[2023-06-13 05:49:32,920] [INFO] DFAST_QC pipeline started.
[2023-06-13 05:49:32,923] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 05:49:32,923] [INFO] DQC Reference Directory: /var/lib/cwl/stgb17c4edb-65a5-4a49-a929-8c8ad492871e/dqc_reference
[2023-06-13 05:49:34,228] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 05:49:34,229] [INFO] Task started: Prodigal
[2023-06-13 05:49:34,229] [INFO] Running command: gunzip -c /var/lib/cwl/stgbdca324c-242a-4255-8108-a383b7ec0153/GCA_947253705.1_SRR17635465_bin.2_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947253705.1_SRR17635465_bin.2_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_947253705.1_SRR17635465_bin.2_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 05:49:48,551] [INFO] Task succeeded: Prodigal
[2023-06-13 05:49:48,551] [INFO] Task started: HMMsearch
[2023-06-13 05:49:48,551] [INFO] Running command: hmmsearch --tblout GCA_947253705.1_SRR17635465_bin.2_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb17c4edb-65a5-4a49-a929-8c8ad492871e/dqc_reference/reference_markers.hmm GCA_947253705.1_SRR17635465_bin.2_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 05:49:48,825] [INFO] Task succeeded: HMMsearch
[2023-06-13 05:49:48,827] [INFO] Found 6/6 markers.
[2023-06-13 05:49:48,851] [INFO] Query marker FASTA was written to GCA_947253705.1_SRR17635465_bin.2_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 05:49:48,852] [INFO] Task started: Blastn
[2023-06-13 05:49:48,852] [INFO] Running command: blastn -query GCA_947253705.1_SRR17635465_bin.2_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb17c4edb-65a5-4a49-a929-8c8ad492871e/dqc_reference/reference_markers.fasta -out GCA_947253705.1_SRR17635465_bin.2_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:49:49,474] [INFO] Task succeeded: Blastn
[2023-06-13 05:49:49,479] [INFO] Selected 16 target genomes.
[2023-06-13 05:49:49,479] [INFO] Target genome list was writen to GCA_947253705.1_SRR17635465_bin.2_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 05:49:49,481] [INFO] Task started: fastANI
[2023-06-13 05:49:49,481] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdca324c-242a-4255-8108-a383b7ec0153/GCA_947253705.1_SRR17635465_bin.2_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947253705.1_SRR17635465_bin.2_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947253705.1_SRR17635465_bin.2_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 05:49:59,765] [INFO] Task succeeded: fastANI
[2023-06-13 05:49:59,765] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb17c4edb-65a5-4a49-a929-8c8ad492871e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 05:49:59,766] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb17c4edb-65a5-4a49-a929-8c8ad492871e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 05:49:59,777] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2023-06-13 05:49:59,778] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 05:49:59,778] [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 timonensis	strain=DSM 22865	GCA_000430565.1	386414	386414	suspected-type	True	96.0869	708	811	95	conclusive
Prevotella timonensis	strain=4401737	GCA_000455445.1	386414	386414	type	True	96.0561	735	811	95	conclusive
Prevotella timonensis	strain=JCM 15640	GCA_000614005.1	386414	386414	type	True	95.9797	709	811	95	conclusive
Prevotella ihumii	strain=Marseille-P3385	GCA_900155655.1	1917878	1917878	type	True	80.9541	104	811	95	below_threshold
Prevotella maculosa	strain=DSM 19339	GCA_000382385.1	439703	439703	type	True	79.3422	58	811	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	78.882	78	811	95	below_threshold
Prevotella maculosa	strain=JCM 15638	GCA_000613965.1	439703	439703	type	True	78.7358	60	811	95	below_threshold
Prevotella vespertina	strain=A2879	GCA_009728485.1	2608404	2608404	type	True	78.3819	75	811	95	below_threshold
Prevotella shahii	strain=JCM 12083	GCA_000613445.1	228603	228603	type	True	78.372	73	811	95	below_threshold
Prevotella oris	strain=DSM 18711	GCA_000377685.1	28135	28135	type	True	77.8348	66	811	95	below_threshold
Prevotella loescheii	strain=DSM 19665	GCA_000378085.1	840	840	type	True	77.463	53	811	95	below_threshold
Prevotella loescheii	strain=ATCC 15930	GCA_000698925.1	840	840	type	True	77.3354	50	811	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 05:49:59,780] [INFO] DFAST Taxonomy check result was written to GCA_947253705.1_SRR17635465_bin.2_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 05:49:59,781] [INFO] ===== Taxonomy check completed =====
[2023-06-13 05:49:59,781] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 05:49:59,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb17c4edb-65a5-4a49-a929-8c8ad492871e/dqc_reference/checkm_data
[2023-06-13 05:49:59,783] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 05:49:59,817] [INFO] Task started: CheckM
[2023-06-13 05:49:59,817] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947253705.1_SRR17635465_bin.2_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947253705.1_SRR17635465_bin.2_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_947253705.1_SRR17635465_bin.2_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 05:50:44,306] [INFO] Task succeeded: CheckM
[2023-06-13 05:50:44,308] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 05:50:44,327] [INFO] ===== Completeness check finished =====
[2023-06-13 05:50:44,328] [INFO] ===== Start GTDB Search =====
[2023-06-13 05:50:44,328] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947253705.1_SRR17635465_bin.2_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 05:50:44,329] [INFO] Task started: Blastn
[2023-06-13 05:50:44,329] [INFO] Running command: blastn -query GCA_947253705.1_SRR17635465_bin.2_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb17c4edb-65a5-4a49-a929-8c8ad492871e/dqc_reference/reference_markers_gtdb.fasta -out GCA_947253705.1_SRR17635465_bin.2_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:50:45,107] [INFO] Task succeeded: Blastn
[2023-06-13 05:50:45,112] [INFO] Selected 16 target genomes.
[2023-06-13 05:50:45,112] [INFO] Target genome list was writen to GCA_947253705.1_SRR17635465_bin.2_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 05:50:45,123] [INFO] Task started: fastANI
[2023-06-13 05:50:45,124] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdca324c-242a-4255-8108-a383b7ec0153/GCA_947253705.1_SRR17635465_bin.2_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947253705.1_SRR17635465_bin.2_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947253705.1_SRR17635465_bin.2_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 05:50:53,862] [INFO] Task succeeded: fastANI
[2023-06-13 05:50:53,875] [INFO] Found 11 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-13 05:50:53,875] [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_000455445.1	s__Prevotella timonensis	96.04	736	811	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0025	97.81	95.47	0.90	0.82	5	inconclusive
GCF_000762405.1	s__Prevotella timonensis_A	95.2642	644	811	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0025	96.56	96.39	0.83	0.81	3	inconclusive
GCF_000177075.1	s__Prevotella buccalis	84.4126	344	811	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.19	95.19	0.85	0.85	2	-
GCF_000479005.1	s__Prevotella sp000479005	84.0674	314	811	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.86	96.42	0.92	0.87	3	-
GCA_900547085.1	s__Prevotella sp900547085	84.0655	237	811	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000163055.2	s__Prevotella sp000163055	80.168	52	811	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000599605.1	s__Prevotella sp000599605	80.1393	78	811	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.66	96.63	0.93	0.92	3	-
GCF_000382385.1	s__Prevotella maculosa	79.339	60	811	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.13	97.00	0.93	0.87	4	-
GCF_000613725.1	s__Prevotella pleuritidis	77.7702	54	811	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.72	98.65	0.96	0.96	4	-
GCF_000378085.1	s__Prevotella loescheii	77.463	53	811	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.09	95.73	0.96	0.93	5	-
GCA_002449845.1	s__Prevotella sp002449845	76.7428	55	811	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.15	96.99	0.89	0.86	3	-
--------------------------------------------------------------------------------
[2023-06-13 05:50:53,877] [INFO] GTDB search result was written to GCA_947253705.1_SRR17635465_bin.2_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 05:50:53,878] [INFO] ===== GTDB Search completed =====
[2023-06-13 05:50:53,881] [INFO] DFAST_QC result json was written to GCA_947253705.1_SRR17635465_bin.2_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 05:50:53,882] [INFO] DFAST_QC completed!
[2023-06-13 05:50:53,882] [INFO] Total running time: 0h1m21s