[2023-03-18 03:28:30,803] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:28:30,803] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:28:30,803] [INFO] DQC Reference Directory: /var/lib/cwl/stg202c63ce-07b7-47de-b54e-c0999f3b3b6b/dqc_reference
[2023-03-18 03:28:31,886] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:28:31,887] [INFO] Task started: Prodigal
[2023-03-18 03:28:31,887] [INFO] Running command: cat /var/lib/cwl/stgfbd7b1f1-9f36-48b8-a2c3-cc20acefa21c/OceanDNA-b16696.fa | prodigal -d OceanDNA-b16696/cds.fna -a OceanDNA-b16696/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:28:47,086] [INFO] Task succeeded: Prodigal
[2023-03-18 03:28:47,086] [INFO] Task started: HMMsearch
[2023-03-18 03:28:47,086] [INFO] Running command: hmmsearch --tblout OceanDNA-b16696/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg202c63ce-07b7-47de-b54e-c0999f3b3b6b/dqc_reference/reference_markers.hmm OceanDNA-b16696/protein.faa > /dev/null
[2023-03-18 03:28:47,241] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:28:47,242] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfbd7b1f1-9f36-48b8-a2c3-cc20acefa21c/OceanDNA-b16696.fa]
[2023-03-18 03:28:47,256] [INFO] Query marker FASTA was written to OceanDNA-b16696/markers.fasta
[2023-03-18 03:28:47,257] [INFO] Task started: Blastn
[2023-03-18 03:28:47,257] [INFO] Running command: blastn -query OceanDNA-b16696/markers.fasta -db /var/lib/cwl/stg202c63ce-07b7-47de-b54e-c0999f3b3b6b/dqc_reference/reference_markers.fasta -out OceanDNA-b16696/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:28:47,768] [INFO] Task succeeded: Blastn
[2023-03-18 03:28:47,769] [INFO] Selected 19 target genomes.
[2023-03-18 03:28:47,769] [INFO] Target genome list was writen to OceanDNA-b16696/target_genomes.txt
[2023-03-18 03:28:47,781] [INFO] Task started: fastANI
[2023-03-18 03:28:47,782] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbd7b1f1-9f36-48b8-a2c3-cc20acefa21c/OceanDNA-b16696.fa --refList OceanDNA-b16696/target_genomes.txt --output OceanDNA-b16696/fastani_result.tsv --threads 1
[2023-03-18 03:29:00,644] [INFO] Task succeeded: fastANI
[2023-03-18 03:29:00,644] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg202c63ce-07b7-47de-b54e-c0999f3b3b6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:29:00,645] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg202c63ce-07b7-47de-b54e-c0999f3b3b6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:29:00,648] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:29:00,648] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:29:00,648] [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	77.7673	171	509	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:29:00,648] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16696/tc_result.tsv
[2023-03-18 03:29:00,648] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:29:00,648] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:29:00,648] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg202c63ce-07b7-47de-b54e-c0999f3b3b6b/dqc_reference/checkm_data
[2023-03-18 03:29:00,649] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:29:00,652] [INFO] Task started: CheckM
[2023-03-18 03:29:00,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16696/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16696/checkm_input OceanDNA-b16696/checkm_result
[2023-03-18 03:29:43,092] [INFO] Task succeeded: CheckM
[2023-03-18 03:29:43,092] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:29:43,094] [INFO] ===== Completeness check finished =====
[2023-03-18 03:29:43,094] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:29:43,094] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16696/markers.fasta)
[2023-03-18 03:29:43,094] [INFO] Task started: Blastn
[2023-03-18 03:29:43,094] [INFO] Running command: blastn -query OceanDNA-b16696/markers.fasta -db /var/lib/cwl/stg202c63ce-07b7-47de-b54e-c0999f3b3b6b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16696/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:29:43,795] [INFO] Task succeeded: Blastn
[2023-03-18 03:29:43,796] [INFO] Selected 13 target genomes.
[2023-03-18 03:29:43,796] [INFO] Target genome list was writen to OceanDNA-b16696/target_genomes_gtdb.txt
[2023-03-18 03:29:43,827] [INFO] Task started: fastANI
[2023-03-18 03:29:43,827] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbd7b1f1-9f36-48b8-a2c3-cc20acefa21c/OceanDNA-b16696.fa --refList OceanDNA-b16696/target_genomes_gtdb.txt --output OceanDNA-b16696/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:29:48,925] [INFO] Task succeeded: fastANI
[2023-03-18 03:29:48,933] [INFO] Found 13 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-18 03:29:48,933] [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_003208835.1	s__Synechococcus_E sp003208835	96.3293	354	509	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	inconclusive
GCA_016777265.1	s__Synechococcus_E sp016777265	95.5416	307	509	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	inconclusive
GCF_000012505.1	s__Synechococcus_E sp000012505	87.3753	476	509	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	87.1345	465	509	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	78.1398	175	509	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	78.061	174	509	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	78.0127	150	509	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_013911515.1	s__Synechococcus_E sp013911515	77.851	153	509	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_014279775.1	s__Synechococcus_C sp002500205	77.6075	93	509	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	-
GCF_014279875.1	s__Synechococcus_C sp002172935	77.4913	113	509	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_000153045.1	s__WH-5701 sp000153045	77.1853	66	509	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	-
GCF_019104765.1	s__Vulcanococcus sp019104765	76.9356	86	509	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014654725.1	s__Vulcanococcus sp014654725	76.8351	88	509	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:29:48,934] [INFO] GTDB search result was written to OceanDNA-b16696/result_gtdb.tsv
[2023-03-18 03:29:48,934] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:29:48,935] [INFO] DFAST_QC result json was written to OceanDNA-b16696/dqc_result.json
[2023-03-18 03:29:48,935] [INFO] DFAST_QC completed!
[2023-03-18 03:29:48,935] [INFO] Total running time: 0h1m18s