[2023-06-30 12:22:36,845] [INFO] DFAST_QC pipeline started.
[2023-06-30 12:22:36,853] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 12:22:36,853] [INFO] DQC Reference Directory: /var/lib/cwl/stg755b73c7-075b-4473-8a04-885b9536930b/dqc_reference
[2023-06-30 12:22:38,529] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 12:22:38,531] [INFO] Task started: Prodigal
[2023-06-30 12:22:38,531] [INFO] Running command: gunzip -c /var/lib/cwl/stg684e6269-f936-469d-9e92-880f44acd44d/GCA_903913175.1_freshwater_MAG_---_Loclat_bin-05792_genomic.fna.gz | prodigal -d GCA_903913175.1_freshwater_MAG_---_Loclat_bin-05792_genomic.fna/cds.fna -a GCA_903913175.1_freshwater_MAG_---_Loclat_bin-05792_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 12:22:40,723] [INFO] Task succeeded: Prodigal
[2023-06-30 12:22:40,723] [INFO] Task started: HMMsearch
[2023-06-30 12:22:40,723] [INFO] Running command: hmmsearch --tblout GCA_903913175.1_freshwater_MAG_---_Loclat_bin-05792_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg755b73c7-075b-4473-8a04-885b9536930b/dqc_reference/reference_markers.hmm GCA_903913175.1_freshwater_MAG_---_Loclat_bin-05792_genomic.fna/protein.faa > /dev/null
[2023-06-30 12:22:40,927] [INFO] Task succeeded: HMMsearch
[2023-06-30 12:22:40,928] [INFO] Found 6/6 markers.
[2023-06-30 12:22:40,939] [INFO] Query marker FASTA was written to GCA_903913175.1_freshwater_MAG_---_Loclat_bin-05792_genomic.fna/markers.fasta
[2023-06-30 12:22:40,939] [INFO] Task started: Blastn
[2023-06-30 12:22:40,939] [INFO] Running command: blastn -query GCA_903913175.1_freshwater_MAG_---_Loclat_bin-05792_genomic.fna/markers.fasta -db /var/lib/cwl/stg755b73c7-075b-4473-8a04-885b9536930b/dqc_reference/reference_markers.fasta -out GCA_903913175.1_freshwater_MAG_---_Loclat_bin-05792_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:22:41,900] [INFO] Task succeeded: Blastn
[2023-06-30 12:22:41,903] [INFO] Selected 7 target genomes.
[2023-06-30 12:22:41,903] [INFO] Target genome list was writen to GCA_903913175.1_freshwater_MAG_---_Loclat_bin-05792_genomic.fna/target_genomes.txt
[2023-06-30 12:22:41,905] [INFO] Task started: fastANI
[2023-06-30 12:22:41,905] [INFO] Running command: fastANI --query /var/lib/cwl/stg684e6269-f936-469d-9e92-880f44acd44d/GCA_903913175.1_freshwater_MAG_---_Loclat_bin-05792_genomic.fna.gz --refList GCA_903913175.1_freshwater_MAG_---_Loclat_bin-05792_genomic.fna/target_genomes.txt --output GCA_903913175.1_freshwater_MAG_---_Loclat_bin-05792_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 12:22:44,412] [INFO] Task succeeded: fastANI
[2023-06-30 12:22:44,413] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg755b73c7-075b-4473-8a04-885b9536930b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 12:22:44,413] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg755b73c7-075b-4473-8a04-885b9536930b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 12:22:44,414] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 12:22:44,414] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 12:22:44,414] [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
--------------------------------------------------------------------------------
[2023-06-30 12:22:44,416] [INFO] DFAST Taxonomy check result was written to GCA_903913175.1_freshwater_MAG_---_Loclat_bin-05792_genomic.fna/tc_result.tsv
[2023-06-30 12:22:44,417] [INFO] ===== Taxonomy check completed =====
[2023-06-30 12:22:44,417] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 12:22:44,417] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg755b73c7-075b-4473-8a04-885b9536930b/dqc_reference/checkm_data
[2023-06-30 12:22:44,419] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 12:22:44,431] [INFO] Task started: CheckM
[2023-06-30 12:22:44,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903913175.1_freshwater_MAG_---_Loclat_bin-05792_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903913175.1_freshwater_MAG_---_Loclat_bin-05792_genomic.fna/checkm_input GCA_903913175.1_freshwater_MAG_---_Loclat_bin-05792_genomic.fna/checkm_result
[2023-06-30 12:22:59,615] [INFO] Task succeeded: CheckM
[2023-06-30 12:22:59,616] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.78%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 12:22:59,674] [INFO] ===== Completeness check finished =====
[2023-06-30 12:22:59,675] [INFO] ===== Start GTDB Search =====
[2023-06-30 12:22:59,675] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903913175.1_freshwater_MAG_---_Loclat_bin-05792_genomic.fna/markers.fasta)
[2023-06-30 12:22:59,675] [INFO] Task started: Blastn
[2023-06-30 12:22:59,675] [INFO] Running command: blastn -query GCA_903913175.1_freshwater_MAG_---_Loclat_bin-05792_genomic.fna/markers.fasta -db /var/lib/cwl/stg755b73c7-075b-4473-8a04-885b9536930b/dqc_reference/reference_markers_gtdb.fasta -out GCA_903913175.1_freshwater_MAG_---_Loclat_bin-05792_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:23:00,518] [INFO] Task succeeded: Blastn
[2023-06-30 12:23:00,522] [INFO] Selected 16 target genomes.
[2023-06-30 12:23:00,522] [INFO] Target genome list was writen to GCA_903913175.1_freshwater_MAG_---_Loclat_bin-05792_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 12:23:00,532] [INFO] Task started: fastANI
[2023-06-30 12:23:00,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg684e6269-f936-469d-9e92-880f44acd44d/GCA_903913175.1_freshwater_MAG_---_Loclat_bin-05792_genomic.fna.gz --refList GCA_903913175.1_freshwater_MAG_---_Loclat_bin-05792_genomic.fna/target_genomes_gtdb.txt --output GCA_903913175.1_freshwater_MAG_---_Loclat_bin-05792_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 12:23:02,775] [INFO] Task succeeded: fastANI
[2023-06-30 12:23:02,783] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 12:23:02,783] [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_903913175.1	s__XYB1-FULL-32-11 sp903913175	99.9999	197	199	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Paceibacterales;f__Staskawiczbacteraceae;g__XYB1-FULL-32-11	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001820485.1	s__XYB1-FULL-32-11 sp001820485	79.0439	72	199	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Paceibacterales;f__Staskawiczbacteraceae;g__XYB1-FULL-32-11	95.0	99.90	99.90	0.90	0.90	2	-
GCA_903850725.1	s__XYB1-FULL-32-11 sp903850725	78.0487	51	199	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Paceibacterales;f__Staskawiczbacteraceae;g__XYB1-FULL-32-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903854535.1	s__XYB1-FULL-32-11 sp903854535	77.1823	59	199	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Paceibacterales;f__Staskawiczbacteraceae;g__XYB1-FULL-32-11	95.0	99.84	99.80	0.95	0.93	4	-
--------------------------------------------------------------------------------
[2023-06-30 12:23:02,785] [INFO] GTDB search result was written to GCA_903913175.1_freshwater_MAG_---_Loclat_bin-05792_genomic.fna/result_gtdb.tsv
[2023-06-30 12:23:02,785] [INFO] ===== GTDB Search completed =====
[2023-06-30 12:23:02,788] [INFO] DFAST_QC result json was written to GCA_903913175.1_freshwater_MAG_---_Loclat_bin-05792_genomic.fna/dqc_result.json
[2023-06-30 12:23:02,788] [INFO] DFAST_QC completed!
[2023-06-30 12:23:02,788] [INFO] Total running time: 0h0m26s