[2023-03-15 03:54:07,372] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:54:07,374] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:54:07,374] [INFO] DQC Reference Directory: /var/lib/cwl/stg36938ae5-f2d6-447b-90bf-5cdfe1aed20f/dqc_reference
[2023-03-15 03:54:08,477] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:54:08,478] [INFO] Task started: Prodigal
[2023-03-15 03:54:08,478] [INFO] Running command: cat /var/lib/cwl/stg93a45464-653a-4ef5-a79a-a4be2eb06d93/OceanDNA-b12504.fa | prodigal -d OceanDNA-b12504/cds.fna -a OceanDNA-b12504/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:54:39,096] [INFO] Task succeeded: Prodigal
[2023-03-15 03:54:39,096] [INFO] Task started: HMMsearch
[2023-03-15 03:54:39,096] [INFO] Running command: hmmsearch --tblout OceanDNA-b12504/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36938ae5-f2d6-447b-90bf-5cdfe1aed20f/dqc_reference/reference_markers.hmm OceanDNA-b12504/protein.faa > /dev/null
[2023-03-15 03:54:39,309] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:54:39,310] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg93a45464-653a-4ef5-a79a-a4be2eb06d93/OceanDNA-b12504.fa]
[2023-03-15 03:54:39,358] [INFO] Query marker FASTA was written to OceanDNA-b12504/markers.fasta
[2023-03-15 03:54:39,360] [INFO] Task started: Blastn
[2023-03-15 03:54:39,360] [INFO] Running command: blastn -query OceanDNA-b12504/markers.fasta -db /var/lib/cwl/stg36938ae5-f2d6-447b-90bf-5cdfe1aed20f/dqc_reference/reference_markers.fasta -out OceanDNA-b12504/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:54:39,934] [INFO] Task succeeded: Blastn
[2023-03-15 03:54:39,943] [INFO] Selected 23 target genomes.
[2023-03-15 03:54:39,943] [INFO] Target genome list was writen to OceanDNA-b12504/target_genomes.txt
[2023-03-15 03:54:39,959] [INFO] Task started: fastANI
[2023-03-15 03:54:39,959] [INFO] Running command: fastANI --query /var/lib/cwl/stg93a45464-653a-4ef5-a79a-a4be2eb06d93/OceanDNA-b12504.fa --refList OceanDNA-b12504/target_genomes.txt --output OceanDNA-b12504/fastani_result.tsv --threads 1
[2023-03-15 03:54:55,672] [INFO] Task succeeded: fastANI
[2023-03-15 03:54:55,672] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36938ae5-f2d6-447b-90bf-5cdfe1aed20f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:54:55,672] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36938ae5-f2d6-447b-90bf-5cdfe1aed20f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:54:55,672] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:54:55,672] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 03:54:55,672] [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
--------------------------------------------------------------------------------
[2023-03-15 03:54:55,676] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12504/tc_result.tsv
[2023-03-15 03:54:55,683] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:54:55,683] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:54:55,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36938ae5-f2d6-447b-90bf-5cdfe1aed20f/dqc_reference/checkm_data
[2023-03-15 03:54:55,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:54:55,746] [INFO] Task started: CheckM
[2023-03-15 03:54:55,746] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12504/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12504/checkm_input OceanDNA-b12504/checkm_result
[2023-03-15 03:56:13,550] [INFO] Task succeeded: CheckM
[2023-03-15 03:56:13,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:56:13,585] [INFO] ===== Completeness check finished =====
[2023-03-15 03:56:13,585] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:56:13,585] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12504/markers.fasta)
[2023-03-15 03:56:13,587] [INFO] Task started: Blastn
[2023-03-15 03:56:13,587] [INFO] Running command: blastn -query OceanDNA-b12504/markers.fasta -db /var/lib/cwl/stg36938ae5-f2d6-447b-90bf-5cdfe1aed20f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12504/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:56:14,611] [INFO] Task succeeded: Blastn
[2023-03-15 03:56:14,632] [INFO] Selected 24 target genomes.
[2023-03-15 03:56:14,632] [INFO] Target genome list was writen to OceanDNA-b12504/target_genomes_gtdb.txt
[2023-03-15 03:56:14,664] [INFO] Task started: fastANI
[2023-03-15 03:56:14,664] [INFO] Running command: fastANI --query /var/lib/cwl/stg93a45464-653a-4ef5-a79a-a4be2eb06d93/OceanDNA-b12504.fa --refList OceanDNA-b12504/target_genomes_gtdb.txt --output OceanDNA-b12504/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:56:27,207] [INFO] Task succeeded: fastANI
[2023-03-15 03:56:27,210] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:56:27,210] [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_016124845.1	s__UBA10329 sp016124845	78.5241	335	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10329;g__UBA10329	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402015.1	s__UBA10329 sp018402015	77.2346	216	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10329;g__UBA10329	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003456455.1	s__UBA10329 sp003456455	77.0666	130	1255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10329;g__UBA10329	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 03:56:27,215] [INFO] GTDB search result was written to OceanDNA-b12504/result_gtdb.tsv
[2023-03-15 03:56:27,227] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:56:27,232] [INFO] DFAST_QC result json was written to OceanDNA-b12504/dqc_result.json
[2023-03-15 03:56:27,233] [INFO] DFAST_QC completed!
[2023-03-15 03:56:27,233] [INFO] Total running time: 0h2m20s