[2023-03-18 01:41:20,960] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:41:20,960] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:41:20,960] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4c0f321-097a-47a6-a5b6-dcf9fb5c40c7/dqc_reference
[2023-03-18 01:41:22,074] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:41:22,075] [INFO] Task started: Prodigal
[2023-03-18 01:41:22,075] [INFO] Running command: cat /var/lib/cwl/stg23c85b59-a751-41e0-aaf3-54a5d8a68c54/OceanDNA-b34269.fa | prodigal -d OceanDNA-b34269/cds.fna -a OceanDNA-b34269/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:41:33,642] [INFO] Task succeeded: Prodigal
[2023-03-18 01:41:33,643] [INFO] Task started: HMMsearch
[2023-03-18 01:41:33,643] [INFO] Running command: hmmsearch --tblout OceanDNA-b34269/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4c0f321-097a-47a6-a5b6-dcf9fb5c40c7/dqc_reference/reference_markers.hmm OceanDNA-b34269/protein.faa > /dev/null
[2023-03-18 01:41:33,846] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:41:33,846] [INFO] Found 6/6 markers.
[2023-03-18 01:41:33,864] [INFO] Query marker FASTA was written to OceanDNA-b34269/markers.fasta
[2023-03-18 01:41:33,866] [INFO] Task started: Blastn
[2023-03-18 01:41:33,866] [INFO] Running command: blastn -query OceanDNA-b34269/markers.fasta -db /var/lib/cwl/stgb4c0f321-097a-47a6-a5b6-dcf9fb5c40c7/dqc_reference/reference_markers.fasta -out OceanDNA-b34269/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:41:34,561] [INFO] Task succeeded: Blastn
[2023-03-18 01:41:34,562] [INFO] Selected 33 target genomes.
[2023-03-18 01:41:34,562] [INFO] Target genome list was writen to OceanDNA-b34269/target_genomes.txt
[2023-03-18 01:41:34,580] [INFO] Task started: fastANI
[2023-03-18 01:41:34,580] [INFO] Running command: fastANI --query /var/lib/cwl/stg23c85b59-a751-41e0-aaf3-54a5d8a68c54/OceanDNA-b34269.fa --refList OceanDNA-b34269/target_genomes.txt --output OceanDNA-b34269/fastani_result.tsv --threads 1
[2023-03-18 01:41:58,950] [INFO] Task succeeded: fastANI
[2023-03-18 01:41:58,950] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4c0f321-097a-47a6-a5b6-dcf9fb5c40c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:41:58,950] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4c0f321-097a-47a6-a5b6-dcf9fb5c40c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:41:58,957] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:41:58,957] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:41:58,957] [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
Alteromonas lipolytica	strain=JW12	GCA_001758465.1	1856405	1856405	type	True	77.3118	51	619	95	below_threshold
Alteromonas lipolytica	strain=CGMCC 1.15735	GCA_014643555.1	1856405	1856405	type	True	77.1946	52	619	95	below_threshold
Alteromonas alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	76.5639	65	619	95	below_threshold
Aestuariibacter halophilus	strain=JC2043	GCA_020687825.1	226011	226011	type	True	76.5553	74	619	95	below_threshold
Alteromonas oceani	strain=S35	GCA_003731635.1	2071609	2071609	type	True	76.4797	57	619	95	below_threshold
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	76.4234	56	619	95	below_threshold
Bowmanella pacifica	strain=CGMCC 1.7086	GCA_014645355.1	502051	502051	type	True	76.3802	67	619	95	below_threshold
Neptunicella marina	strain=S27-2	GCA_014270035.1	2125989	2125989	type	True	76.3582	71	619	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:41:58,957] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34269/tc_result.tsv
[2023-03-18 01:41:58,957] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:41:58,957] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:41:58,957] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4c0f321-097a-47a6-a5b6-dcf9fb5c40c7/dqc_reference/checkm_data
[2023-03-18 01:41:58,958] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:41:58,962] [INFO] Task started: CheckM
[2023-03-18 01:41:58,962] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34269/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34269/checkm_input OceanDNA-b34269/checkm_result
[2023-03-18 01:42:32,004] [INFO] Task succeeded: CheckM
[2023-03-18 01:42:32,005] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:42:32,007] [INFO] ===== Completeness check finished =====
[2023-03-18 01:42:32,007] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:42:32,007] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34269/markers.fasta)
[2023-03-18 01:42:32,008] [INFO] Task started: Blastn
[2023-03-18 01:42:32,008] [INFO] Running command: blastn -query OceanDNA-b34269/markers.fasta -db /var/lib/cwl/stgb4c0f321-097a-47a6-a5b6-dcf9fb5c40c7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34269/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:42:33,128] [INFO] Task succeeded: Blastn
[2023-03-18 01:42:33,129] [INFO] Selected 25 target genomes.
[2023-03-18 01:42:33,129] [INFO] Target genome list was writen to OceanDNA-b34269/target_genomes_gtdb.txt
[2023-03-18 01:42:33,152] [INFO] Task started: fastANI
[2023-03-18 01:42:33,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg23c85b59-a751-41e0-aaf3-54a5d8a68c54/OceanDNA-b34269.fa --refList OceanDNA-b34269/target_genomes_gtdb.txt --output OceanDNA-b34269/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:42:50,281] [INFO] Task succeeded: fastANI
[2023-03-18 01:42:50,289] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:42:50,289] [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_004329715.1	s__JS7-9 sp004329715	97.5658	607	619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__JS7-9	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001758465.1	s__Alteromonas lipolytica	77.3118	51	619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.99	99.99	1.00	1.00	2	-
GCA_001660395.1	s__XY-R5 sp001660395	77.0228	62	619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__XY-R5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222405.1	s__Alteromonas sp018222405	76.6572	57	619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002993365.1	s__Alteromonas alba	76.5979	64	619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584565.2	s__Alteromonas sp002729795	76.4624	53	619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.21	97.21	0.92	0.92	2	-
GCF_018531185.1	s__Bowmanella sp018531185	76.4542	68	619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Bowmanella	95.0	96.11	96.11	0.88	0.88	2	-
GCF_014645355.1	s__Bowmanella pacifica	76.4105	66	619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Bowmanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014270035.1	s__Neptunicella marina	76.3582	71	619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Neptunicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017794925.1	s__Alteromonas sp017794925	76.3478	56	619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339125.1	s__Alteromonas sp002335925	76.285	57	619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.57	96.36	0.89	0.83	19	-
GCF_002887595.1	s__Bowmanella denitrificans	76.2558	62	619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Bowmanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691625.1	s__Alteromonas sp002691625	76.2048	58	619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.62	99.31	0.91	0.90	3	-
--------------------------------------------------------------------------------
[2023-03-18 01:42:50,289] [INFO] GTDB search result was written to OceanDNA-b34269/result_gtdb.tsv
[2023-03-18 01:42:50,289] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:42:50,291] [INFO] DFAST_QC result json was written to OceanDNA-b34269/dqc_result.json
[2023-03-18 01:42:50,291] [INFO] DFAST_QC completed!
[2023-03-18 01:42:50,291] [INFO] Total running time: 0h1m29s