[2023-03-14 14:53:36,440] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:53:36,440] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:53:36,440] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa8ffed8-12f6-49ac-9171-1febdb1dd948/dqc_reference
[2023-03-14 14:53:37,528] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:53:37,529] [INFO] Task started: Prodigal
[2023-03-14 14:53:37,529] [INFO] Running command: cat /var/lib/cwl/stgd78a40cb-64a7-4d06-9725-628d5936abf2/OceanDNA-b16170.fa | prodigal -d OceanDNA-b16170/cds.fna -a OceanDNA-b16170/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:54:01,568] [INFO] Task succeeded: Prodigal
[2023-03-14 14:54:01,569] [INFO] Task started: HMMsearch
[2023-03-14 14:54:01,569] [INFO] Running command: hmmsearch --tblout OceanDNA-b16170/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa8ffed8-12f6-49ac-9171-1febdb1dd948/dqc_reference/reference_markers.hmm OceanDNA-b16170/protein.faa > /dev/null
[2023-03-14 14:54:01,825] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:54:01,826] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd78a40cb-64a7-4d06-9725-628d5936abf2/OceanDNA-b16170.fa]
[2023-03-14 14:54:01,849] [INFO] Query marker FASTA was written to OceanDNA-b16170/markers.fasta
[2023-03-14 14:54:01,849] [INFO] Task started: Blastn
[2023-03-14 14:54:01,850] [INFO] Running command: blastn -query OceanDNA-b16170/markers.fasta -db /var/lib/cwl/stgfa8ffed8-12f6-49ac-9171-1febdb1dd948/dqc_reference/reference_markers.fasta -out OceanDNA-b16170/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:54:02,362] [INFO] Task succeeded: Blastn
[2023-03-14 14:54:02,362] [INFO] Selected 13 target genomes.
[2023-03-14 14:54:02,363] [INFO] Target genome list was writen to OceanDNA-b16170/target_genomes.txt
[2023-03-14 14:54:02,371] [INFO] Task started: fastANI
[2023-03-14 14:54:02,371] [INFO] Running command: fastANI --query /var/lib/cwl/stgd78a40cb-64a7-4d06-9725-628d5936abf2/OceanDNA-b16170.fa --refList OceanDNA-b16170/target_genomes.txt --output OceanDNA-b16170/fastani_result.tsv --threads 1
[2023-03-14 14:54:13,843] [INFO] Task succeeded: fastANI
[2023-03-14 14:54:13,843] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa8ffed8-12f6-49ac-9171-1febdb1dd948/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:54:13,844] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa8ffed8-12f6-49ac-9171-1febdb1dd948/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:54:13,848] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:54:13,848] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 14:54:13,848] [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	76.2305	181	1358	95	below_threshold
Stanieria cyanosphaera	strain=PCC 7437	GCA_000317575.1	102116	102116	type	True	75.8803	210	1358	95	below_threshold
Crocosphaera chwakensis	strain=CCY0110	GCA_000169335.1	2546361	2546361	type	True	75.4288	78	1358	95	below_threshold
Crocosphaera watsonii	strain=WH 8501	GCA_000167195.1	263511	263511	suspected-type	True	75.1473	63	1358	95	below_threshold
Gloeothece citriformis	strain=PCC 7424	GCA_000021825.1	2546356	2546356	type	True	75.0193	57	1358	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 14:54:13,848] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16170/tc_result.tsv
[2023-03-14 14:54:13,848] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:54:13,849] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:54:13,849] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa8ffed8-12f6-49ac-9171-1febdb1dd948/dqc_reference/checkm_data
[2023-03-14 14:54:13,849] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:54:13,854] [INFO] Task started: CheckM
[2023-03-14 14:54:13,854] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16170/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16170/checkm_input OceanDNA-b16170/checkm_result
[2023-03-14 14:55:34,951] [INFO] Task succeeded: CheckM
[2023-03-14 14:55:34,952] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:55:34,954] [INFO] ===== Completeness check finished =====
[2023-03-14 14:55:34,955] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:55:34,955] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16170/markers.fasta)
[2023-03-14 14:55:34,959] [INFO] Task started: Blastn
[2023-03-14 14:55:34,959] [INFO] Running command: blastn -query OceanDNA-b16170/markers.fasta -db /var/lib/cwl/stgfa8ffed8-12f6-49ac-9171-1febdb1dd948/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16170/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:55:35,734] [INFO] Task succeeded: Blastn
[2023-03-14 14:55:35,735] [INFO] Selected 17 target genomes.
[2023-03-14 14:55:35,735] [INFO] Target genome list was writen to OceanDNA-b16170/target_genomes_gtdb.txt
[2023-03-14 14:55:35,775] [INFO] Task started: fastANI
[2023-03-14 14:55:35,775] [INFO] Running command: fastANI --query /var/lib/cwl/stgd78a40cb-64a7-4d06-9725-628d5936abf2/OceanDNA-b16170.fa --refList OceanDNA-b16170/target_genomes_gtdb.txt --output OceanDNA-b16170/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:55:53,903] [INFO] Task succeeded: fastANI
[2023-03-14 14:55:53,911] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 14:55:53,911] [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	78.6318	641	1358	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	77.8031	524	1358	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Hyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015207195.1	s__Pleurocapsa sp015207195	76.3318	197	1358	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355455.1	s__Stanieria sp002355455	75.9543	195	1358	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	75.8791	210	1358	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Stanieria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003995.1	s__Pleurocapsa sp003003995	75.7768	143	1358	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	75.7271	182	1358	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	75.6602	147	1358	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	99.36	99.13	0.90	0.87	3	-
GCA_015207585.1	s__LEGE-06147 sp015207585	75.5429	102	1358	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_000169335.1	s__Crocosphaera chwakensis	75.4446	74	1358	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002172675.1	s__Crocosphaera sp002172675	75.1245	64	1358	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003013815.1	s__Crocosphaera sp003013815	75.0792	63	1358	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:55:53,911] [INFO] GTDB search result was written to OceanDNA-b16170/result_gtdb.tsv
[2023-03-14 14:55:53,911] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:55:53,913] [INFO] DFAST_QC result json was written to OceanDNA-b16170/dqc_result.json
[2023-03-14 14:55:53,913] [INFO] DFAST_QC completed!
[2023-03-14 14:55:53,913] [INFO] Total running time: 0h2m17s