[2023-06-08 02:20:03,313] [INFO] DFAST_QC pipeline started.
[2023-06-08 02:20:03,315] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 02:20:03,315] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0c4ca66-e0d9-456c-8725-b14d90338002/dqc_reference
[2023-06-08 02:20:04,555] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 02:20:04,556] [INFO] Task started: Prodigal
[2023-06-08 02:20:04,556] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f5abd84-98a3-4024-a87b-bdab7f41c818/GCA_947166345.1_SRR8387719_bin.11_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947166345.1_SRR8387719_bin.11_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_947166345.1_SRR8387719_bin.11_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 02:20:17,223] [INFO] Task succeeded: Prodigal
[2023-06-08 02:20:17,224] [INFO] Task started: HMMsearch
[2023-06-08 02:20:17,224] [INFO] Running command: hmmsearch --tblout GCA_947166345.1_SRR8387719_bin.11_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0c4ca66-e0d9-456c-8725-b14d90338002/dqc_reference/reference_markers.hmm GCA_947166345.1_SRR8387719_bin.11_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 02:20:17,467] [INFO] Task succeeded: HMMsearch
[2023-06-08 02:20:17,468] [INFO] Found 6/6 markers.
[2023-06-08 02:20:17,493] [INFO] Query marker FASTA was written to GCA_947166345.1_SRR8387719_bin.11_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 02:20:17,494] [INFO] Task started: Blastn
[2023-06-08 02:20:17,494] [INFO] Running command: blastn -query GCA_947166345.1_SRR8387719_bin.11_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0c4ca66-e0d9-456c-8725-b14d90338002/dqc_reference/reference_markers.fasta -out GCA_947166345.1_SRR8387719_bin.11_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 02:20:18,092] [INFO] Task succeeded: Blastn
[2023-06-08 02:20:18,097] [INFO] Selected 26 target genomes.
[2023-06-08 02:20:18,098] [INFO] Target genome list was writen to GCA_947166345.1_SRR8387719_bin.11_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 02:20:18,099] [INFO] Task started: fastANI
[2023-06-08 02:20:18,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f5abd84-98a3-4024-a87b-bdab7f41c818/GCA_947166345.1_SRR8387719_bin.11_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947166345.1_SRR8387719_bin.11_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947166345.1_SRR8387719_bin.11_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 02:20:29,588] [INFO] Task succeeded: fastANI
[2023-06-08 02:20:29,588] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0c4ca66-e0d9-456c-8725-b14d90338002/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 02:20:29,589] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0c4ca66-e0d9-456c-8725-b14d90338002/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 02:20:29,601] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 02:20:29,601] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 02:20:29,602] [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 brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	78.9856	240	730	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	78.5544	194	730	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	78.5083	193	730	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.5333	71	730	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.449	77	730	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.329	81	730	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.2462	96	730	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.2407	59	730	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.0788	68	730	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	75.8098	87	730	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 02:20:29,604] [INFO] DFAST Taxonomy check result was written to GCA_947166345.1_SRR8387719_bin.11_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 02:20:29,605] [INFO] ===== Taxonomy check completed =====
[2023-06-08 02:20:29,605] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 02:20:29,605] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0c4ca66-e0d9-456c-8725-b14d90338002/dqc_reference/checkm_data
[2023-06-08 02:20:29,606] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 02:20:29,637] [INFO] Task started: CheckM
[2023-06-08 02:20:29,637] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947166345.1_SRR8387719_bin.11_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947166345.1_SRR8387719_bin.11_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_947166345.1_SRR8387719_bin.11_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 02:21:10,200] [INFO] Task succeeded: CheckM
[2023-06-08 02:21:10,202] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.55%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 02:21:10,223] [INFO] ===== Completeness check finished =====
[2023-06-08 02:21:10,223] [INFO] ===== Start GTDB Search =====
[2023-06-08 02:21:10,223] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947166345.1_SRR8387719_bin.11_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 02:21:10,224] [INFO] Task started: Blastn
[2023-06-08 02:21:10,224] [INFO] Running command: blastn -query GCA_947166345.1_SRR8387719_bin.11_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0c4ca66-e0d9-456c-8725-b14d90338002/dqc_reference/reference_markers_gtdb.fasta -out GCA_947166345.1_SRR8387719_bin.11_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 02:21:11,143] [INFO] Task succeeded: Blastn
[2023-06-08 02:21:11,148] [INFO] Selected 27 target genomes.
[2023-06-08 02:21:11,148] [INFO] Target genome list was writen to GCA_947166345.1_SRR8387719_bin.11_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 02:21:11,152] [INFO] Task started: fastANI
[2023-06-08 02:21:11,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f5abd84-98a3-4024-a87b-bdab7f41c818/GCA_947166345.1_SRR8387719_bin.11_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947166345.1_SRR8387719_bin.11_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947166345.1_SRR8387719_bin.11_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 02:21:26,057] [INFO] Task succeeded: fastANI
[2023-06-08 02:21:26,081] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 02:21:26,082] [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_902799905.1	s__Prevotella sp902799905	79.4055	295	730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.33	98.29	0.89	0.87	3	-
GCF_900100635.1	s__Prevotella sp900100635	79.2106	282	730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.15	96.60	0.86	0.83	10	-
GCA_902785695.1	s__Prevotella sp902785695	79.0644	198	730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902788605.1	s__Prevotella sp902788605	79.06	250	730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.22	98.10	0.87	0.84	7	-
GCA_017483805.1	s__Prevotella sp017483805	78.97	274	730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775605.1	s__Prevotella sp902775605	78.849	243	730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775475.1	s__Prevotella sp902775475	78.6364	278	730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.69	98.51	0.89	0.87	7	-
GCA_017467535.1	s__Prevotella sp017467535	78.6233	219	730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780025.1	s__Prevotella sp902780025	78.5638	251	730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016285055.1	s__Prevotella sp016285055	78.423	280	730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002361655.1	s__Prevotella sp002361655	78.4183	191	730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902778535.1	s__Prevotella sp902778535	78.3966	271	730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.92	97.92	0.83	0.83	2	-
GCA_900318815.1	s__Prevotella sp900318815	78.3545	264	730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.58	97.15	0.91	0.81	3	-
GCA_017455845.1	s__Prevotella sp017455845	78.3426	249	730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017554385.1	s__Prevotella sp017554385	78.3172	206	730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017458225.1	s__Prevotella sp017458225	78.3063	182	730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902798285.1	s__Prevotella sp902798285	78.2352	178	730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.28	98.28	0.87	0.87	2	-
GCA_017478085.1	s__Prevotella sp017478085	78.2128	230	730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902784615.1	s__Prevotella sp902784615	78.1971	193	730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902771785.1	s__Prevotella sp902771785	78.1606	237	730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.01	98.01	0.87	0.87	2	-
GCA_017471465.1	s__Prevotella sp017471465	78.1196	182	730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017458195.1	s__Prevotella sp017458195	78.0963	189	730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017417465.1	s__Prevotella sp017417465	78.0343	267	730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017470345.1	s__Prevotella sp017470345	77.871	169	730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233425.1	s__Prevotella sp905233425	77.7464	233	730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318585.1	s__Prevotella sp900318585	77.6425	174	730	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.57	99.14	0.92	0.85	3	-
GCA_905235905.1	s__Prevotella sp905235905	77.6246	211	730	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 02:21:26,084] [INFO] GTDB search result was written to GCA_947166345.1_SRR8387719_bin.11_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 02:21:26,085] [INFO] ===== GTDB Search completed =====
[2023-06-08 02:21:26,089] [INFO] DFAST_QC result json was written to GCA_947166345.1_SRR8387719_bin.11_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 02:21:26,089] [INFO] DFAST_QC completed!
[2023-06-08 02:21:26,089] [INFO] Total running time: 0h1m23s