[2023-03-18 20:13:32,232] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:13:32,232] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:13:32,233] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a0ed859-7400-4b90-a5f7-5077d58b096a/dqc_reference
[2023-03-18 20:13:33,402] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:13:33,430] [INFO] Task started: Prodigal
[2023-03-18 20:13:33,430] [INFO] Running command: cat /var/lib/cwl/stge0a64b4d-efba-4b19-9581-665d667f3ed6/OceanDNA-b16125.fa | prodigal -d OceanDNA-b16125/cds.fna -a OceanDNA-b16125/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:13:53,808] [INFO] Task succeeded: Prodigal
[2023-03-18 20:13:53,808] [INFO] Task started: HMMsearch
[2023-03-18 20:13:53,808] [INFO] Running command: hmmsearch --tblout OceanDNA-b16125/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a0ed859-7400-4b90-a5f7-5077d58b096a/dqc_reference/reference_markers.hmm OceanDNA-b16125/protein.faa > /dev/null
[2023-03-18 20:13:54,085] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:13:54,085] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge0a64b4d-efba-4b19-9581-665d667f3ed6/OceanDNA-b16125.fa]
[2023-03-18 20:13:54,110] [INFO] Query marker FASTA was written to OceanDNA-b16125/markers.fasta
[2023-03-18 20:13:54,110] [INFO] Task started: Blastn
[2023-03-18 20:13:54,110] [INFO] Running command: blastn -query OceanDNA-b16125/markers.fasta -db /var/lib/cwl/stg7a0ed859-7400-4b90-a5f7-5077d58b096a/dqc_reference/reference_markers.fasta -out OceanDNA-b16125/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:13:54,629] [INFO] Task succeeded: Blastn
[2023-03-18 20:13:54,630] [INFO] Selected 19 target genomes.
[2023-03-18 20:13:54,630] [INFO] Target genome list was writen to OceanDNA-b16125/target_genomes.txt
[2023-03-18 20:13:54,642] [INFO] Task started: fastANI
[2023-03-18 20:13:54,642] [INFO] Running command: fastANI --query /var/lib/cwl/stge0a64b4d-efba-4b19-9581-665d667f3ed6/OceanDNA-b16125.fa --refList OceanDNA-b16125/target_genomes.txt --output OceanDNA-b16125/fastani_result.tsv --threads 1
[2023-03-18 20:14:08,079] [INFO] Task succeeded: fastANI
[2023-03-18 20:14:08,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a0ed859-7400-4b90-a5f7-5077d58b096a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:14:08,080] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a0ed859-7400-4b90-a5f7-5077d58b096a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:14:08,083] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:14:08,083] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 20:14:08,084] [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	77.426	414	1332	95	below_threshold
Stanieria cyanosphaera	strain=PCC 7437	GCA_000317575.1	102116	102116	type	True	75.7637	174	1332	95	below_threshold
Gloeothece citriformis	strain=PCC 7424	GCA_000021825.1	2546356	2546356	type	True	75.2937	53	1332	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:14:08,084] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16125/tc_result.tsv
[2023-03-18 20:14:08,084] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:14:08,084] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:14:08,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a0ed859-7400-4b90-a5f7-5077d58b096a/dqc_reference/checkm_data
[2023-03-18 20:14:08,085] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:14:08,091] [INFO] Task started: CheckM
[2023-03-18 20:14:08,091] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16125/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16125/checkm_input OceanDNA-b16125/checkm_result
[2023-03-18 20:14:59,421] [INFO] Task succeeded: CheckM
[2023-03-18 20:14:59,421] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:14:59,425] [INFO] ===== Completeness check finished =====
[2023-03-18 20:14:59,425] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:14:59,425] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16125/markers.fasta)
[2023-03-18 20:14:59,425] [INFO] Task started: Blastn
[2023-03-18 20:14:59,425] [INFO] Running command: blastn -query OceanDNA-b16125/markers.fasta -db /var/lib/cwl/stg7a0ed859-7400-4b90-a5f7-5077d58b096a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16125/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:15:00,138] [INFO] Task succeeded: Blastn
[2023-03-18 20:15:00,139] [INFO] Selected 17 target genomes.
[2023-03-18 20:15:00,139] [INFO] Target genome list was writen to OceanDNA-b16125/target_genomes_gtdb.txt
[2023-03-18 20:15:00,422] [INFO] Task started: fastANI
[2023-03-18 20:15:00,422] [INFO] Running command: fastANI --query /var/lib/cwl/stge0a64b4d-efba-4b19-9581-665d667f3ed6/OceanDNA-b16125.fa --refList OceanDNA-b16125/target_genomes_gtdb.txt --output OceanDNA-b16125/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:15:17,351] [INFO] Task succeeded: fastANI
[2023-03-18 20:15:17,357] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:15:17,357] [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_015207195.1	s__Pleurocapsa sp015207195	78.326	604	1332	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012034765.1	s__Pleurocapsa sp012034765	77.4865	375	1332	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	99.36	99.13	0.90	0.87	3	-
GCF_003003995.1	s__Pleurocapsa sp003003995	77.319	414	1332	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332195.1	s__Pleurocapsa sp000332195	77.0185	403	1332	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368355.1	s__Pleurocapsa sp002368355	76.8921	328	1332	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756305.1	s__Myxosarcina sp000756305	76.7232	265	1332	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Myxosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015207585.1	s__LEGE-06147 sp015207585	75.8682	99	1332	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__LEGE-06147	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932785.1	s__Hyella disjuncta	75.8116	155	1332	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	75.7827	163	1332	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	75.7637	174	1332	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Stanieria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 20:15:17,358] [INFO] GTDB search result was written to OceanDNA-b16125/result_gtdb.tsv
[2023-03-18 20:15:17,358] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:15:17,359] [INFO] DFAST_QC result json was written to OceanDNA-b16125/dqc_result.json
[2023-03-18 20:15:17,359] [INFO] DFAST_QC completed!
[2023-03-18 20:15:17,359] [INFO] Total running time: 0h1m45s