[2023-03-18 10:46:22,154] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:46:22,156] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:46:22,156] [INFO] DQC Reference Directory: /var/lib/cwl/stgf35393b3-2570-4e79-b320-ead1ee551fe3/dqc_reference
[2023-03-18 10:46:23,266] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:46:23,266] [INFO] Task started: Prodigal
[2023-03-18 10:46:23,267] [INFO] Running command: cat /var/lib/cwl/stg121c447f-3eb6-49dc-b0f6-de6b98a34f17/OceanDNA-b16673.fa | prodigal -d OceanDNA-b16673/cds.fna -a OceanDNA-b16673/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:46:32,039] [INFO] Task succeeded: Prodigal
[2023-03-18 10:46:32,039] [INFO] Task started: HMMsearch
[2023-03-18 10:46:32,039] [INFO] Running command: hmmsearch --tblout OceanDNA-b16673/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf35393b3-2570-4e79-b320-ead1ee551fe3/dqc_reference/reference_markers.hmm OceanDNA-b16673/protein.faa > /dev/null
[2023-03-18 10:46:32,173] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:46:32,173] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg121c447f-3eb6-49dc-b0f6-de6b98a34f17/OceanDNA-b16673.fa]
[2023-03-18 10:46:32,201] [INFO] Query marker FASTA was written to OceanDNA-b16673/markers.fasta
[2023-03-18 10:46:32,201] [INFO] Task started: Blastn
[2023-03-18 10:46:32,201] [INFO] Running command: blastn -query OceanDNA-b16673/markers.fasta -db /var/lib/cwl/stgf35393b3-2570-4e79-b320-ead1ee551fe3/dqc_reference/reference_markers.fasta -out OceanDNA-b16673/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:46:32,648] [INFO] Task succeeded: Blastn
[2023-03-18 10:46:32,660] [INFO] Selected 12 target genomes.
[2023-03-18 10:46:32,660] [INFO] Target genome list was writen to OceanDNA-b16673/target_genomes.txt
[2023-03-18 10:46:32,666] [INFO] Task started: fastANI
[2023-03-18 10:46:32,667] [INFO] Running command: fastANI --query /var/lib/cwl/stg121c447f-3eb6-49dc-b0f6-de6b98a34f17/OceanDNA-b16673.fa --refList OceanDNA-b16673/target_genomes.txt --output OceanDNA-b16673/fastani_result.tsv --threads 1
[2023-03-18 10:46:39,489] [INFO] Task succeeded: fastANI
[2023-03-18 10:46:39,490] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf35393b3-2570-4e79-b320-ead1ee551fe3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:46:39,490] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf35393b3-2570-4e79-b320-ead1ee551fe3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:46:39,493] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:46:39,493] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 10:46:39,493] [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	77.217	125	258	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 10:46:39,495] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16673/tc_result.tsv
[2023-03-18 10:46:39,499] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:46:39,499] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:46:39,499] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf35393b3-2570-4e79-b320-ead1ee551fe3/dqc_reference/checkm_data
[2023-03-18 10:46:39,500] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:46:39,535] [INFO] Task started: CheckM
[2023-03-18 10:46:39,535] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16673/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16673/checkm_input OceanDNA-b16673/checkm_result
[2023-03-18 10:47:02,464] [INFO] Task succeeded: CheckM
[2023-03-18 10:47:02,464] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.51%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:47:02,488] [INFO] ===== Completeness check finished =====
[2023-03-18 10:47:02,488] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:47:02,488] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16673/markers.fasta)
[2023-03-18 10:47:02,488] [INFO] Task started: Blastn
[2023-03-18 10:47:02,488] [INFO] Running command: blastn -query OceanDNA-b16673/markers.fasta -db /var/lib/cwl/stgf35393b3-2570-4e79-b320-ead1ee551fe3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16673/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:47:02,964] [INFO] Task succeeded: Blastn
[2023-03-18 10:47:02,968] [INFO] Selected 15 target genomes.
[2023-03-18 10:47:02,968] [INFO] Target genome list was writen to OceanDNA-b16673/target_genomes_gtdb.txt
[2023-03-18 10:47:02,982] [INFO] Task started: fastANI
[2023-03-18 10:47:02,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg121c447f-3eb6-49dc-b0f6-de6b98a34f17/OceanDNA-b16673.fa --refList OceanDNA-b16673/target_genomes_gtdb.txt --output OceanDNA-b16673/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:47:09,183] [INFO] Task succeeded: fastANI
[2023-03-18 10:47:09,192] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 10:47:09,192] [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_002700765.1	s__Synechococcus_E sp002700765	99.0694	205	258	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_014280175.1	s__Synechococcus_E sp004212765	78.1137	109	258	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.21	96.96	0.98	0.97	4	-
GCF_000737535.1	s__Synechococcus_E sp000737535	78.0343	107	258	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	77.7863	121	258	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	-
GCF_014280195.1	s__Synechococcus_E sp014280195	77.7495	109	258	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_003211535.1	s__Synechococcus_E sp003211535	77.4952	86	258	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_014279755.1	s__Synechococcus_E sp014279755	77.4905	93	258	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_002170825.1	s__Synechococcus_E sp002170825	77.4548	73	258	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.06	98.06	0.77	0.77	2	-
GCF_000195975.1	s__Synechococcus_E sp000195975	77.217	125	258	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	-
GCF_000316515.1	s__Cyanobium gracile	76.7138	60	258	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153825.1	s__Synechococcus_C sp000153825	76.6341	71	258	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_000155635.1	s__NIES-981 sp000155635	76.3807	56	258	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:47:09,193] [INFO] GTDB search result was written to OceanDNA-b16673/result_gtdb.tsv
[2023-03-18 10:47:09,195] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:47:09,197] [INFO] DFAST_QC result json was written to OceanDNA-b16673/dqc_result.json
[2023-03-18 10:47:09,197] [INFO] DFAST_QC completed!
[2023-03-18 10:47:09,197] [INFO] Total running time: 0h0m47s