[2023-03-16 10:48:50,397] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:48:50,398] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:48:50,398] [INFO] DQC Reference Directory: /var/lib/cwl/stg25751e04-d752-4bf4-b675-4e526fc7b590/dqc_reference
[2023-03-16 10:48:52,973] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:48:52,973] [INFO] Task started: Prodigal
[2023-03-16 10:48:52,973] [INFO] Running command: cat /var/lib/cwl/stg50de4a1e-ed46-4409-b605-9fff2cdb6cec/OceanDNA-b3547.fa | prodigal -d OceanDNA-b3547/cds.fna -a OceanDNA-b3547/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:49:19,489] [INFO] Task succeeded: Prodigal
[2023-03-16 10:49:19,489] [INFO] Task started: HMMsearch
[2023-03-16 10:49:19,489] [INFO] Running command: hmmsearch --tblout OceanDNA-b3547/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25751e04-d752-4bf4-b675-4e526fc7b590/dqc_reference/reference_markers.hmm OceanDNA-b3547/protein.faa > /dev/null
[2023-03-16 10:49:19,719] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:49:19,720] [INFO] Found 6/6 markers.
[2023-03-16 10:49:19,748] [INFO] Query marker FASTA was written to OceanDNA-b3547/markers.fasta
[2023-03-16 10:49:19,749] [INFO] Task started: Blastn
[2023-03-16 10:49:19,749] [INFO] Running command: blastn -query OceanDNA-b3547/markers.fasta -db /var/lib/cwl/stg25751e04-d752-4bf4-b675-4e526fc7b590/dqc_reference/reference_markers.fasta -out OceanDNA-b3547/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:49:20,283] [INFO] Task succeeded: Blastn
[2023-03-16 10:49:20,284] [INFO] Selected 29 target genomes.
[2023-03-16 10:49:20,284] [INFO] Target genome list was writen to OceanDNA-b3547/target_genomes.txt
[2023-03-16 10:49:20,346] [INFO] Task started: fastANI
[2023-03-16 10:49:20,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg50de4a1e-ed46-4409-b605-9fff2cdb6cec/OceanDNA-b3547.fa --refList OceanDNA-b3547/target_genomes.txt --output OceanDNA-b3547/fastani_result.tsv --threads 1
[2023-03-16 10:49:38,001] [INFO] Task succeeded: fastANI
[2023-03-16 10:49:38,001] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25751e04-d752-4bf4-b675-4e526fc7b590/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:49:38,001] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25751e04-d752-4bf4-b675-4e526fc7b590/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:49:38,002] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:49:38,002] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:49:38,002] [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
--------------------------------------------------------------------------------
[2023-03-16 10:49:38,002] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3547/tc_result.tsv
[2023-03-16 10:49:38,003] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:49:38,003] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:49:38,003] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25751e04-d752-4bf4-b675-4e526fc7b590/dqc_reference/checkm_data
[2023-03-16 10:49:38,008] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:49:38,015] [INFO] Task started: CheckM
[2023-03-16 10:49:38,015] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3547/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3547/checkm_input OceanDNA-b3547/checkm_result
[2023-03-16 10:50:39,512] [INFO] Task succeeded: CheckM
[2023-03-16 10:50:39,512] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:50:39,519] [INFO] ===== Completeness check finished =====
[2023-03-16 10:50:39,519] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:50:39,519] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3547/markers.fasta)
[2023-03-16 10:50:39,522] [INFO] Task started: Blastn
[2023-03-16 10:50:39,523] [INFO] Running command: blastn -query OceanDNA-b3547/markers.fasta -db /var/lib/cwl/stg25751e04-d752-4bf4-b675-4e526fc7b590/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3547/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:50:42,405] [INFO] Task succeeded: Blastn
[2023-03-16 10:50:42,407] [INFO] Selected 23 target genomes.
[2023-03-16 10:50:42,407] [INFO] Target genome list was writen to OceanDNA-b3547/target_genomes_gtdb.txt
[2023-03-16 10:50:42,543] [INFO] Task started: fastANI
[2023-03-16 10:50:42,544] [INFO] Running command: fastANI --query /var/lib/cwl/stg50de4a1e-ed46-4409-b605-9fff2cdb6cec/OceanDNA-b3547.fa --refList OceanDNA-b3547/target_genomes_gtdb.txt --output OceanDNA-b3547/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:51:06,040] [INFO] Task succeeded: fastANI
[2023-03-16 10:51:06,045] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:51:06,045] [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_016845105.1	s__GCA-002708315 sp016845105	77.5387	287	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013203805.1	s__GCA-002708315 sp013203805	77.1812	238	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018661505.1	s__GCA-002708315 sp018661505	76.4575	101	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	99.95	99.92	0.97	0.96	16	-
GCA_014382445.1	s__GCA-002708315 sp014382445	76.3822	131	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	99.88	99.88	0.96	0.96	2	-
GCA_002708315.1	s__GCA-002708315 sp002708315	76.3649	77	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686705.1	s__GCA-002708315 sp002686705	76.0815	102	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:51:06,046] [INFO] GTDB search result was written to OceanDNA-b3547/result_gtdb.tsv
[2023-03-16 10:51:06,047] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:51:06,048] [INFO] DFAST_QC result json was written to OceanDNA-b3547/dqc_result.json
[2023-03-16 10:51:06,048] [INFO] DFAST_QC completed!
[2023-03-16 10:51:06,048] [INFO] Total running time: 0h2m16s