[2023-06-30 10:37:51,170] [INFO] DFAST_QC pipeline started.
[2023-06-30 10:37:51,173] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 10:37:51,173] [INFO] DQC Reference Directory: /var/lib/cwl/stg640b95c6-fe99-4c59-bb00-907559e84f98/dqc_reference
[2023-06-30 10:37:52,528] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 10:37:52,529] [INFO] Task started: Prodigal
[2023-06-30 10:37:52,529] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a712b9d-9e3a-41f0-8bc0-854a38777873/GCA_903894045.1_freshwater_MAG_---_AM-lipid-02-D1_bin-1196_genomic.fna.gz | prodigal -d GCA_903894045.1_freshwater_MAG_---_AM-lipid-02-D1_bin-1196_genomic.fna/cds.fna -a GCA_903894045.1_freshwater_MAG_---_AM-lipid-02-D1_bin-1196_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 10:38:01,169] [INFO] Task succeeded: Prodigal
[2023-06-30 10:38:01,169] [INFO] Task started: HMMsearch
[2023-06-30 10:38:01,170] [INFO] Running command: hmmsearch --tblout GCA_903894045.1_freshwater_MAG_---_AM-lipid-02-D1_bin-1196_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg640b95c6-fe99-4c59-bb00-907559e84f98/dqc_reference/reference_markers.hmm GCA_903894045.1_freshwater_MAG_---_AM-lipid-02-D1_bin-1196_genomic.fna/protein.faa > /dev/null
[2023-06-30 10:38:01,465] [INFO] Task succeeded: HMMsearch
[2023-06-30 10:38:01,467] [INFO] Found 6/6 markers.
[2023-06-30 10:38:01,504] [INFO] Query marker FASTA was written to GCA_903894045.1_freshwater_MAG_---_AM-lipid-02-D1_bin-1196_genomic.fna/markers.fasta
[2023-06-30 10:38:01,505] [INFO] Task started: Blastn
[2023-06-30 10:38:01,505] [INFO] Running command: blastn -query GCA_903894045.1_freshwater_MAG_---_AM-lipid-02-D1_bin-1196_genomic.fna/markers.fasta -db /var/lib/cwl/stg640b95c6-fe99-4c59-bb00-907559e84f98/dqc_reference/reference_markers.fasta -out GCA_903894045.1_freshwater_MAG_---_AM-lipid-02-D1_bin-1196_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:38:02,284] [INFO] Task succeeded: Blastn
[2023-06-30 10:38:02,289] [INFO] Selected 21 target genomes.
[2023-06-30 10:38:02,289] [INFO] Target genome list was writen to GCA_903894045.1_freshwater_MAG_---_AM-lipid-02-D1_bin-1196_genomic.fna/target_genomes.txt
[2023-06-30 10:38:02,294] [INFO] Task started: fastANI
[2023-06-30 10:38:02,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a712b9d-9e3a-41f0-8bc0-854a38777873/GCA_903894045.1_freshwater_MAG_---_AM-lipid-02-D1_bin-1196_genomic.fna.gz --refList GCA_903894045.1_freshwater_MAG_---_AM-lipid-02-D1_bin-1196_genomic.fna/target_genomes.txt --output GCA_903894045.1_freshwater_MAG_---_AM-lipid-02-D1_bin-1196_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 10:38:17,490] [INFO] Task succeeded: fastANI
[2023-06-30 10:38:17,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg640b95c6-fe99-4c59-bb00-907559e84f98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 10:38:17,492] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg640b95c6-fe99-4c59-bb00-907559e84f98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 10:38:17,501] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2023-06-30 10:38:17,501] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-30 10:38:17,502] [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
Jezberella montanilacus	strain=MWH-P2sevCIIIb	GCA_003003055.1	323426	323426	type	True	99.2754	830	964	95	conclusive
Zwartia hollandica	strain=LF4-65	GCA_019923725.1	324606	324606	type	True	77.9135	79	964	95	below_threshold
Sheuella amnicola	strain=NBD-18	GCA_010499255.1	2707330	2707330	type	True	77.3368	73	964	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 10:38:17,504] [INFO] DFAST Taxonomy check result was written to GCA_903894045.1_freshwater_MAG_---_AM-lipid-02-D1_bin-1196_genomic.fna/tc_result.tsv
[2023-06-30 10:38:17,505] [INFO] ===== Taxonomy check completed =====
[2023-06-30 10:38:17,505] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 10:38:17,505] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg640b95c6-fe99-4c59-bb00-907559e84f98/dqc_reference/checkm_data
[2023-06-30 10:38:17,507] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 10:38:17,547] [INFO] Task started: CheckM
[2023-06-30 10:38:17,547] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903894045.1_freshwater_MAG_---_AM-lipid-02-D1_bin-1196_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903894045.1_freshwater_MAG_---_AM-lipid-02-D1_bin-1196_genomic.fna/checkm_input GCA_903894045.1_freshwater_MAG_---_AM-lipid-02-D1_bin-1196_genomic.fna/checkm_result
[2023-06-30 10:38:49,541] [INFO] Task succeeded: CheckM
[2023-06-30 10:38:49,543] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 10:38:49,566] [INFO] ===== Completeness check finished =====
[2023-06-30 10:38:49,566] [INFO] ===== Start GTDB Search =====
[2023-06-30 10:38:49,567] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903894045.1_freshwater_MAG_---_AM-lipid-02-D1_bin-1196_genomic.fna/markers.fasta)
[2023-06-30 10:38:49,567] [INFO] Task started: Blastn
[2023-06-30 10:38:49,567] [INFO] Running command: blastn -query GCA_903894045.1_freshwater_MAG_---_AM-lipid-02-D1_bin-1196_genomic.fna/markers.fasta -db /var/lib/cwl/stg640b95c6-fe99-4c59-bb00-907559e84f98/dqc_reference/reference_markers_gtdb.fasta -out GCA_903894045.1_freshwater_MAG_---_AM-lipid-02-D1_bin-1196_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:38:50,724] [INFO] Task succeeded: Blastn
[2023-06-30 10:38:50,729] [INFO] Selected 20 target genomes.
[2023-06-30 10:38:50,730] [INFO] Target genome list was writen to GCA_903894045.1_freshwater_MAG_---_AM-lipid-02-D1_bin-1196_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 10:38:50,739] [INFO] Task started: fastANI
[2023-06-30 10:38:50,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a712b9d-9e3a-41f0-8bc0-854a38777873/GCA_903894045.1_freshwater_MAG_---_AM-lipid-02-D1_bin-1196_genomic.fna.gz --refList GCA_903894045.1_freshwater_MAG_---_AM-lipid-02-D1_bin-1196_genomic.fna/target_genomes_gtdb.txt --output GCA_903894045.1_freshwater_MAG_---_AM-lipid-02-D1_bin-1196_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 10:39:02,315] [INFO] Task succeeded: fastANI
[2023-06-30 10:39:02,328] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 10:39:02,328] [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_003003055.1	s__NBD-18 sp003003055	99.2754	830	964	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	99.26	99.12	0.90	0.84	10	conclusive
GCA_903924715.1	s__NBD-18 sp903924715	77.9419	66	964	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013205565.1	s__NBD-18 sp013205565	77.4184	86	964	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010499255.1	s__NBD-18 sp003507735	77.4156	71	964	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	99.47	99.47	0.95	0.95	2	-
GCA_903958565.1	s__NBD-18 sp903958565	77.387	83	964	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	99.16	98.92	0.86	0.85	5	-
GCA_002292845.1	s__NBD-18 sp002292845	76.9636	60	964	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002737415.1	s__NBD-18 sp002737415	76.9371	92	964	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903821335.1	s__NBD-18 sp903821335	76.8871	92	964	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	99.43	99.29	0.86	0.84	5	-
--------------------------------------------------------------------------------
[2023-06-30 10:39:02,330] [INFO] GTDB search result was written to GCA_903894045.1_freshwater_MAG_---_AM-lipid-02-D1_bin-1196_genomic.fna/result_gtdb.tsv
[2023-06-30 10:39:02,331] [INFO] ===== GTDB Search completed =====
[2023-06-30 10:39:02,334] [INFO] DFAST_QC result json was written to GCA_903894045.1_freshwater_MAG_---_AM-lipid-02-D1_bin-1196_genomic.fna/dqc_result.json
[2023-06-30 10:39:02,335] [INFO] DFAST_QC completed!
[2023-06-30 10:39:02,335] [INFO] Total running time: 0h1m11s