[2023-03-16 06:24:06,017] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:24:06,017] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:24:06,017] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc17abc7-778f-4d77-b061-6ef4cc18a568/dqc_reference
[2023-03-16 06:24:07,123] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:24:07,123] [INFO] Task started: Prodigal
[2023-03-16 06:24:07,123] [INFO] Running command: cat /var/lib/cwl/stg3d8ccc23-8d32-4b2a-a74b-aea3d19588b8/OceanDNA-b16700.fa | prodigal -d OceanDNA-b16700/cds.fna -a OceanDNA-b16700/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:24:18,056] [INFO] Task succeeded: Prodigal
[2023-03-16 06:24:18,057] [INFO] Task started: HMMsearch
[2023-03-16 06:24:18,057] [INFO] Running command: hmmsearch --tblout OceanDNA-b16700/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc17abc7-778f-4d77-b061-6ef4cc18a568/dqc_reference/reference_markers.hmm OceanDNA-b16700/protein.faa > /dev/null
[2023-03-16 06:24:18,201] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:24:18,201] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3d8ccc23-8d32-4b2a-a74b-aea3d19588b8/OceanDNA-b16700.fa]
[2023-03-16 06:24:18,213] [INFO] Query marker FASTA was written to OceanDNA-b16700/markers.fasta
[2023-03-16 06:24:18,214] [INFO] Task started: Blastn
[2023-03-16 06:24:18,214] [INFO] Running command: blastn -query OceanDNA-b16700/markers.fasta -db /var/lib/cwl/stgdc17abc7-778f-4d77-b061-6ef4cc18a568/dqc_reference/reference_markers.fasta -out OceanDNA-b16700/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:24:18,744] [INFO] Task succeeded: Blastn
[2023-03-16 06:24:18,744] [INFO] Selected 19 target genomes.
[2023-03-16 06:24:18,745] [INFO] Target genome list was writen to OceanDNA-b16700/target_genomes.txt
[2023-03-16 06:24:18,753] [INFO] Task started: fastANI
[2023-03-16 06:24:18,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d8ccc23-8d32-4b2a-a74b-aea3d19588b8/OceanDNA-b16700.fa --refList OceanDNA-b16700/target_genomes.txt --output OceanDNA-b16700/fastani_result.tsv --threads 1
[2023-03-16 06:24:30,186] [INFO] Task succeeded: fastANI
[2023-03-16 06:24:30,186] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc17abc7-778f-4d77-b061-6ef4cc18a568/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:24:30,186] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc17abc7-778f-4d77-b061-6ef4cc18a568/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:24:30,190] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:24:30,190] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 06:24:30,190] [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
Parasynechococcus marenigrum	strain=WH 8102	GCA_000195975.1	2881428	2881428	type	True	77.4997	88	313	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:24:30,190] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16700/tc_result.tsv
[2023-03-16 06:24:30,190] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:24:30,190] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:24:30,190] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc17abc7-778f-4d77-b061-6ef4cc18a568/dqc_reference/checkm_data
[2023-03-16 06:24:30,191] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:24:30,211] [INFO] Task started: CheckM
[2023-03-16 06:24:30,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16700/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16700/checkm_input OceanDNA-b16700/checkm_result
[2023-03-16 06:25:03,734] [INFO] Task succeeded: CheckM
[2023-03-16 06:25:03,734] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.38%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 06:25:03,756] [INFO] ===== Completeness check finished =====
[2023-03-16 06:25:03,756] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:25:03,756] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16700/markers.fasta)
[2023-03-16 06:25:03,757] [INFO] Task started: Blastn
[2023-03-16 06:25:03,757] [INFO] Running command: blastn -query OceanDNA-b16700/markers.fasta -db /var/lib/cwl/stgdc17abc7-778f-4d77-b061-6ef4cc18a568/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16700/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:25:04,516] [INFO] Task succeeded: Blastn
[2023-03-16 06:25:04,517] [INFO] Selected 7 target genomes.
[2023-03-16 06:25:04,517] [INFO] Target genome list was writen to OceanDNA-b16700/target_genomes_gtdb.txt
[2023-03-16 06:25:04,523] [INFO] Task started: fastANI
[2023-03-16 06:25:04,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d8ccc23-8d32-4b2a-a74b-aea3d19588b8/OceanDNA-b16700.fa --refList OceanDNA-b16700/target_genomes_gtdb.txt --output OceanDNA-b16700/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:25:07,629] [INFO] Task succeeded: fastANI
[2023-03-16 06:25:07,634] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-16 06:25:07,634] [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_003211275.1	s__Synechococcus_C sp003209155	97.5315	217	313	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	97.35	96.97	0.64	0.60	6	inconclusive
GCA_003211205.1	s__Synechococcus_C sp003211205	95.8668	245	313	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_014304815.1	s__Synechococcus_C sp001632165	93.815	305	313	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	97.31	96.03	0.90	0.85	7	-
GCA_003210775.1	s__Synechococcus_C sp003210775	88.9786	231	313	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014279995.1	s__Synechococcus_C sp001631935	88.2278	302	313	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	96.61	96.58	0.90	0.90	3	-
GCF_900473965.1	s__Synechococcus_C sp900473965	87.7345	306	313	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014279975.1	s__Synechococcus_C sp014279975	87.5605	302	313	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:25:07,634] [INFO] GTDB search result was written to OceanDNA-b16700/result_gtdb.tsv
[2023-03-16 06:25:07,634] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:25:07,635] [INFO] DFAST_QC result json was written to OceanDNA-b16700/dqc_result.json
[2023-03-16 06:25:07,635] [INFO] DFAST_QC completed!
[2023-03-16 06:25:07,635] [INFO] Total running time: 0h1m2s