[2023-03-16 00:59:57,173] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:59:57,173] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:59:57,173] [INFO] DQC Reference Directory: /var/lib/cwl/stgaec588b4-b8a8-4afe-bda5-d8f807e52a1f/dqc_reference
[2023-03-16 00:59:59,434] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:59:59,447] [INFO] Task started: Prodigal
[2023-03-16 00:59:59,447] [INFO] Running command: cat /var/lib/cwl/stge87ecc5e-1330-4258-993a-7a6ba2e3e968/OceanDNA-b16518.fa | prodigal -d OceanDNA-b16518/cds.fna -a OceanDNA-b16518/protein.faa -g 11 -q > /dev/null
[2023-03-16 01:00:08,369] [INFO] Task succeeded: Prodigal
[2023-03-16 01:00:08,369] [INFO] Task started: HMMsearch
[2023-03-16 01:00:08,369] [INFO] Running command: hmmsearch --tblout OceanDNA-b16518/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaec588b4-b8a8-4afe-bda5-d8f807e52a1f/dqc_reference/reference_markers.hmm OceanDNA-b16518/protein.faa > /dev/null
[2023-03-16 01:00:08,504] [INFO] Task succeeded: HMMsearch
[2023-03-16 01:00:08,505] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge87ecc5e-1330-4258-993a-7a6ba2e3e968/OceanDNA-b16518.fa]
[2023-03-16 01:00:08,515] [INFO] Query marker FASTA was written to OceanDNA-b16518/markers.fasta
[2023-03-16 01:00:08,517] [INFO] Task started: Blastn
[2023-03-16 01:00:08,517] [INFO] Running command: blastn -query OceanDNA-b16518/markers.fasta -db /var/lib/cwl/stgaec588b4-b8a8-4afe-bda5-d8f807e52a1f/dqc_reference/reference_markers.fasta -out OceanDNA-b16518/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:00:08,958] [INFO] Task succeeded: Blastn
[2023-03-16 01:00:08,959] [INFO] Selected 14 target genomes.
[2023-03-16 01:00:08,959] [INFO] Target genome list was writen to OceanDNA-b16518/target_genomes.txt
[2023-03-16 01:00:08,972] [INFO] Task started: fastANI
[2023-03-16 01:00:08,972] [INFO] Running command: fastANI --query /var/lib/cwl/stge87ecc5e-1330-4258-993a-7a6ba2e3e968/OceanDNA-b16518.fa --refList OceanDNA-b16518/target_genomes.txt --output OceanDNA-b16518/fastani_result.tsv --threads 1
[2023-03-16 01:00:19,707] [INFO] Task succeeded: fastANI
[2023-03-16 01:00:19,707] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaec588b4-b8a8-4afe-bda5-d8f807e52a1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 01:00:19,707] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaec588b4-b8a8-4afe-bda5-d8f807e52a1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 01:00:19,711] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 01:00:19,711] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 01:00:19,711] [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	77.2819	66	220	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 01:00:19,711] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16518/tc_result.tsv
[2023-03-16 01:00:19,711] [INFO] ===== Taxonomy check completed =====
[2023-03-16 01:00:19,711] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 01:00:19,711] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaec588b4-b8a8-4afe-bda5-d8f807e52a1f/dqc_reference/checkm_data
[2023-03-16 01:00:19,712] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 01:00:19,715] [INFO] Task started: CheckM
[2023-03-16 01:00:19,715] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16518/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16518/checkm_input OceanDNA-b16518/checkm_result
[2023-03-16 01:00:47,819] [INFO] Task succeeded: CheckM
[2023-03-16 01:00:47,820] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.02%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 01:00:47,822] [INFO] ===== Completeness check finished =====
[2023-03-16 01:00:47,822] [INFO] ===== Start GTDB Search =====
[2023-03-16 01:00:47,822] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16518/markers.fasta)
[2023-03-16 01:00:47,823] [INFO] Task started: Blastn
[2023-03-16 01:00:47,823] [INFO] Running command: blastn -query OceanDNA-b16518/markers.fasta -db /var/lib/cwl/stgaec588b4-b8a8-4afe-bda5-d8f807e52a1f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16518/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:00:48,283] [INFO] Task succeeded: Blastn
[2023-03-16 01:00:48,283] [INFO] Selected 10 target genomes.
[2023-03-16 01:00:48,284] [INFO] Target genome list was writen to OceanDNA-b16518/target_genomes_gtdb.txt
[2023-03-16 01:00:48,335] [INFO] Task started: fastANI
[2023-03-16 01:00:48,335] [INFO] Running command: fastANI --query /var/lib/cwl/stge87ecc5e-1330-4258-993a-7a6ba2e3e968/OceanDNA-b16518.fa --refList OceanDNA-b16518/target_genomes_gtdb.txt --output OceanDNA-b16518/fastani_result_gtdb.tsv --threads 1
[2023-03-16 01:00:52,227] [INFO] Task succeeded: fastANI
[2023-03-16 01:00:52,233] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 01:00:52,233] [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_018623675.1	s__Synechococcus_C sp018623675	93.8635	135	220	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_000153825.1	s__Synechococcus_C sp000153825	80.1416	152	220	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_900473935.1	s__Synechococcus_C sp002171995	78.4334	110	220	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	98.95	98.80	0.86	0.67	4	-
GCF_014279595.1	s__Synechococcus_C sp000153065	78.1589	100	220	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	-
GCF_900474295.1	s__Synechococcus_C sp900474295	78.142	119	220	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	78.128	89	220	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_004209775.1	s__Synechococcus_C sp004209775	77.9205	107	220	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014279815.1	s__Synechococcus_C sp014279815	77.8439	77	220	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_000737575.1	s__Synechococcus_E sp000737575	77.2147	75	220	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	-
--------------------------------------------------------------------------------
[2023-03-16 01:00:52,236] [INFO] GTDB search result was written to OceanDNA-b16518/result_gtdb.tsv
[2023-03-16 01:00:52,241] [INFO] ===== GTDB Search completed =====
[2023-03-16 01:00:52,244] [INFO] DFAST_QC result json was written to OceanDNA-b16518/dqc_result.json
[2023-03-16 01:00:52,244] [INFO] DFAST_QC completed!
[2023-03-16 01:00:52,244] [INFO] Total running time: 0h0m55s