[2023-06-30 13:24:10,092] [INFO] DFAST_QC pipeline started.
[2023-06-30 13:24:10,095] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 13:24:10,095] [INFO] DQC Reference Directory: /var/lib/cwl/stge3346f77-3125-4500-b472-44fac6751003/dqc_reference
[2023-06-30 13:24:11,338] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 13:24:11,340] [INFO] Task started: Prodigal
[2023-06-30 13:24:11,341] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf4dbfe5-9ca0-4e4f-9393-3f440551ed23/GCA_900751035.1_SRS820614_56_genomic.fna.gz | prodigal -d GCA_900751035.1_SRS820614_56_genomic.fna/cds.fna -a GCA_900751035.1_SRS820614_56_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 13:24:17,315] [INFO] Task succeeded: Prodigal
[2023-06-30 13:24:17,316] [INFO] Task started: HMMsearch
[2023-06-30 13:24:17,316] [INFO] Running command: hmmsearch --tblout GCA_900751035.1_SRS820614_56_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3346f77-3125-4500-b472-44fac6751003/dqc_reference/reference_markers.hmm GCA_900751035.1_SRS820614_56_genomic.fna/protein.faa > /dev/null
[2023-06-30 13:24:17,579] [INFO] Task succeeded: HMMsearch
[2023-06-30 13:24:17,581] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgcf4dbfe5-9ca0-4e4f-9393-3f440551ed23/GCA_900751035.1_SRS820614_56_genomic.fna.gz]
[2023-06-30 13:24:17,608] [INFO] Query marker FASTA was written to GCA_900751035.1_SRS820614_56_genomic.fna/markers.fasta
[2023-06-30 13:24:17,609] [INFO] Task started: Blastn
[2023-06-30 13:24:17,609] [INFO] Running command: blastn -query GCA_900751035.1_SRS820614_56_genomic.fna/markers.fasta -db /var/lib/cwl/stge3346f77-3125-4500-b472-44fac6751003/dqc_reference/reference_markers.fasta -out GCA_900751035.1_SRS820614_56_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:24:18,216] [INFO] Task succeeded: Blastn
[2023-06-30 13:24:18,220] [INFO] Selected 20 target genomes.
[2023-06-30 13:24:18,220] [INFO] Target genome list was writen to GCA_900751035.1_SRS820614_56_genomic.fna/target_genomes.txt
[2023-06-30 13:24:18,223] [INFO] Task started: fastANI
[2023-06-30 13:24:18,224] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf4dbfe5-9ca0-4e4f-9393-3f440551ed23/GCA_900751035.1_SRS820614_56_genomic.fna.gz --refList GCA_900751035.1_SRS820614_56_genomic.fna/target_genomes.txt --output GCA_900751035.1_SRS820614_56_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 13:24:30,480] [INFO] Task succeeded: fastANI
[2023-06-30 13:24:30,481] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3346f77-3125-4500-b472-44fac6751003/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 13:24:30,481] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3346f77-3125-4500-b472-44fac6751003/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 13:24:30,483] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 13:24:30,484] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 13:24:30,484] [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 13:24:30,486] [INFO] DFAST Taxonomy check result was written to GCA_900751035.1_SRS820614_56_genomic.fna/tc_result.tsv
[2023-06-30 13:24:30,487] [INFO] ===== Taxonomy check completed =====
[2023-06-30 13:24:30,487] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 13:24:30,488] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3346f77-3125-4500-b472-44fac6751003/dqc_reference/checkm_data
[2023-06-30 13:24:30,492] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 13:24:30,535] [INFO] Task started: CheckM
[2023-06-30 13:24:30,536] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900751035.1_SRS820614_56_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900751035.1_SRS820614_56_genomic.fna/checkm_input GCA_900751035.1_SRS820614_56_genomic.fna/checkm_result
[2023-06-30 13:24:54,669] [INFO] Task succeeded: CheckM
[2023-06-30 13:24:54,670] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.77%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 13:24:54,693] [INFO] ===== Completeness check finished =====
[2023-06-30 13:24:54,694] [INFO] ===== Start GTDB Search =====
[2023-06-30 13:24:54,694] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900751035.1_SRS820614_56_genomic.fna/markers.fasta)
[2023-06-30 13:24:54,694] [INFO] Task started: Blastn
[2023-06-30 13:24:54,695] [INFO] Running command: blastn -query GCA_900751035.1_SRS820614_56_genomic.fna/markers.fasta -db /var/lib/cwl/stge3346f77-3125-4500-b472-44fac6751003/dqc_reference/reference_markers_gtdb.fasta -out GCA_900751035.1_SRS820614_56_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:24:55,634] [INFO] Task succeeded: Blastn
[2023-06-30 13:24:55,638] [INFO] Selected 7 target genomes.
[2023-06-30 13:24:55,638] [INFO] Target genome list was writen to GCA_900751035.1_SRS820614_56_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 13:24:55,642] [INFO] Task started: fastANI
[2023-06-30 13:24:55,643] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf4dbfe5-9ca0-4e4f-9393-3f440551ed23/GCA_900751035.1_SRS820614_56_genomic.fna.gz --refList GCA_900751035.1_SRS820614_56_genomic.fna/target_genomes_gtdb.txt --output GCA_900751035.1_SRS820614_56_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 13:24:59,420] [INFO] Task succeeded: fastANI
[2023-06-30 13:24:59,433] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 13:24:59,433] [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_900751035.1	s__CAG-170 sp900751035	100.0	661	668	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000432135.1	s__CAG-170 sp000432135	91.5753	414	668	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	98.47	98.15	0.85	0.82	4	-
GCA_902796245.1	s__CAG-170 sp902796245	88.8883	318	668	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545925.1	s__CAG-170 sp900545925	88.7995	444	668	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	98.27	97.70	0.79	0.64	4	-
GCA_002404795.1	s__CAG-170 sp002404795	84.145	316	668	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	95.77	95.28	0.76	0.71	13	-
GCA_002437575.1	s__CAG-170 sp002437575	79.7877	167	668	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549635.1	s__CAG-170 sp900549635	79.0707	166	668	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	97.02	95.99	0.80	0.73	4	-
--------------------------------------------------------------------------------
[2023-06-30 13:24:59,436] [INFO] GTDB search result was written to GCA_900751035.1_SRS820614_56_genomic.fna/result_gtdb.tsv
[2023-06-30 13:24:59,437] [INFO] ===== GTDB Search completed =====
[2023-06-30 13:24:59,441] [INFO] DFAST_QC result json was written to GCA_900751035.1_SRS820614_56_genomic.fna/dqc_result.json
[2023-06-30 13:24:59,441] [INFO] DFAST_QC completed!
[2023-06-30 13:24:59,441] [INFO] Total running time: 0h0m49s