[2023-06-08 13:17:20,366] [INFO] DFAST_QC pipeline started.
[2023-06-08 13:17:20,370] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 13:17:20,370] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c15b192-9499-4278-a2ca-0d078bd9310e/dqc_reference
[2023-06-08 13:17:21,729] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 13:17:21,738] [INFO] Task started: Prodigal
[2023-06-08 13:17:21,738] [INFO] Running command: gunzip -c /var/lib/cwl/stgde7f14f0-2a20-48c5-8bca-5a8f7d021997/GCA_945836585.1_SRR5666659_bin.30_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945836585.1_SRR5666659_bin.30_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945836585.1_SRR5666659_bin.30_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 13:17:36,386] [INFO] Task succeeded: Prodigal
[2023-06-08 13:17:36,387] [INFO] Task started: HMMsearch
[2023-06-08 13:17:36,387] [INFO] Running command: hmmsearch --tblout GCA_945836585.1_SRR5666659_bin.30_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c15b192-9499-4278-a2ca-0d078bd9310e/dqc_reference/reference_markers.hmm GCA_945836585.1_SRR5666659_bin.30_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 13:17:36,661] [INFO] Task succeeded: HMMsearch
[2023-06-08 13:17:36,663] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgde7f14f0-2a20-48c5-8bca-5a8f7d021997/GCA_945836585.1_SRR5666659_bin.30_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 13:17:36,687] [INFO] Query marker FASTA was written to GCA_945836585.1_SRR5666659_bin.30_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 13:17:36,688] [INFO] Task started: Blastn
[2023-06-08 13:17:36,688] [INFO] Running command: blastn -query GCA_945836585.1_SRR5666659_bin.30_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c15b192-9499-4278-a2ca-0d078bd9310e/dqc_reference/reference_markers.fasta -out GCA_945836585.1_SRR5666659_bin.30_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:17:37,301] [INFO] Task succeeded: Blastn
[2023-06-08 13:17:37,304] [INFO] Selected 22 target genomes.
[2023-06-08 13:17:37,305] [INFO] Target genome list was writen to GCA_945836585.1_SRR5666659_bin.30_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 13:17:37,306] [INFO] Task started: fastANI
[2023-06-08 13:17:37,307] [INFO] Running command: fastANI --query /var/lib/cwl/stgde7f14f0-2a20-48c5-8bca-5a8f7d021997/GCA_945836585.1_SRR5666659_bin.30_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945836585.1_SRR5666659_bin.30_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945836585.1_SRR5666659_bin.30_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 13:17:52,136] [INFO] Task succeeded: fastANI
[2023-06-08 13:17:52,136] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c15b192-9499-4278-a2ca-0d078bd9310e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 13:17:52,136] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c15b192-9499-4278-a2ca-0d078bd9310e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 13:17:52,140] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 13:17:52,141] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 13:17:52,141] [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
Palleniella intestinalis	strain=PINT	GCA_013166595.1	2736291	2736291	type	True	77.0096	64	716	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	76.1502	54	716	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 13:17:52,143] [INFO] DFAST Taxonomy check result was written to GCA_945836585.1_SRR5666659_bin.30_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 13:17:52,143] [INFO] ===== Taxonomy check completed =====
[2023-06-08 13:17:52,144] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 13:17:52,144] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c15b192-9499-4278-a2ca-0d078bd9310e/dqc_reference/checkm_data
[2023-06-08 13:17:52,145] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 13:17:52,179] [INFO] Task started: CheckM
[2023-06-08 13:17:52,180] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945836585.1_SRR5666659_bin.30_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945836585.1_SRR5666659_bin.30_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945836585.1_SRR5666659_bin.30_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 13:18:34,975] [INFO] Task succeeded: CheckM
[2023-06-08 13:18:34,977] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 13:18:34,998] [INFO] ===== Completeness check finished =====
[2023-06-08 13:18:34,999] [INFO] ===== Start GTDB Search =====
[2023-06-08 13:18:34,999] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945836585.1_SRR5666659_bin.30_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 13:18:34,999] [INFO] Task started: Blastn
[2023-06-08 13:18:35,000] [INFO] Running command: blastn -query GCA_945836585.1_SRR5666659_bin.30_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c15b192-9499-4278-a2ca-0d078bd9310e/dqc_reference/reference_markers_gtdb.fasta -out GCA_945836585.1_SRR5666659_bin.30_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:18:35,759] [INFO] Task succeeded: Blastn
[2023-06-08 13:18:35,764] [INFO] Selected 24 target genomes.
[2023-06-08 13:18:35,765] [INFO] Target genome list was writen to GCA_945836585.1_SRR5666659_bin.30_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 13:18:35,775] [INFO] Task started: fastANI
[2023-06-08 13:18:35,776] [INFO] Running command: fastANI --query /var/lib/cwl/stgde7f14f0-2a20-48c5-8bca-5a8f7d021997/GCA_945836585.1_SRR5666659_bin.30_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945836585.1_SRR5666659_bin.30_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945836585.1_SRR5666659_bin.30_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 13:18:46,000] [INFO] Task succeeded: fastANI
[2023-06-08 13:18:46,013] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 13:18:46,014] [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_017623655.1	s__Prevotella sp017623655	80.6775	289	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002353585.1	s__Prevotella sp002353585	77.3508	93	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.91	95.27	0.85	0.76	8	-
GCA_017479675.1	s__Prevotella sp017479675	77.317	123	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.31	98.13	0.63	0.60	3	-
GCA_017413085.1	s__Prevotella sp017413085	77.1238	113	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.36	98.36	0.87	0.87	2	-
GCA_017642485.1	s__Prevotella sp017642485	77.0721	80	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013166595.1	s__Prevotella sp002298815	77.0559	63	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.88	99.76	0.99	0.99	4	-
GCA_002392645.1	s__Prevotella sp002392645	76.8971	78	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.38	96.38	0.66	0.66	2	-
GCA_900769275.1	s__Prevotella sp900769275	76.8604	88	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017478025.1	s__Prevotella sp017478025	76.8483	101	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.24	95.24	0.74	0.74	2	-
GCA_002353975.1	s__Prevotella sp002353975	76.8387	91	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.61	96.48	0.79	0.75	4	-
GCA_016281055.1	s__Prevotella sp016281055	76.786	131	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017475005.1	s__Prevotella sp017475005	76.6679	55	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.77	98.77	0.88	0.88	2	-
GCA_018065145.1	s__Prevotella sp018065145	76.5961	137	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002373375.1	s__Prevotella sp002373375	76.3099	93	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.88	95.14	0.78	0.66	9	-
GCA_900552965.1	s__Prevotella sp900552965	76.2777	73	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.78	99.78	0.83	0.83	2	-
GCA_900315565.1	s__Prevotella sp900315565	76.1142	51	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.12	96.25	0.91	0.84	3	-
--------------------------------------------------------------------------------
[2023-06-08 13:18:46,016] [INFO] GTDB search result was written to GCA_945836585.1_SRR5666659_bin.30_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 13:18:46,017] [INFO] ===== GTDB Search completed =====
[2023-06-08 13:18:46,020] [INFO] DFAST_QC result json was written to GCA_945836585.1_SRR5666659_bin.30_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 13:18:46,020] [INFO] DFAST_QC completed!
[2023-06-08 13:18:46,020] [INFO] Total running time: 0h1m26s