[2023-03-16 19:57:56,496] [INFO] DFAST_QC pipeline started.
[2023-03-16 19:57:56,496] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 19:57:56,496] [INFO] DQC Reference Directory: /var/lib/cwl/stg1eefb04c-2386-41c6-8b16-d970dfdc4542/dqc_reference
[2023-03-16 19:57:57,576] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 19:57:57,577] [INFO] Task started: Prodigal
[2023-03-16 19:57:57,577] [INFO] Running command: cat /var/lib/cwl/stg331f2694-55b5-4656-a045-9691710f3b74/OceanDNA-b34564.fa | prodigal -d OceanDNA-b34564/cds.fna -a OceanDNA-b34564/protein.faa -g 11 -q > /dev/null
[2023-03-16 19:58:16,429] [INFO] Task succeeded: Prodigal
[2023-03-16 19:58:16,429] [INFO] Task started: HMMsearch
[2023-03-16 19:58:16,429] [INFO] Running command: hmmsearch --tblout OceanDNA-b34564/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1eefb04c-2386-41c6-8b16-d970dfdc4542/dqc_reference/reference_markers.hmm OceanDNA-b34564/protein.faa > /dev/null
[2023-03-16 19:58:16,635] [INFO] Task succeeded: HMMsearch
[2023-03-16 19:58:16,636] [INFO] Found 6/6 markers.
[2023-03-16 19:58:16,658] [INFO] Query marker FASTA was written to OceanDNA-b34564/markers.fasta
[2023-03-16 19:58:16,659] [INFO] Task started: Blastn
[2023-03-16 19:58:16,659] [INFO] Running command: blastn -query OceanDNA-b34564/markers.fasta -db /var/lib/cwl/stg1eefb04c-2386-41c6-8b16-d970dfdc4542/dqc_reference/reference_markers.fasta -out OceanDNA-b34564/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:58:17,268] [INFO] Task succeeded: Blastn
[2023-03-16 19:58:17,269] [INFO] Selected 21 target genomes.
[2023-03-16 19:58:17,269] [INFO] Target genome list was writen to OceanDNA-b34564/target_genomes.txt
[2023-03-16 19:58:17,282] [INFO] Task started: fastANI
[2023-03-16 19:58:17,282] [INFO] Running command: fastANI --query /var/lib/cwl/stg331f2694-55b5-4656-a045-9691710f3b74/OceanDNA-b34564.fa --refList OceanDNA-b34564/target_genomes.txt --output OceanDNA-b34564/fastani_result.tsv --threads 1
[2023-03-16 19:58:31,974] [INFO] Task succeeded: fastANI
[2023-03-16 19:58:31,974] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1eefb04c-2386-41c6-8b16-d970dfdc4542/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 19:58:31,974] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1eefb04c-2386-41c6-8b16-d970dfdc4542/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 19:58:31,983] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 19:58:31,983] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 19:58:31,983] [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 naphthalenivorans	strain=SN2	GCA_000213655.1	715451	715451	type	True	90.7872	1042	1151	95	below_threshold
Alteromonas lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	89.6363	1051	1151	95	below_threshold
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	78.9477	355	1151	95	below_threshold
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	78.8688	331	1151	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	78.8263	321	1151	95	below_threshold
Alteromonas genovensis	strain=LMG 24078	GCA_010500895.1	471225	471225	type	True	78.7516	272	1151	95	below_threshold
Alteromonas profundi	strain=345S023	GCA_010500865.1	2696062	2696062	type	True	78.7381	325	1151	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	78.6175	337	1151	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	78.5436	334	1151	95	below_threshold
Alteromonas hispanica	strain=LMG 22958	GCA_010500915.1	315421	315421	type	True	78.5054	257	1151	95	below_threshold
Paraglaciecola mesophila	strain=KMM 241	GCA_000315015.1	197222	197222	type	True	76.7113	82	1151	95	below_threshold
Alteromonas alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	76.6648	101	1151	95	below_threshold
Alteromonas facilis	strain=P0213	GCA_002807665.1	2048004	2048004	type	True	76.574	75	1151	95	below_threshold
Glaciecola pallidula	strain=ACAM 615	GCA_000315035.1	56807	56807	type	True	76.3629	50	1151	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 19:58:31,983] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34564/tc_result.tsv
[2023-03-16 19:58:31,983] [INFO] ===== Taxonomy check completed =====
[2023-03-16 19:58:31,983] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 19:58:31,983] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1eefb04c-2386-41c6-8b16-d970dfdc4542/dqc_reference/checkm_data
[2023-03-16 19:58:31,984] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 19:58:32,006] [INFO] Task started: CheckM
[2023-03-16 19:58:32,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34564/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34564/checkm_input OceanDNA-b34564/checkm_result
[2023-03-16 19:59:20,191] [INFO] Task succeeded: CheckM
[2023-03-16 19:59:20,192] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 19:59:20,195] [INFO] ===== Completeness check finished =====
[2023-03-16 19:59:20,195] [INFO] ===== Start GTDB Search =====
[2023-03-16 19:59:20,195] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34564/markers.fasta)
[2023-03-16 19:59:20,196] [INFO] Task started: Blastn
[2023-03-16 19:59:20,197] [INFO] Running command: blastn -query OceanDNA-b34564/markers.fasta -db /var/lib/cwl/stg1eefb04c-2386-41c6-8b16-d970dfdc4542/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34564/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:59:21,158] [INFO] Task succeeded: Blastn
[2023-03-16 19:59:21,159] [INFO] Selected 10 target genomes.
[2023-03-16 19:59:21,160] [INFO] Target genome list was writen to OceanDNA-b34564/target_genomes_gtdb.txt
[2023-03-16 19:59:21,172] [INFO] Task started: fastANI
[2023-03-16 19:59:21,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg331f2694-55b5-4656-a045-9691710f3b74/OceanDNA-b34564.fa --refList OceanDNA-b34564/target_genomes_gtdb.txt --output OceanDNA-b34564/fastani_result_gtdb.tsv --threads 1
[2023-03-16 19:59:29,880] [INFO] Task succeeded: fastANI
[2023-03-16 19:59:29,887] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 19:59:29,887] [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_001562115.1	s__Alteromonas stellipolaris	98.871	1125	1151	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.45	98.97	0.97	0.94	8	conclusive
GCF_018100795.1	s__Alteromonas sp018100795	94.06	1068	1151	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000213655.1	s__Alteromonas naphthalenivorans	90.7872	1042	1151	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.31	95.95	0.86	0.84	6	-
GCF_902506055.1	s__Alteromonas lipotrueae	89.6593	1065	1151	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.66	99.49	0.97	0.95	4	-
GCF_000730385.1	s__Alteromonas australica	78.9538	354	1151	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.80	98.45	0.91	0.74	29	-
GCF_000020585.3	s__Alteromonas mediterranea	78.8622	330	1151	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.15	97.41	0.86	0.82	24	-
GCF_016405965.1	s__Alteromonas sp016405965	78.7773	303	1151	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500865.1	s__Alteromonas profundi	78.7344	324	1151	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002993325.1	s__Alteromonas gracilis	78.6402	317	1151	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	96.94	96.21	0.87	0.84	4	-
GCF_003443615.1	s__Alteromonas sp003443615	78.552	322	1151	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-16 19:59:29,887] [INFO] GTDB search result was written to OceanDNA-b34564/result_gtdb.tsv
[2023-03-16 19:59:29,887] [INFO] ===== GTDB Search completed =====
[2023-03-16 19:59:29,889] [INFO] DFAST_QC result json was written to OceanDNA-b34564/dqc_result.json
[2023-03-16 19:59:29,889] [INFO] DFAST_QC completed!
[2023-03-16 19:59:29,890] [INFO] Total running time: 0h1m33s