[2023-03-16 07:55:45,194] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:55:45,194] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:55:45,194] [INFO] DQC Reference Directory: /var/lib/cwl/stg7289bb77-d3e6-45c6-bbcc-d27c2e996879/dqc_reference
[2023-03-16 07:55:46,322] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:55:46,323] [INFO] Task started: Prodigal
[2023-03-16 07:55:46,323] [INFO] Running command: cat /var/lib/cwl/stg7198549c-3917-4be1-8852-9cb9943205f9/OceanDNA-b16662.fa | prodigal -d OceanDNA-b16662/cds.fna -a OceanDNA-b16662/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:56:01,354] [INFO] Task succeeded: Prodigal
[2023-03-16 07:56:01,355] [INFO] Task started: HMMsearch
[2023-03-16 07:56:01,355] [INFO] Running command: hmmsearch --tblout OceanDNA-b16662/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7289bb77-d3e6-45c6-bbcc-d27c2e996879/dqc_reference/reference_markers.hmm OceanDNA-b16662/protein.faa > /dev/null
[2023-03-16 07:56:01,516] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:56:01,517] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7198549c-3917-4be1-8852-9cb9943205f9/OceanDNA-b16662.fa]
[2023-03-16 07:56:01,530] [INFO] Query marker FASTA was written to OceanDNA-b16662/markers.fasta
[2023-03-16 07:56:01,532] [INFO] Task started: Blastn
[2023-03-16 07:56:01,532] [INFO] Running command: blastn -query OceanDNA-b16662/markers.fasta -db /var/lib/cwl/stg7289bb77-d3e6-45c6-bbcc-d27c2e996879/dqc_reference/reference_markers.fasta -out OceanDNA-b16662/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:56:02,060] [INFO] Task succeeded: Blastn
[2023-03-16 07:56:02,061] [INFO] Selected 15 target genomes.
[2023-03-16 07:56:02,061] [INFO] Target genome list was writen to OceanDNA-b16662/target_genomes.txt
[2023-03-16 07:56:02,071] [INFO] Task started: fastANI
[2023-03-16 07:56:02,071] [INFO] Running command: fastANI --query /var/lib/cwl/stg7198549c-3917-4be1-8852-9cb9943205f9/OceanDNA-b16662.fa --refList OceanDNA-b16662/target_genomes.txt --output OceanDNA-b16662/fastani_result.tsv --threads 1
[2023-03-16 07:56:12,769] [INFO] Task succeeded: fastANI
[2023-03-16 07:56:12,769] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7289bb77-d3e6-45c6-bbcc-d27c2e996879/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:56:12,769] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7289bb77-d3e6-45c6-bbcc-d27c2e996879/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:56:12,773] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:56:12,773] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:56:12,773] [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	77.7834	201	530	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:56:12,773] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16662/tc_result.tsv
[2023-03-16 07:56:12,773] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:56:12,773] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:56:12,773] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7289bb77-d3e6-45c6-bbcc-d27c2e996879/dqc_reference/checkm_data
[2023-03-16 07:56:12,774] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:56:12,777] [INFO] Task started: CheckM
[2023-03-16 07:56:12,777] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16662/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16662/checkm_input OceanDNA-b16662/checkm_result
[2023-03-16 07:56:55,254] [INFO] Task succeeded: CheckM
[2023-03-16 07:56:55,255] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.53%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 07:56:55,266] [INFO] ===== Completeness check finished =====
[2023-03-16 07:56:55,266] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:56:55,266] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16662/markers.fasta)
[2023-03-16 07:56:55,268] [INFO] Task started: Blastn
[2023-03-16 07:56:55,268] [INFO] Running command: blastn -query OceanDNA-b16662/markers.fasta -db /var/lib/cwl/stg7289bb77-d3e6-45c6-bbcc-d27c2e996879/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16662/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:56:56,054] [INFO] Task succeeded: Blastn
[2023-03-16 07:56:56,055] [INFO] Selected 20 target genomes.
[2023-03-16 07:56:56,055] [INFO] Target genome list was writen to OceanDNA-b16662/target_genomes_gtdb.txt
[2023-03-16 07:56:56,171] [INFO] Task started: fastANI
[2023-03-16 07:56:56,171] [INFO] Running command: fastANI --query /var/lib/cwl/stg7198549c-3917-4be1-8852-9cb9943205f9/OceanDNA-b16662.fa --refList OceanDNA-b16662/target_genomes_gtdb.txt --output OceanDNA-b16662/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:57:03,853] [INFO] Task succeeded: fastANI
[2023-03-16 07:57:03,865] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 07:57:03,865] [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_002690325.1	s__Synechococcus_E sp002690325	99.4418	487	530	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	conclusive
GCF_014279895.1	s__Synechococcus_E sp002724845	78.1396	182	530	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	96.37	95.03	0.93	0.89	13	-
GCA_016779825.1	s__Synechococcus_E sp016779825	78.0818	144	530	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	77.9662	186	530	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	-
GCF_000737595.1	s__Synechococcus_E sp000737595	77.9573	172	530	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	77.8937	109	530	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_014280195.1	s__Synechococcus_E sp014280195	77.8265	195	530	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_000161795.2	s__Synechococcus_E sp000161795	77.8057	181	530	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_000195975.1	s__Synechococcus_E sp000195975	77.8005	200	530	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	77.7034	144	530	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_014280175.1	s__Synechococcus_E sp004212765	77.6255	197	530	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	-
GCA_003211535.1	s__Synechococcus_E sp003211535	77.4593	130	530	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_003211235.1	s__Synechococcus_E sp003211235	77.4163	86	530	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_014280035.1	s__Synechococcus_C sp002693285	77.1553	98	530	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	98.95	98.86	0.95	0.94	3	-
GCF_000012505.1	s__Synechococcus_E sp000012505	77.0632	126	530	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_014217855.1	s__Synechococcus_C sp004332415	76.9656	115	530	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_000737535.1	s__Synechococcus_E sp000737535	76.9105	142	530	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_014279595.1	s__Synechococcus_C sp000153065	76.8243	119	530	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	99.83	99.83	0.99	0.99	2	-
GCA_003211515.1	s__Synechococcus_E sp003211515	76.8123	95	530	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_000230675.1	s__Synechococcus_C sp000230675	76.4875	76	530	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	96.29	95.09	0.90	0.84	8	-
--------------------------------------------------------------------------------
[2023-03-16 07:57:03,870] [INFO] GTDB search result was written to OceanDNA-b16662/result_gtdb.tsv
[2023-03-16 07:57:03,871] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:57:03,872] [INFO] DFAST_QC result json was written to OceanDNA-b16662/dqc_result.json
[2023-03-16 07:57:03,872] [INFO] DFAST_QC completed!
[2023-03-16 07:57:03,872] [INFO] Total running time: 0h1m19s