[2023-03-16 04:31:43,752] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:31:43,752] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:31:43,753] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ab28ef3-5c72-42fd-88d0-ffef41e249b1/dqc_reference
[2023-03-16 04:31:45,528] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:31:45,528] [INFO] Task started: Prodigal
[2023-03-16 04:31:45,528] [INFO] Running command: cat /var/lib/cwl/stgcba236de-2aac-41d3-a5fc-b589731c90f1/OceanDNA-b16418.fa | prodigal -d OceanDNA-b16418/cds.fna -a OceanDNA-b16418/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:31:59,031] [INFO] Task succeeded: Prodigal
[2023-03-16 04:31:59,032] [INFO] Task started: HMMsearch
[2023-03-16 04:31:59,032] [INFO] Running command: hmmsearch --tblout OceanDNA-b16418/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ab28ef3-5c72-42fd-88d0-ffef41e249b1/dqc_reference/reference_markers.hmm OceanDNA-b16418/protein.faa > /dev/null
[2023-03-16 04:31:59,203] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:31:59,203] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcba236de-2aac-41d3-a5fc-b589731c90f1/OceanDNA-b16418.fa]
[2023-03-16 04:31:59,217] [INFO] Query marker FASTA was written to OceanDNA-b16418/markers.fasta
[2023-03-16 04:31:59,218] [INFO] Task started: Blastn
[2023-03-16 04:31:59,219] [INFO] Running command: blastn -query OceanDNA-b16418/markers.fasta -db /var/lib/cwl/stg0ab28ef3-5c72-42fd-88d0-ffef41e249b1/dqc_reference/reference_markers.fasta -out OceanDNA-b16418/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:31:59,820] [INFO] Task succeeded: Blastn
[2023-03-16 04:31:59,821] [INFO] Selected 21 target genomes.
[2023-03-16 04:31:59,821] [INFO] Target genome list was writen to OceanDNA-b16418/target_genomes.txt
[2023-03-16 04:31:59,865] [INFO] Task started: fastANI
[2023-03-16 04:31:59,865] [INFO] Running command: fastANI --query /var/lib/cwl/stgcba236de-2aac-41d3-a5fc-b589731c90f1/OceanDNA-b16418.fa --refList OceanDNA-b16418/target_genomes.txt --output OceanDNA-b16418/fastani_result.tsv --threads 1
[2023-03-16 04:32:12,218] [INFO] Task succeeded: fastANI
[2023-03-16 04:32:12,219] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ab28ef3-5c72-42fd-88d0-ffef41e249b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:32:12,219] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ab28ef3-5c72-42fd-88d0-ffef41e249b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:32:12,222] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:32:12,222] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:32:12,222] [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	76.7326	83	476	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:32:12,222] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16418/tc_result.tsv
[2023-03-16 04:32:12,222] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:32:12,222] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:32:12,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ab28ef3-5c72-42fd-88d0-ffef41e249b1/dqc_reference/checkm_data
[2023-03-16 04:32:12,223] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:32:12,278] [INFO] Task started: CheckM
[2023-03-16 04:32:12,279] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16418/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16418/checkm_input OceanDNA-b16418/checkm_result
[2023-03-16 04:32:51,876] [INFO] Task succeeded: CheckM
[2023-03-16 04:32:51,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:32:51,879] [INFO] ===== Completeness check finished =====
[2023-03-16 04:32:51,879] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:32:51,879] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16418/markers.fasta)
[2023-03-16 04:32:51,880] [INFO] Task started: Blastn
[2023-03-16 04:32:51,881] [INFO] Running command: blastn -query OceanDNA-b16418/markers.fasta -db /var/lib/cwl/stg0ab28ef3-5c72-42fd-88d0-ffef41e249b1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16418/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:32:52,817] [INFO] Task succeeded: Blastn
[2023-03-16 04:32:52,818] [INFO] Selected 15 target genomes.
[2023-03-16 04:32:52,818] [INFO] Target genome list was writen to OceanDNA-b16418/target_genomes_gtdb.txt
[2023-03-16 04:32:52,832] [INFO] Task started: fastANI
[2023-03-16 04:32:52,832] [INFO] Running command: fastANI --query /var/lib/cwl/stgcba236de-2aac-41d3-a5fc-b589731c90f1/OceanDNA-b16418.fa --refList OceanDNA-b16418/target_genomes_gtdb.txt --output OceanDNA-b16418/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:32:58,997] [INFO] Task succeeded: fastANI
[2023-03-16 04:32:59,006] [INFO] Found 10 fastANI hits (3 hits with ANI > circumscription radius)
[2023-03-16 04:32:59,006] [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_000011485.1	s__Prochlorococcus_C marinus_B	96.4654	467	476	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_C	95.0	96.34	95.12	0.90	0.85	19	inconclusive
GCA_003214855.1	s__Prochlorococcus_C sp003214855	95.6349	341	476	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_C	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_000760295.1	s__Prochlorococcus_C sp000760295	95.4243	463	476	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_C	95.0	99.99	99.99	0.99	0.99	3	inconclusive
GCF_014279875.1	s__Synechococcus_C sp002172935	77.0244	72	476	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	98.09	98.09	0.93	0.93	2	-
GCF_014304815.1	s__Synechococcus_C sp001632165	76.8839	70	476	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	-
GCF_900474295.1	s__Synechococcus_C sp900474295	76.7938	78	476	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_014217855.1	s__Synechococcus_C sp004332415	76.7534	96	476	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	97.38	96.99	0.88	0.86	3	-
GCF_000195975.1	s__Synechococcus_E sp000195975	76.7326	83	476	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.37	97.74	0.92	0.91	7	-
GCA_002691345.1	s__Synechococcus_E sp002691345	76.7153	51	476	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	100.00	100.00	0.96	0.96	2	-
GCF_014279775.1	s__Synechococcus_C sp002500205	76.5941	63	476	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	99.03	97.76	0.95	0.86	9	-
--------------------------------------------------------------------------------
[2023-03-16 04:32:59,009] [INFO] GTDB search result was written to OceanDNA-b16418/result_gtdb.tsv
[2023-03-16 04:32:59,012] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:32:59,013] [INFO] DFAST_QC result json was written to OceanDNA-b16418/dqc_result.json
[2023-03-16 04:32:59,013] [INFO] DFAST_QC completed!
[2023-03-16 04:32:59,014] [INFO] Total running time: 0h1m15s