[2023-06-04 23:16:09,054] [INFO] DFAST_QC pipeline started.
[2023-06-04 23:16:09,057] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 23:16:09,057] [INFO] DQC Reference Directory: /var/lib/cwl/stg41dd7ed6-a329-4e35-b7d2-305bd1e00090/dqc_reference
[2023-06-04 23:16:10,284] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 23:16:10,285] [INFO] Task started: Prodigal
[2023-06-04 23:16:10,285] [INFO] Running command: gunzip -c /var/lib/cwl/stg8faf2e9f-a675-4c6b-9e10-950d35403fb0/GCA_934561095.1_ERR7738191_bin.21_genomic.fna.gz | prodigal -d GCA_934561095.1_ERR7738191_bin.21_genomic.fna/cds.fna -a GCA_934561095.1_ERR7738191_bin.21_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 23:16:13,551] [INFO] Task succeeded: Prodigal
[2023-06-04 23:16:13,552] [INFO] Task started: HMMsearch
[2023-06-04 23:16:13,552] [INFO] Running command: hmmsearch --tblout GCA_934561095.1_ERR7738191_bin.21_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41dd7ed6-a329-4e35-b7d2-305bd1e00090/dqc_reference/reference_markers.hmm GCA_934561095.1_ERR7738191_bin.21_genomic.fna/protein.faa > /dev/null
[2023-06-04 23:16:13,747] [INFO] Task succeeded: HMMsearch
[2023-06-04 23:16:13,748] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8faf2e9f-a675-4c6b-9e10-950d35403fb0/GCA_934561095.1_ERR7738191_bin.21_genomic.fna.gz]
[2023-06-04 23:16:13,771] [INFO] Query marker FASTA was written to GCA_934561095.1_ERR7738191_bin.21_genomic.fna/markers.fasta
[2023-06-04 23:16:13,771] [INFO] Task started: Blastn
[2023-06-04 23:16:13,771] [INFO] Running command: blastn -query GCA_934561095.1_ERR7738191_bin.21_genomic.fna/markers.fasta -db /var/lib/cwl/stg41dd7ed6-a329-4e35-b7d2-305bd1e00090/dqc_reference/reference_markers.fasta -out GCA_934561095.1_ERR7738191_bin.21_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:16:14,436] [INFO] Task succeeded: Blastn
[2023-06-04 23:16:14,440] [INFO] Selected 22 target genomes.
[2023-06-04 23:16:14,441] [INFO] Target genome list was writen to GCA_934561095.1_ERR7738191_bin.21_genomic.fna/target_genomes.txt
[2023-06-04 23:16:14,444] [INFO] Task started: fastANI
[2023-06-04 23:16:14,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg8faf2e9f-a675-4c6b-9e10-950d35403fb0/GCA_934561095.1_ERR7738191_bin.21_genomic.fna.gz --refList GCA_934561095.1_ERR7738191_bin.21_genomic.fna/target_genomes.txt --output GCA_934561095.1_ERR7738191_bin.21_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 23:16:24,271] [INFO] Task succeeded: fastANI
[2023-06-04 23:16:24,272] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41dd7ed6-a329-4e35-b7d2-305bd1e00090/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 23:16:24,272] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41dd7ed6-a329-4e35-b7d2-305bd1e00090/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 23:16:24,274] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 23:16:24,275] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 23:16:24,275] [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
--------------------------------------------------------------------------------
[2023-06-04 23:16:24,280] [INFO] DFAST Taxonomy check result was written to GCA_934561095.1_ERR7738191_bin.21_genomic.fna/tc_result.tsv
[2023-06-04 23:16:24,281] [INFO] ===== Taxonomy check completed =====
[2023-06-04 23:16:24,281] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 23:16:24,281] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41dd7ed6-a329-4e35-b7d2-305bd1e00090/dqc_reference/checkm_data
[2023-06-04 23:16:24,284] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 23:16:24,304] [INFO] Task started: CheckM
[2023-06-04 23:16:24,304] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934561095.1_ERR7738191_bin.21_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934561095.1_ERR7738191_bin.21_genomic.fna/checkm_input GCA_934561095.1_ERR7738191_bin.21_genomic.fna/checkm_result
[2023-06-04 23:16:40,848] [INFO] Task succeeded: CheckM
[2023-06-04 23:16:40,849] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 23:16:40,870] [INFO] ===== Completeness check finished =====
[2023-06-04 23:16:40,870] [INFO] ===== Start GTDB Search =====
[2023-06-04 23:16:40,871] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934561095.1_ERR7738191_bin.21_genomic.fna/markers.fasta)
[2023-06-04 23:16:40,871] [INFO] Task started: Blastn
[2023-06-04 23:16:40,871] [INFO] Running command: blastn -query GCA_934561095.1_ERR7738191_bin.21_genomic.fna/markers.fasta -db /var/lib/cwl/stg41dd7ed6-a329-4e35-b7d2-305bd1e00090/dqc_reference/reference_markers_gtdb.fasta -out GCA_934561095.1_ERR7738191_bin.21_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:16:41,936] [INFO] Task succeeded: Blastn
[2023-06-04 23:16:41,940] [INFO] Selected 9 target genomes.
[2023-06-04 23:16:41,940] [INFO] Target genome list was writen to GCA_934561095.1_ERR7738191_bin.21_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 23:16:41,943] [INFO] Task started: fastANI
[2023-06-04 23:16:41,943] [INFO] Running command: fastANI --query /var/lib/cwl/stg8faf2e9f-a675-4c6b-9e10-950d35403fb0/GCA_934561095.1_ERR7738191_bin.21_genomic.fna.gz --refList GCA_934561095.1_ERR7738191_bin.21_genomic.fna/target_genomes_gtdb.txt --output GCA_934561095.1_ERR7738191_bin.21_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 23:16:44,878] [INFO] Task succeeded: fastANI
[2023-06-04 23:16:44,890] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-04 23:16:44,890] [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_003522945.1	s__UBA738 sp003522945	89.5044	146	213	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738	95.0	97.42	97.25	0.82	0.69	7	-
GCA_002404605.1	s__UBA738 sp002404605	89.374	181	213	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738	95.0	99.68	99.62	0.91	0.89	3	-
GCA_004557735.1	s__UBA738 sp004557735	88.4794	180	213	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738	95.0	96.30	95.55	0.89	0.83	10	-
GCA_900763675.1	s__UBA738 sp900763675	85.7863	163	213	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017541825.1	s__UBA738 sp017541825	77.9477	64	213	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017411265.1	s__UBA738 sp017411265	77.5414	60	213	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 23:16:44,892] [INFO] GTDB search result was written to GCA_934561095.1_ERR7738191_bin.21_genomic.fna/result_gtdb.tsv
[2023-06-04 23:16:44,893] [INFO] ===== GTDB Search completed =====
[2023-06-04 23:16:44,895] [INFO] DFAST_QC result json was written to GCA_934561095.1_ERR7738191_bin.21_genomic.fna/dqc_result.json
[2023-06-04 23:16:44,896] [INFO] DFAST_QC completed!
[2023-06-04 23:16:44,896] [INFO] Total running time: 0h0m36s