[2023-03-18 21:07:03,640] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:07:03,641] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:07:03,641] [INFO] DQC Reference Directory: /var/lib/cwl/stg3720eba8-90bd-45fa-99e9-99cdb4024bee/dqc_reference
[2023-03-18 21:07:05,389] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:07:05,389] [INFO] Task started: Prodigal
[2023-03-18 21:07:05,389] [INFO] Running command: cat /var/lib/cwl/stg7f026b39-24c9-4432-8487-de6a966b0c57/OceanDNA-b4170.fa | prodigal -d OceanDNA-b4170/cds.fna -a OceanDNA-b4170/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:07:24,830] [INFO] Task succeeded: Prodigal
[2023-03-18 21:07:24,830] [INFO] Task started: HMMsearch
[2023-03-18 21:07:24,830] [INFO] Running command: hmmsearch --tblout OceanDNA-b4170/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3720eba8-90bd-45fa-99e9-99cdb4024bee/dqc_reference/reference_markers.hmm OceanDNA-b4170/protein.faa > /dev/null
[2023-03-18 21:07:25,036] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:07:25,036] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7f026b39-24c9-4432-8487-de6a966b0c57/OceanDNA-b4170.fa]
[2023-03-18 21:07:25,055] [INFO] Query marker FASTA was written to OceanDNA-b4170/markers.fasta
[2023-03-18 21:07:25,056] [INFO] Task started: Blastn
[2023-03-18 21:07:25,056] [INFO] Running command: blastn -query OceanDNA-b4170/markers.fasta -db /var/lib/cwl/stg3720eba8-90bd-45fa-99e9-99cdb4024bee/dqc_reference/reference_markers.fasta -out OceanDNA-b4170/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:07:25,610] [INFO] Task succeeded: Blastn
[2023-03-18 21:07:25,611] [INFO] Selected 22 target genomes.
[2023-03-18 21:07:25,611] [INFO] Target genome list was writen to OceanDNA-b4170/target_genomes.txt
[2023-03-18 21:07:25,625] [INFO] Task started: fastANI
[2023-03-18 21:07:25,625] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f026b39-24c9-4432-8487-de6a966b0c57/OceanDNA-b4170.fa --refList OceanDNA-b4170/target_genomes.txt --output OceanDNA-b4170/fastani_result.tsv --threads 1
[2023-03-18 21:07:41,020] [INFO] Task succeeded: fastANI
[2023-03-18 21:07:41,021] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3720eba8-90bd-45fa-99e9-99cdb4024bee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:07:41,021] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3720eba8-90bd-45fa-99e9-99cdb4024bee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:07:41,021] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:07:41,021] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:07:41,021] [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
--------------------------------------------------------------------------------
[2023-03-18 21:07:41,021] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4170/tc_result.tsv
[2023-03-18 21:07:41,021] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:07:41,021] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:07:41,022] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3720eba8-90bd-45fa-99e9-99cdb4024bee/dqc_reference/checkm_data
[2023-03-18 21:07:41,024] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:07:41,036] [INFO] Task started: CheckM
[2023-03-18 21:07:41,036] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4170/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4170/checkm_input OceanDNA-b4170/checkm_result
[2023-03-18 21:08:32,752] [INFO] Task succeeded: CheckM
[2023-03-18 21:08:32,752] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:08:32,807] [INFO] ===== Completeness check finished =====
[2023-03-18 21:08:32,807] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:08:32,807] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4170/markers.fasta)
[2023-03-18 21:08:32,808] [INFO] Task started: Blastn
[2023-03-18 21:08:32,808] [INFO] Running command: blastn -query OceanDNA-b4170/markers.fasta -db /var/lib/cwl/stg3720eba8-90bd-45fa-99e9-99cdb4024bee/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4170/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:08:33,708] [INFO] Task succeeded: Blastn
[2023-03-18 21:08:33,709] [INFO] Selected 8 target genomes.
[2023-03-18 21:08:33,709] [INFO] Target genome list was writen to OceanDNA-b4170/target_genomes_gtdb.txt
[2023-03-18 21:08:33,774] [INFO] Task started: fastANI
[2023-03-18 21:08:33,774] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f026b39-24c9-4432-8487-de6a966b0c57/OceanDNA-b4170.fa --refList OceanDNA-b4170/target_genomes_gtdb.txt --output OceanDNA-b4170/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:08:38,464] [INFO] Task succeeded: fastANI
[2023-03-18 21:08:38,468] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:08:38,468] [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_905182375.1	s__UBA4465 sp905182375	99.083	758	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905479015.1	s__UBA4465 sp002470835	93.5588	805	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	99.62	98.40	0.95	0.92	11	-
GCA_002292365.1	s__UBA4465 sp002292365	93.4355	689	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	99.58	99.58	0.82	0.82	2	-
GCA_905182655.1	s__UBA4465 sp905182655	87.7302	464	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691385.1	s__UBA4465 sp002691385	83.5216	610	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902605755.1	s__UBA4465 sp902605755	80.1637	326	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:08:38,474] [INFO] GTDB search result was written to OceanDNA-b4170/result_gtdb.tsv
[2023-03-18 21:08:38,475] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:08:38,475] [INFO] DFAST_QC result json was written to OceanDNA-b4170/dqc_result.json
[2023-03-18 21:08:38,475] [INFO] DFAST_QC completed!
[2023-03-18 21:08:38,475] [INFO] Total running time: 0h1m35s