[2023-06-29 16:18:37,266] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:18:37,277] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:18:37,277] [INFO] DQC Reference Directory: /var/lib/cwl/stgde2c4cb5-9eb5-482b-af5d-9ae8f73b24cd/dqc_reference
[2023-06-29 16:18:38,759] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:18:38,760] [INFO] Task started: Prodigal
[2023-06-29 16:18:38,761] [INFO] Running command: gunzip -c /var/lib/cwl/stgee4280b4-5948-495a-848c-6f0ae22ea37b/GCA_937897985.1_SRR3330157_bin.134_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937897985.1_SRR3330157_bin.134_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937897985.1_SRR3330157_bin.134_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:18:56,434] [INFO] Task succeeded: Prodigal
[2023-06-29 16:18:56,434] [INFO] Task started: HMMsearch
[2023-06-29 16:18:56,435] [INFO] Running command: hmmsearch --tblout GCA_937897985.1_SRR3330157_bin.134_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde2c4cb5-9eb5-482b-af5d-9ae8f73b24cd/dqc_reference/reference_markers.hmm GCA_937897985.1_SRR3330157_bin.134_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:18:56,740] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:18:56,741] [INFO] Found 6/6 markers.
[2023-06-29 16:18:56,787] [INFO] Query marker FASTA was written to GCA_937897985.1_SRR3330157_bin.134_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 16:18:56,788] [INFO] Task started: Blastn
[2023-06-29 16:18:56,788] [INFO] Running command: blastn -query GCA_937897985.1_SRR3330157_bin.134_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgde2c4cb5-9eb5-482b-af5d-9ae8f73b24cd/dqc_reference/reference_markers.fasta -out GCA_937897985.1_SRR3330157_bin.134_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:18:57,454] [INFO] Task succeeded: Blastn
[2023-06-29 16:18:57,458] [INFO] Selected 33 target genomes.
[2023-06-29 16:18:57,459] [INFO] Target genome list was writen to GCA_937897985.1_SRR3330157_bin.134_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 16:18:57,461] [INFO] Task started: fastANI
[2023-06-29 16:18:57,462] [INFO] Running command: fastANI --query /var/lib/cwl/stgee4280b4-5948-495a-848c-6f0ae22ea37b/GCA_937897985.1_SRR3330157_bin.134_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937897985.1_SRR3330157_bin.134_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937897985.1_SRR3330157_bin.134_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:19:19,446] [INFO] Task succeeded: fastANI
[2023-06-29 16:19:19,447] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde2c4cb5-9eb5-482b-af5d-9ae8f73b24cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:19:19,447] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde2c4cb5-9eb5-482b-af5d-9ae8f73b24cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:19:19,450] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:19:19,451] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 16:19:19,451] [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
Paludibacter propionicigenes	strain=WB4	GCA_000183135.1	185300	185300	type	True	77.1365	129	1349	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:19:19,453] [INFO] DFAST Taxonomy check result was written to GCA_937897985.1_SRR3330157_bin.134_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 16:19:19,454] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:19:19,454] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:19:19,454] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde2c4cb5-9eb5-482b-af5d-9ae8f73b24cd/dqc_reference/checkm_data
[2023-06-29 16:19:19,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:19:19,500] [INFO] Task started: CheckM
[2023-06-29 16:19:19,500] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937897985.1_SRR3330157_bin.134_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937897985.1_SRR3330157_bin.134_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937897985.1_SRR3330157_bin.134_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 16:20:11,734] [INFO] Task succeeded: CheckM
[2023-06-29 16:20:11,736] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:20:11,757] [INFO] ===== Completeness check finished =====
[2023-06-29 16:20:11,758] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:20:11,758] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937897985.1_SRR3330157_bin.134_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 16:20:11,758] [INFO] Task started: Blastn
[2023-06-29 16:20:11,758] [INFO] Running command: blastn -query GCA_937897985.1_SRR3330157_bin.134_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgde2c4cb5-9eb5-482b-af5d-9ae8f73b24cd/dqc_reference/reference_markers_gtdb.fasta -out GCA_937897985.1_SRR3330157_bin.134_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:20:12,558] [INFO] Task succeeded: Blastn
[2023-06-29 16:20:12,563] [INFO] Selected 17 target genomes.
[2023-06-29 16:20:12,563] [INFO] Target genome list was writen to GCA_937897985.1_SRR3330157_bin.134_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:20:12,568] [INFO] Task started: fastANI
[2023-06-29 16:20:12,568] [INFO] Running command: fastANI --query /var/lib/cwl/stgee4280b4-5948-495a-848c-6f0ae22ea37b/GCA_937897985.1_SRR3330157_bin.134_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937897985.1_SRR3330157_bin.134_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937897985.1_SRR3330157_bin.134_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:20:22,750] [INFO] Task succeeded: fastANI
[2023-06-29 16:20:22,766] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 16:20:22,766] [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_903912795.1	s__Paludibacter sp903912795	77.6509	153	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002427615.1	s__Paludibacter sp002427615	77.5663	222	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	99.75	99.75	0.80	0.80	2	-
GCA_009929375.1	s__Paludibacter sp009929375	77.5417	208	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017989795.1	s__Paludibacter sp017989795	77.4117	86	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016937795.1	s__Paludibacter sp016937795	77.3287	186	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018054805.1	s__Paludibacter sp018054805	77.3095	82	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873355.1	s__Paludibacter sp903873355	77.2597	110	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000183135.1	s__Paludibacter propionicigenes	77.1365	129	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903929065.1	s__Paludibacter sp903929065	77.1223	131	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903830915.1	s__Paludibacter sp903830915	77.0645	127	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002427885.1	s__Paludibacter sp002427885	77.0301	119	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903911085.1	s__Paludibacter sp903911085	77.0219	139	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	99.91	99.87	0.95	0.95	3	-
GCA_903901975.1	s__Paludibacter sp903901975	77.0082	140	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	99.91	99.88	0.94	0.92	6	-
GCA_010365115.1	s__Paludibacter sp010365115	76.8605	145	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882285.1	s__Paludibacter sp017882285	76.7966	164	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Paludibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 16:20:22,768] [INFO] GTDB search result was written to GCA_937897985.1_SRR3330157_bin.134_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 16:20:22,769] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:20:22,772] [INFO] DFAST_QC result json was written to GCA_937897985.1_SRR3330157_bin.134_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 16:20:22,772] [INFO] DFAST_QC completed!
[2023-06-29 16:20:22,772] [INFO] Total running time: 0h1m46s