[2023-06-08 10:52:39,290] [INFO] DFAST_QC pipeline started.
[2023-06-08 10:52:39,293] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 10:52:39,294] [INFO] DQC Reference Directory: /var/lib/cwl/stgc964d429-5393-4d02-8c62-8438462575c4/dqc_reference
[2023-06-08 10:52:40,650] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 10:52:40,650] [INFO] Task started: Prodigal
[2023-06-08 10:52:40,651] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2498266-e49d-4b7c-b164-73055baa5943/GCA_945831005.1_SRR5240748_bin.8_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945831005.1_SRR5240748_bin.8_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945831005.1_SRR5240748_bin.8_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 10:52:52,726] [INFO] Task succeeded: Prodigal
[2023-06-08 10:52:52,726] [INFO] Task started: HMMsearch
[2023-06-08 10:52:52,726] [INFO] Running command: hmmsearch --tblout GCA_945831005.1_SRR5240748_bin.8_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc964d429-5393-4d02-8c62-8438462575c4/dqc_reference/reference_markers.hmm GCA_945831005.1_SRR5240748_bin.8_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 10:52:52,977] [INFO] Task succeeded: HMMsearch
[2023-06-08 10:52:52,978] [INFO] Found 6/6 markers.
[2023-06-08 10:52:53,009] [INFO] Query marker FASTA was written to GCA_945831005.1_SRR5240748_bin.8_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 10:52:53,010] [INFO] Task started: Blastn
[2023-06-08 10:52:53,010] [INFO] Running command: blastn -query GCA_945831005.1_SRR5240748_bin.8_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc964d429-5393-4d02-8c62-8438462575c4/dqc_reference/reference_markers.fasta -out GCA_945831005.1_SRR5240748_bin.8_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:52:53,614] [INFO] Task succeeded: Blastn
[2023-06-08 10:52:53,618] [INFO] Selected 25 target genomes.
[2023-06-08 10:52:53,619] [INFO] Target genome list was writen to GCA_945831005.1_SRR5240748_bin.8_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 10:52:53,620] [INFO] Task started: fastANI
[2023-06-08 10:52:53,621] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2498266-e49d-4b7c-b164-73055baa5943/GCA_945831005.1_SRR5240748_bin.8_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945831005.1_SRR5240748_bin.8_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945831005.1_SRR5240748_bin.8_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 10:53:06,569] [INFO] Task succeeded: fastANI
[2023-06-08 10:53:06,570] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc964d429-5393-4d02-8c62-8438462575c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 10:53:06,571] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc964d429-5393-4d02-8c62-8438462575c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 10:53:06,579] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 10:53:06,580] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 10:53:06,580] [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	77.6613	96	586	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.757	54	586	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 10:53:06,582] [INFO] DFAST Taxonomy check result was written to GCA_945831005.1_SRR5240748_bin.8_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 10:53:06,583] [INFO] ===== Taxonomy check completed =====
[2023-06-08 10:53:06,584] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 10:53:06,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc964d429-5393-4d02-8c62-8438462575c4/dqc_reference/checkm_data
[2023-06-08 10:53:06,586] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 10:53:06,616] [INFO] Task started: CheckM
[2023-06-08 10:53:06,617] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945831005.1_SRR5240748_bin.8_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945831005.1_SRR5240748_bin.8_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945831005.1_SRR5240748_bin.8_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 10:53:46,085] [INFO] Task succeeded: CheckM
[2023-06-08 10:53:46,086] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 10:53:46,106] [INFO] ===== Completeness check finished =====
[2023-06-08 10:53:46,106] [INFO] ===== Start GTDB Search =====
[2023-06-08 10:53:46,106] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945831005.1_SRR5240748_bin.8_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 10:53:46,107] [INFO] Task started: Blastn
[2023-06-08 10:53:46,107] [INFO] Running command: blastn -query GCA_945831005.1_SRR5240748_bin.8_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc964d429-5393-4d02-8c62-8438462575c4/dqc_reference/reference_markers_gtdb.fasta -out GCA_945831005.1_SRR5240748_bin.8_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:53:46,958] [INFO] Task succeeded: Blastn
[2023-06-08 10:53:46,963] [INFO] Selected 16 target genomes.
[2023-06-08 10:53:46,963] [INFO] Target genome list was writen to GCA_945831005.1_SRR5240748_bin.8_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 10:53:46,965] [INFO] Task started: fastANI
[2023-06-08 10:53:46,965] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2498266-e49d-4b7c-b164-73055baa5943/GCA_945831005.1_SRR5240748_bin.8_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945831005.1_SRR5240748_bin.8_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945831005.1_SRR5240748_bin.8_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 10:53:54,266] [INFO] Task succeeded: fastANI
[2023-06-08 10:53:54,276] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 10:53:54,276] [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_004556065.1	s__Prevotella sp004556065	98.1877	453	586	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.27	97.47	0.85	0.76	10	conclusive
GCA_004555245.1	s__Prevotella sp004555245	78.38	172	586	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.26	98.55	0.94	0.92	3	-
GCF_013166595.1	s__Prevotella sp002298815	77.6613	96	586	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.88	99.76	0.99	0.99	4	-
GCA_017462915.1	s__Prevotella sp017462915	77.6415	126	586	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017424205.1	s__Prevotella sp017424205	77.4571	63	586	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004792655.1	s__Prevotella sp004792655	77.3248	102	586	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 10:53:54,278] [INFO] GTDB search result was written to GCA_945831005.1_SRR5240748_bin.8_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 10:53:54,279] [INFO] ===== GTDB Search completed =====
[2023-06-08 10:53:54,281] [INFO] DFAST_QC result json was written to GCA_945831005.1_SRR5240748_bin.8_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 10:53:54,281] [INFO] DFAST_QC completed!
[2023-06-08 10:53:54,281] [INFO] Total running time: 0h1m15s