[2023-06-08 08:43:32,953] [INFO] DFAST_QC pipeline started.
[2023-06-08 08:43:32,956] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 08:43:32,957] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3b89778-4788-4423-8895-fbf115d8ae30/dqc_reference
[2023-06-08 08:43:34,213] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 08:43:34,214] [INFO] Task started: Prodigal
[2023-06-08 08:43:34,214] [INFO] Running command: gunzip -c /var/lib/cwl/stge04e1ca7-a7ae-4e15-90af-09c7bd53cac1/GCA_945981365.1_ERR2020027_bin.11_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945981365.1_ERR2020027_bin.11_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945981365.1_ERR2020027_bin.11_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 08:43:44,305] [INFO] Task succeeded: Prodigal
[2023-06-08 08:43:44,306] [INFO] Task started: HMMsearch
[2023-06-08 08:43:44,306] [INFO] Running command: hmmsearch --tblout GCA_945981365.1_ERR2020027_bin.11_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3b89778-4788-4423-8895-fbf115d8ae30/dqc_reference/reference_markers.hmm GCA_945981365.1_ERR2020027_bin.11_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 08:43:44,547] [INFO] Task succeeded: HMMsearch
[2023-06-08 08:43:44,549] [INFO] Found 6/6 markers.
[2023-06-08 08:43:44,575] [INFO] Query marker FASTA was written to GCA_945981365.1_ERR2020027_bin.11_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 08:43:44,576] [INFO] Task started: Blastn
[2023-06-08 08:43:44,576] [INFO] Running command: blastn -query GCA_945981365.1_ERR2020027_bin.11_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3b89778-4788-4423-8895-fbf115d8ae30/dqc_reference/reference_markers.fasta -out GCA_945981365.1_ERR2020027_bin.11_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:43:45,158] [INFO] Task succeeded: Blastn
[2023-06-08 08:43:45,162] [INFO] Selected 24 target genomes.
[2023-06-08 08:43:45,163] [INFO] Target genome list was writen to GCA_945981365.1_ERR2020027_bin.11_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 08:43:45,164] [INFO] Task started: fastANI
[2023-06-08 08:43:45,164] [INFO] Running command: fastANI --query /var/lib/cwl/stge04e1ca7-a7ae-4e15-90af-09c7bd53cac1/GCA_945981365.1_ERR2020027_bin.11_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945981365.1_ERR2020027_bin.11_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945981365.1_ERR2020027_bin.11_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 08:43:57,809] [INFO] Task succeeded: fastANI
[2023-06-08 08:43:57,809] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3b89778-4788-4423-8895-fbf115d8ae30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 08:43:57,810] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3b89778-4788-4423-8895-fbf115d8ae30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 08:43:57,816] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 08:43:57,816] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 08:43:57,817] [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 pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	77.6722	53	681	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 08:43:57,818] [INFO] DFAST Taxonomy check result was written to GCA_945981365.1_ERR2020027_bin.11_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 08:43:57,819] [INFO] ===== Taxonomy check completed =====
[2023-06-08 08:43:57,820] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 08:43:57,820] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3b89778-4788-4423-8895-fbf115d8ae30/dqc_reference/checkm_data
[2023-06-08 08:43:57,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 08:43:57,851] [INFO] Task started: CheckM
[2023-06-08 08:43:57,852] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945981365.1_ERR2020027_bin.11_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945981365.1_ERR2020027_bin.11_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945981365.1_ERR2020027_bin.11_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 08:44:31,231] [INFO] Task succeeded: CheckM
[2023-06-08 08:44:31,233] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 08:44:31,254] [INFO] ===== Completeness check finished =====
[2023-06-08 08:44:31,254] [INFO] ===== Start GTDB Search =====
[2023-06-08 08:44:31,254] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945981365.1_ERR2020027_bin.11_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 08:44:31,255] [INFO] Task started: Blastn
[2023-06-08 08:44:31,255] [INFO] Running command: blastn -query GCA_945981365.1_ERR2020027_bin.11_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3b89778-4788-4423-8895-fbf115d8ae30/dqc_reference/reference_markers_gtdb.fasta -out GCA_945981365.1_ERR2020027_bin.11_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:44:32,002] [INFO] Task succeeded: Blastn
[2023-06-08 08:44:32,007] [INFO] Selected 29 target genomes.
[2023-06-08 08:44:32,007] [INFO] Target genome list was writen to GCA_945981365.1_ERR2020027_bin.11_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 08:44:32,012] [INFO] Task started: fastANI
[2023-06-08 08:44:32,012] [INFO] Running command: fastANI --query /var/lib/cwl/stge04e1ca7-a7ae-4e15-90af-09c7bd53cac1/GCA_945981365.1_ERR2020027_bin.11_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945981365.1_ERR2020027_bin.11_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945981365.1_ERR2020027_bin.11_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 08:44:44,430] [INFO] Task succeeded: fastANI
[2023-06-08 08:44:44,440] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 08:44:44,440] [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_900768785.1	s__Prevotella sp900768785	98.1906	575	681	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000433175.1	s__Prevotella sp000433175	77.4144	54	681	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.10	97.93	0.86	0.84	3	-
GCF_013166515.1	s__Prevotella sp013166515	77.4113	62	681	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.36	96.74	0.93	0.86	3	-
GCA_017415455.1	s__Prevotella sp017415455	76.7675	65	681	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.31	98.11	0.83	0.82	3	-
GCA_905196835.1	s__Prevotella stercoripullorum	76.7373	55	681	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.53	95.99	0.92	0.86	5	-
GCA_000436695.1	s__Prevotella sp000436695	76.6302	84	681	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.96	98.24	0.85	0.83	3	-
GCA_905215655.1	s__Prevotella sp905215655	76.204	57	681	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 08:44:44,442] [INFO] GTDB search result was written to GCA_945981365.1_ERR2020027_bin.11_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 08:44:44,443] [INFO] ===== GTDB Search completed =====
[2023-06-08 08:44:44,446] [INFO] DFAST_QC result json was written to GCA_945981365.1_ERR2020027_bin.11_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 08:44:44,446] [INFO] DFAST_QC completed!
[2023-06-08 08:44:44,446] [INFO] Total running time: 0h1m11s