[2023-06-07 18:44:39,822] [INFO] DFAST_QC pipeline started.
[2023-06-07 18:44:39,825] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 18:44:39,825] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb7b2f2d-2c0c-4596-b267-1c45d4dbe9b8/dqc_reference
[2023-06-07 18:44:41,979] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 18:44:41,980] [INFO] Task started: Prodigal
[2023-06-07 18:44:41,980] [INFO] Running command: gunzip -c /var/lib/cwl/stg800e5371-b615-47f0-8fc5-cef59e69289b/GCA_945830385.1_SRR5240741_bin.17_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945830385.1_SRR5240741_bin.17_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945830385.1_SRR5240741_bin.17_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 18:45:00,314] [INFO] Task succeeded: Prodigal
[2023-06-07 18:45:00,314] [INFO] Task started: HMMsearch
[2023-06-07 18:45:00,314] [INFO] Running command: hmmsearch --tblout GCA_945830385.1_SRR5240741_bin.17_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb7b2f2d-2c0c-4596-b267-1c45d4dbe9b8/dqc_reference/reference_markers.hmm GCA_945830385.1_SRR5240741_bin.17_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-07 18:45:00,605] [INFO] Task succeeded: HMMsearch
[2023-06-07 18:45:00,606] [INFO] Found 6/6 markers.
[2023-06-07 18:45:00,639] [INFO] Query marker FASTA was written to GCA_945830385.1_SRR5240741_bin.17_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-07 18:45:00,639] [INFO] Task started: Blastn
[2023-06-07 18:45:00,639] [INFO] Running command: blastn -query GCA_945830385.1_SRR5240741_bin.17_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb7b2f2d-2c0c-4596-b267-1c45d4dbe9b8/dqc_reference/reference_markers.fasta -out GCA_945830385.1_SRR5240741_bin.17_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 18:45:01,231] [INFO] Task succeeded: Blastn
[2023-06-07 18:45:01,235] [INFO] Selected 23 target genomes.
[2023-06-07 18:45:01,236] [INFO] Target genome list was writen to GCA_945830385.1_SRR5240741_bin.17_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-07 18:45:01,240] [INFO] Task started: fastANI
[2023-06-07 18:45:01,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg800e5371-b615-47f0-8fc5-cef59e69289b/GCA_945830385.1_SRR5240741_bin.17_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945830385.1_SRR5240741_bin.17_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945830385.1_SRR5240741_bin.17_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 18:45:12,440] [INFO] Task succeeded: fastANI
[2023-06-07 18:45:12,440] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb7b2f2d-2c0c-4596-b267-1c45d4dbe9b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 18:45:12,440] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb7b2f2d-2c0c-4596-b267-1c45d4dbe9b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 18:45:12,456] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 18:45:12,456] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 18:45:12,456] [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	79.1924	203	1013	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.9738	77	1013	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.9429	117	1013	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.9288	112	1013	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.8164	67	1013	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.7394	67	1013	95	below_threshold
Prevotella maculosa	strain=JCM 15638	GCA_000613965.1	439703	439703	type	True	76.7289	55	1013	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	76.7251	61	1013	95	below_threshold
Prevotella maculosa	strain=DSM 19339	GCA_000382385.1	439703	439703	type	True	76.6225	58	1013	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.5147	86	1013	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	76.4916	82	1013	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	76.4841	81	1013	95	below_threshold
Prevotella bergensis	strain=DSM 17361	GCA_000160535.1	242750	242750	type	True	76.3106	60	1013	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	76.0335	55	1013	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	75.9971	53	1013	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 18:45:12,458] [INFO] DFAST Taxonomy check result was written to GCA_945830385.1_SRR5240741_bin.17_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-07 18:45:12,459] [INFO] ===== Taxonomy check completed =====
[2023-06-07 18:45:12,459] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 18:45:12,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb7b2f2d-2c0c-4596-b267-1c45d4dbe9b8/dqc_reference/checkm_data
[2023-06-07 18:45:12,460] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 18:45:12,500] [INFO] Task started: CheckM
[2023-06-07 18:45:12,500] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945830385.1_SRR5240741_bin.17_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945830385.1_SRR5240741_bin.17_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945830385.1_SRR5240741_bin.17_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-07 18:46:06,669] [INFO] Task succeeded: CheckM
[2023-06-07 18:46:06,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 18:46:06,699] [INFO] ===== Completeness check finished =====
[2023-06-07 18:46:06,700] [INFO] ===== Start GTDB Search =====
[2023-06-07 18:46:06,700] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945830385.1_SRR5240741_bin.17_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-07 18:46:06,700] [INFO] Task started: Blastn
[2023-06-07 18:46:06,701] [INFO] Running command: blastn -query GCA_945830385.1_SRR5240741_bin.17_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb7b2f2d-2c0c-4596-b267-1c45d4dbe9b8/dqc_reference/reference_markers_gtdb.fasta -out GCA_945830385.1_SRR5240741_bin.17_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 18:46:07,559] [INFO] Task succeeded: Blastn
[2023-06-07 18:46:07,563] [INFO] Selected 26 target genomes.
[2023-06-07 18:46:07,563] [INFO] Target genome list was writen to GCA_945830385.1_SRR5240741_bin.17_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 18:46:07,574] [INFO] Task started: fastANI
[2023-06-07 18:46:07,574] [INFO] Running command: fastANI --query /var/lib/cwl/stg800e5371-b615-47f0-8fc5-cef59e69289b/GCA_945830385.1_SRR5240741_bin.17_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945830385.1_SRR5240741_bin.17_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945830385.1_SRR5240741_bin.17_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 18:46:20,283] [INFO] Task succeeded: fastANI
[2023-06-07 18:46:20,308] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 18:46:20,309] [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_900314365.1	s__Prevotella sp900314365	97.8823	654	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	100.00	100.00	0.98	0.98	2	conclusive
GCA_900318855.1	s__Prevotella sp900318855	81.1683	436	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.94	98.64	0.80	0.74	4	-
GCA_900546345.1	s__Prevotella sp900546345	80.8767	159	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009695775.1	s__Prevotella mizrahii	79.203	202	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.15	96.87	0.87	0.84	6	-
GCA_900319905.1	s__Prevotella sp900319905	78.3152	148	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.87	98.44	0.89	0.87	7	-
GCF_000424185.1	s__Prevotella sp000424185	77.9725	120	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900322095.1	s__Prevotella sp900322095	77.9211	152	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.50	99.22	0.86	0.85	3	-
GCA_900770845.1	s__Prevotella sp900770845	77.8215	139	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315835.1	s__Prevotella sp900315835	77.7107	157	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.59	98.19	0.88	0.85	9	-
GCA_900199655.1	s__Prevotella sp900199655	77.0912	101	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.91	99.91	0.98	0.98	2	-
GCA_002437285.1	s__Prevotella sp002437285	76.7357	131	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.68	99.38	0.93	0.88	13	-
GCA_002299635.1	s__Prevotella sp002299635	76.6893	56	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.50	98.47	0.80	0.78	3	-
GCF_900113305.1	s__Prevotella sp900113305	76.5289	103	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318915.1	s__Prevotella sp900318915	76.4911	95	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.05	95.26	0.87	0.81	11	-
GCF_900454835.1	s__Prevotella denticola	76.4841	81	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.27	97.69	0.92	0.88	14	-
GCA_002439605.1	s__Prevotella sp002439605	76.4402	65	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.57	99.57	0.81	0.81	2	-
GCA_017635615.1	s__Prevotella sp017635615	76.3289	56	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016302965.1	s__Prevotella sp016302965	76.2738	71	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017476785.1	s__Prevotella sp017476785	76.2685	64	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234355.1	s__Prevotella sp905234355	76.2121	72	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017483805.1	s__Prevotella sp017483805	76.1338	82	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902776475.1	s__Prevotella sp902776475	76.1004	93	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.89	97.89	0.91	0.91	2	-
GCA_900315075.1	s__Prevotella sp900315075	76.066	67	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.96	98.41	0.92	0.87	4	-
GCA_017442765.1	s__Prevotella sp017442765	75.9988	70	1013	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 18:46:20,317] [INFO] GTDB search result was written to GCA_945830385.1_SRR5240741_bin.17_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-07 18:46:20,318] [INFO] ===== GTDB Search completed =====
[2023-06-07 18:46:20,324] [INFO] DFAST_QC result json was written to GCA_945830385.1_SRR5240741_bin.17_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-07 18:46:20,324] [INFO] DFAST_QC completed!
[2023-06-07 18:46:20,324] [INFO] Total running time: 0h1m41s