eca7ae-551c-4412-abe2-e48c54a868d0/GCA_945873435.1_ERR1855540_bin.18_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945873435.1_ERR1855540_bin.18_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945873435.1_ERR1855540_bin.18_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 05:15:02,201] [INFO] Task succeeded: Prodigal
[2023-06-08 05:15:02,202] [INFO] Task started: HMMsearch
[2023-06-08 05:15:02,202] [INFO] Running command: hmmsearch --tblout GCA_945873435.1_ERR1855540_bin.18_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5fef8e1f-b873-4b9a-abb3-d06b10278a57/dqc_reference/reference_markers.hmm GCA_945873435.1_ERR1855540_bin.18_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 05:15:02,463] [INFO] Task succeeded: HMMsearch
[2023-06-08 05:15:02,464] [INFO] Found 6/6 markers.
[2023-06-08 05:15:02,494] [INFO] Query marker FASTA was written to GCA_945873435.1_ERR1855540_bin.18_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 05:15:02,494] [INFO] Task started: Blastn
[2023-06-08 05:15:02,495] [INFO] Running command: blastn -query GCA_945873435.1_ERR1855540_bin.18_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fef8e1f-b873-4b9a-abb3-d06b10278a57/dqc_reference/reference_markers.fasta -out GCA_945873435.1_ERR1855540_bin.18_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:15:03,123] [INFO] Task succeeded: Blastn
[2023-06-08 05:15:03,128] [INFO] Selected 20 target genomes.
[2023-06-08 05:15:03,128] [INFO] Target genome list was writen to GCA_945873435.1_ERR1855540_bin.18_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 05:15:03,134] [INFO] Task started: fastANI
[2023-06-08 05:15:03,135] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1eca7ae-551c-4412-abe2-e48c54a868d0/GCA_945873435.1_ERR1855540_bin.18_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945873435.1_ERR1855540_bin.18_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945873435.1_ERR1855540_bin.18_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 05:15:12,231] [INFO] Task succeeded: fastANI
[2023-06-08 05:15:12,232] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5fef8e1f-b873-4b9a-abb3-d06b10278a57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 05:15:12,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5fef8e1f-b873-4b9a-abb3-d06b10278a57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 05:15:12,248] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 05:15:12,248] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 05:15:12,248] [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 mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	79.5623	192	926	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	77.9019	219	926	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.8994	172	926	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	77.8694	215	926	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	77.7548	210	926	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	77.7074	157	926	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	77.6259	160	926	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	77.5256	149	926	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	77.3876	78	926	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	77.1885	145	926	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.7114	129	926	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	76.6479	110	926	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	76.6404	108	926	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.5887	65	926	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.5315	79	926	95	below_threshold
Prevotella colorans	strain=DSM 100333	GCA_003096815.1	1703337	1703337	type	True	76.5211	55	926	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 05:15:12,257] [INFO] DFAST Taxonomy check result was written to GCA_945873435.1_ERR1855540_bin.18_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 05:15:12,257] [INFO] ===== Taxonomy check completed =====
[2023-06-08 05:15:12,257] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 05:15:12,258] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5fef8e1f-b873-4b9a-abb3-d06b10278a57/dqc_reference/checkm_data
[2023-06-08 05:15:12,258] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 05:15:12,294] [INFO] Task started: CheckM
[2023-06-08 05:15:12,294] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945873435.1_ERR1855540_bin.18_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945873435.1_ERR1855540_bin.18_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945873435.1_ERR1855540_bin.18_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 05:16:07,772] [INFO] Task succeeded: CheckM
[2023-06-08 05:16:07,774] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 05:16:07,803] [INFO] ===== Completeness check finished =====
[2023-06-08 05:16:07,803] [INFO] ===== Start GTDB Search =====
[2023-06-08 05:16:07,804] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945873435.1_ERR1855540_bin.18_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 05:16:07,804] [INFO] Task started: Blastn
[2023-06-08 05:16:07,804] [INFO] Running command: blastn -query GCA_945873435.1_ERR1855540_bin.18_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fef8e1f-b873-4b9a-abb3-d06b10278a57/dqc_reference/reference_markers_gtdb.fasta -out GCA_945873435.1_ERR1855540_bin.18_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:16:08,809] [INFO] Task succeeded: Blastn
[2023-06-08 05:16:08,815] [INFO] Selected 17 target genomes.
[2023-06-08 05:16:08,815] [INFO] Target genome list was writen to GCA_945873435.1_ERR1855540_bin.18_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 05:16:08,834] [INFO] Task started: fastANI
[2023-06-08 05:16:08,834] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1eca7ae-551c-4412-abe2-e48c54a868d0/GCA_945873435.1_ERR1855540_bin.18_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945873435.1_ERR1855540_bin.18_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945873435.1_ERR1855540_bin.18_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 05:16:18,523] [INFO] Task succeeded: fastANI
[2023-06-08 05:16:18,539] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 05:16:18,540] [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_004558865.1	s__Prevotella sp004558865	97.7408	587	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900770845.1	s__Prevotella sp900770845	94.2543	614	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900322035.1	s__Prevotella sp900322035	83.0627	396	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.07	98.30	0.87	0.81	3	-
GCA_900322095.1	s__Prevotella sp900322095	81.1582	422	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.50	99.22	0.86	0.85	3	-
GCF_009695775.1	s__Prevotella mizrahii	79.4568	198	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.15	96.87	0.87	0.84	6	-
GCA_900546345.1	s__Prevotella sp900546345	78.6825	167	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900317685.1	s__Prevotella sp900317685	78.4965	206	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.13	96.10	0.84	0.76	12	-
GCA_002437285.1	s__Prevotella sp002437285	78.3386	172	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.68	99.38	0.93	0.88	13	-
GCA_900762125.1	s__Prevotella sp900762125	77.8385	172	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003447235.1	s__Prevotella sp003447235	77.7894	161	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.02	97.84	0.85	0.82	13	-
GCA_002481295.1	s__Prevotella sp002481295	77.5618	166	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.83	96.70	0.87	0.78	4	-
GCA_900318815.1	s__Prevotella sp900318815	77.5252	157	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.58	97.15	0.91	0.81	3	-
GCF_900113305.1	s__Prevotella sp900113305	77.5042	157	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779455.1	s__Prevotella sp902779455	77.353	187	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900314365.1	s__Prevotella sp900314365	77.1704	132	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	100.00	100.00	0.98	0.98	2	-
GCA_017478085.1	s__Prevotella sp017478085	77.1629	148	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902774815.1	s__Prevotella sp902774815	76.7409	132	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 05:16:18,542] [INFO] GTDB search result was written to GCA_945873435.1_ERR1855540_bin.18_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 05:16:18,542] [INFO] ===== GTDB Search completed =====
[2023-06-08 05:16:18,546] [INFO] DFAST_QC result json was written to GCA_945873435.1_ERR1855540_bin.18_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 05:16:18,547] [INFO] DFAST_QC completed!
[2023-06-08 05:16:18,547] [INFO] Total running time: 0h1m38s