[2023-07-01 04:39:33,193] [INFO] DFAST_QC pipeline started.
[2023-07-01 04:39:33,194] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 04:39:33,195] [INFO] DQC Reference Directory: /var/lib/cwl/stg79394ebf-3c1d-4c0e-80ec-eaaf46182b34/dqc_reference
[2023-07-01 04:39:34,387] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 04:39:34,388] [INFO] Task started: Prodigal
[2023-07-01 04:39:34,388] [INFO] Running command: gunzip -c /var/lib/cwl/stgba57d89d-fcf6-47cd-a3fb-e4cc49938867/GCA_903900355.1_freshwater_MAG_---_MJ120516A_bin-685_genomic.fna.gz | prodigal -d GCA_903900355.1_freshwater_MAG_---_MJ120516A_bin-685_genomic.fna/cds.fna -a GCA_903900355.1_freshwater_MAG_---_MJ120516A_bin-685_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 04:39:36,848] [INFO] Task succeeded: Prodigal
[2023-07-01 04:39:36,849] [INFO] Task started: HMMsearch
[2023-07-01 04:39:36,849] [INFO] Running command: hmmsearch --tblout GCA_903900355.1_freshwater_MAG_---_MJ120516A_bin-685_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79394ebf-3c1d-4c0e-80ec-eaaf46182b34/dqc_reference/reference_markers.hmm GCA_903900355.1_freshwater_MAG_---_MJ120516A_bin-685_genomic.fna/protein.faa > /dev/null
[2023-07-01 04:39:36,997] [INFO] Task succeeded: HMMsearch
[2023-07-01 04:39:36,998] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgba57d89d-fcf6-47cd-a3fb-e4cc49938867/GCA_903900355.1_freshwater_MAG_---_MJ120516A_bin-685_genomic.fna.gz]
[2023-07-01 04:39:37,013] [INFO] Query marker FASTA was written to GCA_903900355.1_freshwater_MAG_---_MJ120516A_bin-685_genomic.fna/markers.fasta
[2023-07-01 04:39:37,014] [INFO] Task started: Blastn
[2023-07-01 04:39:37,014] [INFO] Running command: blastn -query GCA_903900355.1_freshwater_MAG_---_MJ120516A_bin-685_genomic.fna/markers.fasta -db /var/lib/cwl/stg79394ebf-3c1d-4c0e-80ec-eaaf46182b34/dqc_reference/reference_markers.fasta -out GCA_903900355.1_freshwater_MAG_---_MJ120516A_bin-685_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:39:37,565] [INFO] Task succeeded: Blastn
[2023-07-01 04:39:37,568] [INFO] Selected 25 target genomes.
[2023-07-01 04:39:37,569] [INFO] Target genome list was writen to GCA_903900355.1_freshwater_MAG_---_MJ120516A_bin-685_genomic.fna/target_genomes.txt
[2023-07-01 04:39:37,569] [INFO] Task started: fastANI
[2023-07-01 04:39:37,569] [INFO] Running command: fastANI --query /var/lib/cwl/stgba57d89d-fcf6-47cd-a3fb-e4cc49938867/GCA_903900355.1_freshwater_MAG_---_MJ120516A_bin-685_genomic.fna.gz --refList GCA_903900355.1_freshwater_MAG_---_MJ120516A_bin-685_genomic.fna/target_genomes.txt --output GCA_903900355.1_freshwater_MAG_---_MJ120516A_bin-685_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 04:39:49,323] [INFO] Task succeeded: fastANI
[2023-07-01 04:39:49,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79394ebf-3c1d-4c0e-80ec-eaaf46182b34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 04:39:49,324] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79394ebf-3c1d-4c0e-80ec-eaaf46182b34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 04:39:49,326] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 04:39:49,326] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 04:39:49,326] [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
--------------------------------------------------------------------------------
[2023-07-01 04:39:49,327] [INFO] DFAST Taxonomy check result was written to GCA_903900355.1_freshwater_MAG_---_MJ120516A_bin-685_genomic.fna/tc_result.tsv
[2023-07-01 04:39:49,328] [INFO] ===== Taxonomy check completed =====
[2023-07-01 04:39:49,328] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 04:39:49,328] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79394ebf-3c1d-4c0e-80ec-eaaf46182b34/dqc_reference/checkm_data
[2023-07-01 04:39:49,331] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 04:39:49,347] [INFO] Task started: CheckM
[2023-07-01 04:39:49,348] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903900355.1_freshwater_MAG_---_MJ120516A_bin-685_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903900355.1_freshwater_MAG_---_MJ120516A_bin-685_genomic.fna/checkm_input GCA_903900355.1_freshwater_MAG_---_MJ120516A_bin-685_genomic.fna/checkm_result
[2023-07-01 04:40:03,583] [INFO] Task succeeded: CheckM
[2023-07-01 04:40:03,584] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 04:40:03,599] [INFO] ===== Completeness check finished =====
[2023-07-01 04:40:03,599] [INFO] ===== Start GTDB Search =====
[2023-07-01 04:40:03,600] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903900355.1_freshwater_MAG_---_MJ120516A_bin-685_genomic.fna/markers.fasta)
[2023-07-01 04:40:03,600] [INFO] Task started: Blastn
[2023-07-01 04:40:03,600] [INFO] Running command: blastn -query GCA_903900355.1_freshwater_MAG_---_MJ120516A_bin-685_genomic.fna/markers.fasta -db /var/lib/cwl/stg79394ebf-3c1d-4c0e-80ec-eaaf46182b34/dqc_reference/reference_markers_gtdb.fasta -out GCA_903900355.1_freshwater_MAG_---_MJ120516A_bin-685_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:40:04,306] [INFO] Task succeeded: Blastn
[2023-07-01 04:40:04,309] [INFO] Selected 12 target genomes.
[2023-07-01 04:40:04,310] [INFO] Target genome list was writen to GCA_903900355.1_freshwater_MAG_---_MJ120516A_bin-685_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 04:40:04,310] [INFO] Task started: fastANI
[2023-07-01 04:40:04,311] [INFO] Running command: fastANI --query /var/lib/cwl/stgba57d89d-fcf6-47cd-a3fb-e4cc49938867/GCA_903900355.1_freshwater_MAG_---_MJ120516A_bin-685_genomic.fna.gz --refList GCA_903900355.1_freshwater_MAG_---_MJ120516A_bin-685_genomic.fna/target_genomes_gtdb.txt --output GCA_903900355.1_freshwater_MAG_---_MJ120516A_bin-685_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 04:40:09,439] [INFO] Task succeeded: fastANI
[2023-07-01 04:40:09,446] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 04:40:09,446] [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_903863905.1	s__KS41 sp903863905	98.8484	153	157	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.63	99.29	0.91	0.83	33	conclusive
GCA_903839855.1	s__KS41 sp903839855	80.3199	74	157	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.93	99.90	0.95	0.94	3	-
GCA_003584865.1	s__KS41 sp003584865	80.0177	62	157	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.03	97.03	0.84	0.75	9	-
GCA_903917345.1	s__KS41 sp903917345	79.7354	55	157	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.26	98.86	0.95	0.89	10	-
GCA_903859415.1	s__KS41 sp903859415	79.6495	77	157	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.28	98.83	0.89	0.85	3	-
GCA_903866825.1	s__KS41 sp903866825	79.5539	69	157	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.82	99.82	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-07-01 04:40:09,448] [INFO] GTDB search result was written to GCA_903900355.1_freshwater_MAG_---_MJ120516A_bin-685_genomic.fna/result_gtdb.tsv
[2023-07-01 04:40:09,448] [INFO] ===== GTDB Search completed =====
[2023-07-01 04:40:09,450] [INFO] DFAST_QC result json was written to GCA_903900355.1_freshwater_MAG_---_MJ120516A_bin-685_genomic.fna/dqc_result.json
[2023-07-01 04:40:09,450] [INFO] DFAST_QC completed!
[2023-07-01 04:40:09,450] [INFO] Total running time: 0h0m36s