[2023-06-29 22:41:55,587] [INFO] DFAST_QC pipeline started.
[2023-06-29 22:41:55,590] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 22:41:55,590] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe41b782-9460-4c4b-b687-3d318d0621c0/dqc_reference
[2023-06-29 22:41:58,157] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 22:41:58,158] [INFO] Task started: Prodigal
[2023-06-29 22:41:58,158] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e3571d5-f58a-4014-a70c-ae179fe35783/GCA_903867775.1_freshwater_MAG_---_AM-sed-core2-D2_bin-198_genomic.fna.gz | prodigal -d GCA_903867775.1_freshwater_MAG_---_AM-sed-core2-D2_bin-198_genomic.fna/cds.fna -a GCA_903867775.1_freshwater_MAG_---_AM-sed-core2-D2_bin-198_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 22:42:02,116] [INFO] Task succeeded: Prodigal
[2023-06-29 22:42:02,116] [INFO] Task started: HMMsearch
[2023-06-29 22:42:02,117] [INFO] Running command: hmmsearch --tblout GCA_903867775.1_freshwater_MAG_---_AM-sed-core2-D2_bin-198_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe41b782-9460-4c4b-b687-3d318d0621c0/dqc_reference/reference_markers.hmm GCA_903867775.1_freshwater_MAG_---_AM-sed-core2-D2_bin-198_genomic.fna/protein.faa > /dev/null
[2023-06-29 22:42:02,330] [INFO] Task succeeded: HMMsearch
[2023-06-29 22:42:02,332] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg8e3571d5-f58a-4014-a70c-ae179fe35783/GCA_903867775.1_freshwater_MAG_---_AM-sed-core2-D2_bin-198_genomic.fna.gz]
[2023-06-29 22:42:02,364] [INFO] Query marker FASTA was written to GCA_903867775.1_freshwater_MAG_---_AM-sed-core2-D2_bin-198_genomic.fna/markers.fasta
[2023-06-29 22:42:02,364] [INFO] Task started: Blastn
[2023-06-29 22:42:02,365] [INFO] Running command: blastn -query GCA_903867775.1_freshwater_MAG_---_AM-sed-core2-D2_bin-198_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe41b782-9460-4c4b-b687-3d318d0621c0/dqc_reference/reference_markers.fasta -out GCA_903867775.1_freshwater_MAG_---_AM-sed-core2-D2_bin-198_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:42:03,082] [INFO] Task succeeded: Blastn
[2023-06-29 22:42:03,087] [INFO] Selected 5 target genomes.
[2023-06-29 22:42:03,087] [INFO] Target genome list was writen to GCA_903867775.1_freshwater_MAG_---_AM-sed-core2-D2_bin-198_genomic.fna/target_genomes.txt
[2023-06-29 22:42:03,090] [INFO] Task started: fastANI
[2023-06-29 22:42:03,091] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e3571d5-f58a-4014-a70c-ae179fe35783/GCA_903867775.1_freshwater_MAG_---_AM-sed-core2-D2_bin-198_genomic.fna.gz --refList GCA_903867775.1_freshwater_MAG_---_AM-sed-core2-D2_bin-198_genomic.fna/target_genomes.txt --output GCA_903867775.1_freshwater_MAG_---_AM-sed-core2-D2_bin-198_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 22:42:06,102] [INFO] Task succeeded: fastANI
[2023-06-29 22:42:06,102] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe41b782-9460-4c4b-b687-3d318d0621c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 22:42:06,103] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe41b782-9460-4c4b-b687-3d318d0621c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 22:42:06,105] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 22:42:06,105] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 22:42:06,106] [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
--------------------------------------------------------------------------------
[2023-06-29 22:42:06,108] [INFO] DFAST Taxonomy check result was written to GCA_903867775.1_freshwater_MAG_---_AM-sed-core2-D2_bin-198_genomic.fna/tc_result.tsv
[2023-06-29 22:42:06,109] [INFO] ===== Taxonomy check completed =====
[2023-06-29 22:42:06,109] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 22:42:06,110] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe41b782-9460-4c4b-b687-3d318d0621c0/dqc_reference/checkm_data
[2023-06-29 22:42:06,114] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 22:42:06,137] [INFO] Task started: CheckM
[2023-06-29 22:42:06,137] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903867775.1_freshwater_MAG_---_AM-sed-core2-D2_bin-198_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903867775.1_freshwater_MAG_---_AM-sed-core2-D2_bin-198_genomic.fna/checkm_input GCA_903867775.1_freshwater_MAG_---_AM-sed-core2-D2_bin-198_genomic.fna/checkm_result
[2023-06-29 22:42:28,284] [INFO] Task succeeded: CheckM
[2023-06-29 22:42:28,286] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 4.55%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-29 22:42:28,307] [INFO] ===== Completeness check finished =====
[2023-06-29 22:42:28,307] [INFO] ===== Start GTDB Search =====
[2023-06-29 22:42:28,307] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903867775.1_freshwater_MAG_---_AM-sed-core2-D2_bin-198_genomic.fna/markers.fasta)
[2023-06-29 22:42:28,308] [INFO] Task started: Blastn
[2023-06-29 22:42:28,308] [INFO] Running command: blastn -query GCA_903867775.1_freshwater_MAG_---_AM-sed-core2-D2_bin-198_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe41b782-9460-4c4b-b687-3d318d0621c0/dqc_reference/reference_markers_gtdb.fasta -out GCA_903867775.1_freshwater_MAG_---_AM-sed-core2-D2_bin-198_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:42:28,988] [INFO] Task succeeded: Blastn
[2023-06-29 22:42:28,992] [INFO] Selected 7 target genomes.
[2023-06-29 22:42:28,992] [INFO] Target genome list was writen to GCA_903867775.1_freshwater_MAG_---_AM-sed-core2-D2_bin-198_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 22:42:28,997] [INFO] Task started: fastANI
[2023-06-29 22:42:28,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e3571d5-f58a-4014-a70c-ae179fe35783/GCA_903867775.1_freshwater_MAG_---_AM-sed-core2-D2_bin-198_genomic.fna.gz --refList GCA_903867775.1_freshwater_MAG_---_AM-sed-core2-D2_bin-198_genomic.fna/target_genomes_gtdb.txt --output GCA_903867775.1_freshwater_MAG_---_AM-sed-core2-D2_bin-198_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 22:42:32,710] [INFO] Task succeeded: fastANI
[2023-06-29 22:42:32,796] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 22:42:32,797] [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_903871465.1	s__Methanothrix sp903871465	94.8122	346	369	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanotrichales;f__Methanotrichaceae;g__Methanothrix	95.0	99.90	99.77	0.96	0.93	9	-
GCA_016927055.1	s__Methanothrix sp016927055	80.0369	181	369	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanotrichales;f__Methanotrichaceae;g__Methanothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902385025.1	s__Methanothrix sp902385025	78.9058	133	369	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanotrichales;f__Methanotrichaceae;g__Methanothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000204415.1	s__Methanothrix soehngenii	78.8783	160	369	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanotrichales;f__Methanotrichaceae;g__Methanothrix	95.0	98.33	96.33	0.94	0.87	11	-
GCA_002067705.1	s__Methanothrix sp002067705	78.4103	164	369	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanotrichales;f__Methanotrichaceae;g__Methanothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002067755.1	s__Methanothrix sp002067755	78.1813	130	369	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanotrichales;f__Methanotrichaceae;g__Methanothrix	95.0	99.67	99.61	0.92	0.90	3	-
GCA_002067365.1	s__Methanothrix sp002067365	77.6936	104	369	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanotrichales;f__Methanotrichaceae;g__Methanothrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 22:42:32,799] [INFO] GTDB search result was written to GCA_903867775.1_freshwater_MAG_---_AM-sed-core2-D2_bin-198_genomic.fna/result_gtdb.tsv
[2023-06-29 22:42:32,800] [INFO] ===== GTDB Search completed =====
[2023-06-29 22:42:32,808] [INFO] DFAST_QC result json was written to GCA_903867775.1_freshwater_MAG_---_AM-sed-core2-D2_bin-198_genomic.fna/dqc_result.json
[2023-06-29 22:42:32,810] [INFO] DFAST_QC completed!
[2023-06-29 22:42:32,810] [INFO] Total running time: 0h0m37s