[2023-06-08 17:09:30,091] [INFO] DFAST_QC pipeline started.
[2023-06-08 17:09:30,094] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 17:09:30,094] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f485912-6025-4c28-a2c8-94537f0ec18f/dqc_reference
[2023-06-08 17:09:31,368] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 17:09:31,369] [INFO] Task started: Prodigal
[2023-06-08 17:09:31,369] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a65d094-2451-4c7e-a5e7-9bcd65f28a84/GCA_947166295.1_SRR8387717_bin.42_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947166295.1_SRR8387717_bin.42_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_947166295.1_SRR8387717_bin.42_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 17:09:32,985] [INFO] Task succeeded: Prodigal
[2023-06-08 17:09:32,986] [INFO] Task started: HMMsearch
[2023-06-08 17:09:32,986] [INFO] Running command: hmmsearch --tblout GCA_947166295.1_SRR8387717_bin.42_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f485912-6025-4c28-a2c8-94537f0ec18f/dqc_reference/reference_markers.hmm GCA_947166295.1_SRR8387717_bin.42_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 17:09:33,184] [INFO] Task succeeded: HMMsearch
[2023-06-08 17:09:33,185] [INFO] Found 6/6 markers.
[2023-06-08 17:09:33,212] [INFO] Query marker FASTA was written to GCA_947166295.1_SRR8387717_bin.42_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 17:09:33,212] [INFO] Task started: Blastn
[2023-06-08 17:09:33,212] [INFO] Running command: blastn -query GCA_947166295.1_SRR8387717_bin.42_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f485912-6025-4c28-a2c8-94537f0ec18f/dqc_reference/reference_markers.fasta -out GCA_947166295.1_SRR8387717_bin.42_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:09:33,965] [INFO] Task succeeded: Blastn
[2023-06-08 17:09:33,970] [INFO] Selected 15 target genomes.
[2023-06-08 17:09:33,970] [INFO] Target genome list was writen to GCA_947166295.1_SRR8387717_bin.42_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 17:09:33,972] [INFO] Task started: fastANI
[2023-06-08 17:09:33,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a65d094-2451-4c7e-a5e7-9bcd65f28a84/GCA_947166295.1_SRR8387717_bin.42_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947166295.1_SRR8387717_bin.42_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947166295.1_SRR8387717_bin.42_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 17:09:42,603] [INFO] Task succeeded: fastANI
[2023-06-08 17:09:42,604] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f485912-6025-4c28-a2c8-94537f0ec18f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 17:09:42,604] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f485912-6025-4c28-a2c8-94537f0ec18f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 17:09:42,606] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 17:09:42,606] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 17:09:42,606] [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
--------------------------------------------------------------------------------
[2023-06-08 17:09:42,608] [INFO] DFAST Taxonomy check result was written to GCA_947166295.1_SRR8387717_bin.42_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 17:09:42,609] [INFO] ===== Taxonomy check completed =====
[2023-06-08 17:09:42,609] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 17:09:42,609] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f485912-6025-4c28-a2c8-94537f0ec18f/dqc_reference/checkm_data
[2023-06-08 17:09:42,612] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 17:09:42,626] [INFO] Task started: CheckM
[2023-06-08 17:09:42,626] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947166295.1_SRR8387717_bin.42_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947166295.1_SRR8387717_bin.42_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_947166295.1_SRR8387717_bin.42_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 17:09:56,186] [INFO] Task succeeded: CheckM
[2023-06-08 17:09:56,187] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.95%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 17:09:56,205] [INFO] ===== Completeness check finished =====
[2023-06-08 17:09:56,206] [INFO] ===== Start GTDB Search =====
[2023-06-08 17:09:56,206] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947166295.1_SRR8387717_bin.42_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 17:09:56,207] [INFO] Task started: Blastn
[2023-06-08 17:09:56,207] [INFO] Running command: blastn -query GCA_947166295.1_SRR8387717_bin.42_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f485912-6025-4c28-a2c8-94537f0ec18f/dqc_reference/reference_markers_gtdb.fasta -out GCA_947166295.1_SRR8387717_bin.42_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:09:57,051] [INFO] Task succeeded: Blastn
[2023-06-08 17:09:57,056] [INFO] Selected 24 target genomes.
[2023-06-08 17:09:57,057] [INFO] Target genome list was writen to GCA_947166295.1_SRR8387717_bin.42_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 17:09:57,066] [INFO] Task started: fastANI
[2023-06-08 17:09:57,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a65d094-2451-4c7e-a5e7-9bcd65f28a84/GCA_947166295.1_SRR8387717_bin.42_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947166295.1_SRR8387717_bin.42_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947166295.1_SRR8387717_bin.42_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 17:10:00,399] [INFO] Task succeeded: fastANI
[2023-06-08 17:10:00,412] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 17:10:00,413] [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_017421325.1	s__Nanosyncoccus sp017421325	84.6629	166	240	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__Nanosyncoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902761145.1	s__Nanosyncoccus sp902761145	78.9154	61	240	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__Nanosyncoccus	95.0	97.81	97.81	0.96	0.96	2	-
GCA_017511645.1	s__Nanosyncoccus sp017511645	78.8369	76	240	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__Nanosyncoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004138395.1	s__Nanosyncoccus alces	78.7039	111	240	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__Nanosyncoccus	95.0	97.03	97.03	0.89	0.89	2	-
GCA_002363125.1	s__Nanosyncoccus sp002363125	78.4348	85	240	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__Nanosyncoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002350545.1	s__Nanosyncoccus sp002350545	78.4047	57	240	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__Nanosyncoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017511925.1	s__Nanosyncoccus sp017511925	78.0356	73	240	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__Nanosyncoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017962365.1	s__Nanosyncoccus sp017962365	77.5963	50	240	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__Nanosyncoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017510705.1	s__Nanosyncoccus sp017510705	77.5724	60	240	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__Nanosyncoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017431105.1	s__Nanosyncoccus sp017431105	77.3801	68	240	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__Nanosyncoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017545485.1	s__Nanosyncoccus sp017545485	77.376	59	240	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__Nanosyncoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017514025.1	s__Nanosyncoccus sp017514025	77.1879	54	240	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__Nanosyncoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017619315.1	s__Nanosyncoccus sp017619315	77.0973	51	240	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosyncoccaceae;g__Nanosyncoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 17:10:00,415] [INFO] GTDB search result was written to GCA_947166295.1_SRR8387717_bin.42_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 17:10:00,416] [INFO] ===== GTDB Search completed =====
[2023-06-08 17:10:00,419] [INFO] DFAST_QC result json was written to GCA_947166295.1_SRR8387717_bin.42_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 17:10:00,420] [INFO] DFAST_QC completed!
[2023-06-08 17:10:00,420] [INFO] Total running time: 0h0m30s