[2023-03-17 05:10:04,770] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:10:04,770] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:10:04,770] [INFO] DQC Reference Directory: /var/lib/cwl/stg7797b882-6c87-4058-8f14-1c30acc07beb/dqc_reference
[2023-03-17 05:10:05,937] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:10:05,937] [INFO] Task started: Prodigal
[2023-03-17 05:10:05,937] [INFO] Running command: cat /var/lib/cwl/stgda3b5bee-d559-4d9f-acd7-fe6a3ad1be70/OceanDNA-b16182.fa | prodigal -d OceanDNA-b16182/cds.fna -a OceanDNA-b16182/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:10:20,988] [INFO] Task succeeded: Prodigal
[2023-03-17 05:10:20,988] [INFO] Task started: HMMsearch
[2023-03-17 05:10:20,988] [INFO] Running command: hmmsearch --tblout OceanDNA-b16182/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7797b882-6c87-4058-8f14-1c30acc07beb/dqc_reference/reference_markers.hmm OceanDNA-b16182/protein.faa > /dev/null
[2023-03-17 05:10:21,198] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:10:21,198] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgda3b5bee-d559-4d9f-acd7-fe6a3ad1be70/OceanDNA-b16182.fa]
[2023-03-17 05:10:21,219] [INFO] Query marker FASTA was written to OceanDNA-b16182/markers.fasta
[2023-03-17 05:10:21,220] [INFO] Task started: Blastn
[2023-03-17 05:10:21,220] [INFO] Running command: blastn -query OceanDNA-b16182/markers.fasta -db /var/lib/cwl/stg7797b882-6c87-4058-8f14-1c30acc07beb/dqc_reference/reference_markers.fasta -out OceanDNA-b16182/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:10:21,658] [INFO] Task succeeded: Blastn
[2023-03-17 05:10:21,659] [INFO] Selected 10 target genomes.
[2023-03-17 05:10:21,659] [INFO] Target genome list was writen to OceanDNA-b16182/target_genomes.txt
[2023-03-17 05:10:21,666] [INFO] Task started: fastANI
[2023-03-17 05:10:21,666] [INFO] Running command: fastANI --query /var/lib/cwl/stgda3b5bee-d559-4d9f-acd7-fe6a3ad1be70/OceanDNA-b16182.fa --refList OceanDNA-b16182/target_genomes.txt --output OceanDNA-b16182/fastani_result.tsv --threads 1
[2023-03-17 05:10:28,581] [INFO] Task succeeded: fastANI
[2023-03-17 05:10:28,582] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7797b882-6c87-4058-8f14-1c30acc07beb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:10:28,582] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7797b882-6c87-4058-8f14-1c30acc07beb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:10:28,585] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:10:28,585] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:10:28,585] [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
Waterburya agarophytonicola	strain=KI4	GCA_020640915.1	2886916	2886916	type	True	75.4597	59	699	95	below_threshold
Stanieria cyanosphaera	strain=PCC 7437	GCA_000317575.1	102116	102116	type	True	75.389	51	699	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:10:28,585] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16182/tc_result.tsv
[2023-03-17 05:10:28,585] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:10:28,586] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:10:28,586] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7797b882-6c87-4058-8f14-1c30acc07beb/dqc_reference/checkm_data
[2023-03-17 05:10:28,586] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:10:28,664] [INFO] Task started: CheckM
[2023-03-17 05:10:28,664] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16182/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16182/checkm_input OceanDNA-b16182/checkm_result
[2023-03-17 05:11:10,432] [INFO] Task succeeded: CheckM
[2023-03-17 05:11:10,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:11:10,435] [INFO] ===== Completeness check finished =====
[2023-03-17 05:11:10,435] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:11:10,435] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16182/markers.fasta)
[2023-03-17 05:11:10,435] [INFO] Task started: Blastn
[2023-03-17 05:11:10,435] [INFO] Running command: blastn -query OceanDNA-b16182/markers.fasta -db /var/lib/cwl/stg7797b882-6c87-4058-8f14-1c30acc07beb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16182/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:11:10,831] [INFO] Task succeeded: Blastn
[2023-03-17 05:11:10,832] [INFO] Selected 14 target genomes.
[2023-03-17 05:11:10,832] [INFO] Target genome list was writen to OceanDNA-b16182/target_genomes_gtdb.txt
[2023-03-17 05:11:10,909] [INFO] Task started: fastANI
[2023-03-17 05:11:10,909] [INFO] Running command: fastANI --query /var/lib/cwl/stgda3b5bee-d559-4d9f-acd7-fe6a3ad1be70/OceanDNA-b16182.fa --refList OceanDNA-b16182/target_genomes_gtdb.txt --output OceanDNA-b16182/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:11:21,739] [INFO] Task succeeded: fastANI
[2023-03-17 05:11:21,742] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:11:21,742] [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
GCF_900659865.1	s__Hyella patelloides	76.5739	138	699	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Hyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932785.1	s__Hyella disjuncta	76.5167	126	699	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Hyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355455.1	s__Stanieria sp002355455	75.5392	62	699	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Stanieria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317575.1	s__Stanieria cyanosphaera	75.389	51	699	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Stanieria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:11:21,742] [INFO] GTDB search result was written to OceanDNA-b16182/result_gtdb.tsv
[2023-03-17 05:11:21,743] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:11:21,743] [INFO] DFAST_QC result json was written to OceanDNA-b16182/dqc_result.json
[2023-03-17 05:11:21,743] [INFO] DFAST_QC completed!
[2023-03-17 05:11:21,743] [INFO] Total running time: 0h1m17s