[2023-03-14 11:33:34,954] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:33:34,954] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:33:34,954] [INFO] DQC Reference Directory: /var/lib/cwl/stg686766e9-6318-4f65-a31d-aa9dfc04c104/dqc_reference
[2023-03-14 11:33:36,196] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:33:36,196] [INFO] Task started: Prodigal
[2023-03-14 11:33:36,197] [INFO] Running command: cat /var/lib/cwl/stg0ea9e52b-30e3-444c-8876-06e59993385a/OceanDNA-b16470.fa | prodigal -d OceanDNA-b16470/cds.fna -a OceanDNA-b16470/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:33:54,463] [INFO] Task succeeded: Prodigal
[2023-03-14 11:33:54,463] [INFO] Task started: HMMsearch
[2023-03-14 11:33:54,463] [INFO] Running command: hmmsearch --tblout OceanDNA-b16470/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg686766e9-6318-4f65-a31d-aa9dfc04c104/dqc_reference/reference_markers.hmm OceanDNA-b16470/protein.faa > /dev/null
[2023-03-14 11:33:54,670] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:33:54,671] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0ea9e52b-30e3-444c-8876-06e59993385a/OceanDNA-b16470.fa]
[2023-03-14 11:33:54,688] [INFO] Query marker FASTA was written to OceanDNA-b16470/markers.fasta
[2023-03-14 11:33:54,688] [INFO] Task started: Blastn
[2023-03-14 11:33:54,688] [INFO] Running command: blastn -query OceanDNA-b16470/markers.fasta -db /var/lib/cwl/stg686766e9-6318-4f65-a31d-aa9dfc04c104/dqc_reference/reference_markers.fasta -out OceanDNA-b16470/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:33:55,237] [INFO] Task succeeded: Blastn
[2023-03-14 11:33:55,238] [INFO] Selected 29 target genomes.
[2023-03-14 11:33:55,238] [INFO] Target genome list was writen to OceanDNA-b16470/target_genomes.txt
[2023-03-14 11:33:55,254] [INFO] Task started: fastANI
[2023-03-14 11:33:55,254] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ea9e52b-30e3-444c-8876-06e59993385a/OceanDNA-b16470.fa --refList OceanDNA-b16470/target_genomes.txt --output OceanDNA-b16470/fastani_result.tsv --threads 1
[2023-03-14 11:34:18,992] [INFO] Task succeeded: fastANI
[2023-03-14 11:34:18,992] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg686766e9-6318-4f65-a31d-aa9dfc04c104/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:34:18,992] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg686766e9-6318-4f65-a31d-aa9dfc04c104/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:34:18,995] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:34:18,995] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:34:18,995] [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	77.845	190	617	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:34:18,995] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16470/tc_result.tsv
[2023-03-14 11:34:18,996] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:34:18,996] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:34:18,996] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg686766e9-6318-4f65-a31d-aa9dfc04c104/dqc_reference/checkm_data
[2023-03-14 11:34:18,997] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:34:19,015] [INFO] Task started: CheckM
[2023-03-14 11:34:19,015] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16470/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16470/checkm_input OceanDNA-b16470/checkm_result
[2023-03-14 11:35:08,752] [INFO] Task succeeded: CheckM
[2023-03-14 11:35:08,753] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 12.50%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 11:35:08,755] [INFO] ===== Completeness check finished =====
[2023-03-14 11:35:08,755] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:35:08,756] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16470/markers.fasta)
[2023-03-14 11:35:08,757] [INFO] Task started: Blastn
[2023-03-14 11:35:08,757] [INFO] Running command: blastn -query OceanDNA-b16470/markers.fasta -db /var/lib/cwl/stg686766e9-6318-4f65-a31d-aa9dfc04c104/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16470/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:35:09,559] [INFO] Task succeeded: Blastn
[2023-03-14 11:35:09,559] [INFO] Selected 12 target genomes.
[2023-03-14 11:35:09,560] [INFO] Target genome list was writen to OceanDNA-b16470/target_genomes_gtdb.txt
[2023-03-14 11:35:09,569] [INFO] Task started: fastANI
[2023-03-14 11:35:09,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ea9e52b-30e3-444c-8876-06e59993385a/OceanDNA-b16470.fa --refList OceanDNA-b16470/target_genomes_gtdb.txt --output OceanDNA-b16470/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:35:14,984] [INFO] Task succeeded: fastANI
[2023-03-14 11:35:14,991] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:35:14,991] [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_000012505.1	s__Synechococcus_E sp000012505	88.8592	547	617	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	95.61	95.06	0.95	0.89	4	-
GCF_000153805.1	s__Synechococcus_E sp000153805	88.7301	551	617	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016777265.1	s__Synechococcus_E sp016777265	87.2397	323	617	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003208835.1	s__Synechococcus_E sp003208835	86.1886	399	617	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	95.29	95.29	0.71	0.71	2	-
GCF_000161795.2	s__Synechococcus_E sp000161795	78.3556	193	617	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012625.1	s__Synechococcus_E sp000012625	78.2198	196	617	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	95.15	95.15	0.92	0.92	2	-
GCA_013911515.1	s__Synechococcus_E sp013911515	77.9715	162	617	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779825.1	s__Synechococcus_E sp016779825	77.7391	155	617	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737575.1	s__Synechococcus_E sp000737575	77.7184	164	617	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.69	96.21	0.96	0.90	8	-
GCA_002690325.1	s__Synechococcus_E sp002690325	77.4263	150	617	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153045.1	s__WH-5701 sp000153045	76.5013	82	617	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__WH-5701	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:35:14,991] [INFO] GTDB search result was written to OceanDNA-b16470/result_gtdb.tsv
[2023-03-14 11:35:14,991] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:35:14,992] [INFO] DFAST_QC result json was written to OceanDNA-b16470/dqc_result.json
[2023-03-14 11:35:14,992] [INFO] DFAST_QC completed!
[2023-03-14 11:35:14,992] [INFO] Total running time: 0h1m40s