[2023-06-08 09:32:35,388] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:32:35,391] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:32:35,391] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb510ee5-9714-44c4-88bc-ad76be8b56a8/dqc_reference
[2023-06-08 09:32:37,168] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:32:37,169] [INFO] Task started: Prodigal
[2023-06-08 09:32:37,169] [INFO] Running command: gunzip -c /var/lib/cwl/stg2cd3cdac-48e3-4165-9bda-41c96b67acd7/GCA_945831595.1_SRR5976185_bin.18_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945831595.1_SRR5976185_bin.18_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945831595.1_SRR5976185_bin.18_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:32:50,512] [INFO] Task succeeded: Prodigal
[2023-06-08 09:32:50,513] [INFO] Task started: HMMsearch
[2023-06-08 09:32:50,513] [INFO] Running command: hmmsearch --tblout GCA_945831595.1_SRR5976185_bin.18_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb510ee5-9714-44c4-88bc-ad76be8b56a8/dqc_reference/reference_markers.hmm GCA_945831595.1_SRR5976185_bin.18_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:32:50,727] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:32:50,729] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2cd3cdac-48e3-4165-9bda-41c96b67acd7/GCA_945831595.1_SRR5976185_bin.18_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 09:32:50,753] [INFO] Query marker FASTA was written to GCA_945831595.1_SRR5976185_bin.18_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 09:32:50,753] [INFO] Task started: Blastn
[2023-06-08 09:32:50,754] [INFO] Running command: blastn -query GCA_945831595.1_SRR5976185_bin.18_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb510ee5-9714-44c4-88bc-ad76be8b56a8/dqc_reference/reference_markers.fasta -out GCA_945831595.1_SRR5976185_bin.18_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:32:51,330] [INFO] Task succeeded: Blastn
[2023-06-08 09:32:51,335] [INFO] Selected 19 target genomes.
[2023-06-08 09:32:51,335] [INFO] Target genome list was writen to GCA_945831595.1_SRR5976185_bin.18_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 09:32:51,337] [INFO] Task started: fastANI
[2023-06-08 09:32:51,337] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cd3cdac-48e3-4165-9bda-41c96b67acd7/GCA_945831595.1_SRR5976185_bin.18_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945831595.1_SRR5976185_bin.18_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945831595.1_SRR5976185_bin.18_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:33:00,371] [INFO] Task succeeded: fastANI
[2023-06-08 09:33:00,372] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb510ee5-9714-44c4-88bc-ad76be8b56a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:33:00,372] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb510ee5-9714-44c4-88bc-ad76be8b56a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:33:00,380] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:33:00,380] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 09:33:00,380] [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	77.1884	95	666	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.3474	51	666	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 09:33:00,383] [INFO] DFAST Taxonomy check result was written to GCA_945831595.1_SRR5976185_bin.18_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 09:33:00,383] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:33:00,384] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:33:00,384] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb510ee5-9714-44c4-88bc-ad76be8b56a8/dqc_reference/checkm_data
[2023-06-08 09:33:00,386] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:33:00,416] [INFO] Task started: CheckM
[2023-06-08 09:33:00,416] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945831595.1_SRR5976185_bin.18_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945831595.1_SRR5976185_bin.18_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945831595.1_SRR5976185_bin.18_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 09:33:42,679] [INFO] Task succeeded: CheckM
[2023-06-08 09:33:42,680] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:33:42,698] [INFO] ===== Completeness check finished =====
[2023-06-08 09:33:42,699] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:33:42,699] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945831595.1_SRR5976185_bin.18_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 09:33:42,699] [INFO] Task started: Blastn
[2023-06-08 09:33:42,700] [INFO] Running command: blastn -query GCA_945831595.1_SRR5976185_bin.18_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb510ee5-9714-44c4-88bc-ad76be8b56a8/dqc_reference/reference_markers_gtdb.fasta -out GCA_945831595.1_SRR5976185_bin.18_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:33:43,496] [INFO] Task succeeded: Blastn
[2023-06-08 09:33:43,501] [INFO] Selected 14 target genomes.
[2023-06-08 09:33:43,501] [INFO] Target genome list was writen to GCA_945831595.1_SRR5976185_bin.18_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:33:43,502] [INFO] Task started: fastANI
[2023-06-08 09:33:43,503] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cd3cdac-48e3-4165-9bda-41c96b67acd7/GCA_945831595.1_SRR5976185_bin.18_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945831595.1_SRR5976185_bin.18_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945831595.1_SRR5976185_bin.18_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:33:50,515] [INFO] Task succeeded: fastANI
[2023-06-08 09:33:50,527] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 09:33:50,527] [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	98.3384	519	666	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	78.4993	167	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.26	98.55	0.94	0.92	3	-
GCA_017462915.1	s__Prevotella sp017462915	77.5817	115	666	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	77.2814	66	666	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	77.1884	95	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.88	99.76	0.99	0.99	4	-
GCA_004792655.1	s__Prevotella sp004792655	77.0764	94	666	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 09:33:50,529] [INFO] GTDB search result was written to GCA_945831595.1_SRR5976185_bin.18_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 09:33:50,530] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:33:50,532] [INFO] DFAST_QC result json was written to GCA_945831595.1_SRR5976185_bin.18_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 09:33:50,532] [INFO] DFAST_QC completed!
[2023-06-08 09:33:50,532] [INFO] Total running time: 0h1m15s