[2023-03-16 16:43:21,348] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:43:21,349] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:43:21,349] [INFO] DQC Reference Directory: /var/lib/cwl/stg8008b25c-b3d5-441f-bf13-006c04bcf76a/dqc_reference
[2023-03-16 16:43:22,503] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:43:22,503] [INFO] Task started: Prodigal
[2023-03-16 16:43:22,503] [INFO] Running command: cat /var/lib/cwl/stgb614548b-dc73-4c33-b22b-22cb834a6494/OceanDNA-b34798.fa | prodigal -d OceanDNA-b34798/cds.fna -a OceanDNA-b34798/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:43:39,128] [INFO] Task succeeded: Prodigal
[2023-03-16 16:43:39,128] [INFO] Task started: HMMsearch
[2023-03-16 16:43:39,128] [INFO] Running command: hmmsearch --tblout OceanDNA-b34798/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8008b25c-b3d5-441f-bf13-006c04bcf76a/dqc_reference/reference_markers.hmm OceanDNA-b34798/protein.faa > /dev/null
[2023-03-16 16:43:39,317] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:43:39,317] [INFO] Found 6/6 markers.
[2023-03-16 16:43:39,333] [INFO] Query marker FASTA was written to OceanDNA-b34798/markers.fasta
[2023-03-16 16:43:39,334] [INFO] Task started: Blastn
[2023-03-16 16:43:39,334] [INFO] Running command: blastn -query OceanDNA-b34798/markers.fasta -db /var/lib/cwl/stg8008b25c-b3d5-441f-bf13-006c04bcf76a/dqc_reference/reference_markers.fasta -out OceanDNA-b34798/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:43:40,415] [INFO] Task succeeded: Blastn
[2023-03-16 16:43:40,416] [INFO] Selected 30 target genomes.
[2023-03-16 16:43:40,416] [INFO] Target genome list was writen to OceanDNA-b34798/target_genomes.txt
[2023-03-16 16:43:40,455] [INFO] Task started: fastANI
[2023-03-16 16:43:40,455] [INFO] Running command: fastANI --query /var/lib/cwl/stgb614548b-dc73-4c33-b22b-22cb834a6494/OceanDNA-b34798.fa --refList OceanDNA-b34798/target_genomes.txt --output OceanDNA-b34798/fastani_result.tsv --threads 1
[2023-03-16 16:44:06,564] [INFO] Task succeeded: fastANI
[2023-03-16 16:44:06,564] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8008b25c-b3d5-441f-bf13-006c04bcf76a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:44:06,564] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8008b25c-b3d5-441f-bf13-006c04bcf76a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:44:06,575] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:44:06,575] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 16:44:06,575] [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	77.6445	67	866	95	below_threshold
Alteromonas lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	77.5655	60	866	95	below_threshold
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	77.2905	57	866	95	below_threshold
Paraglaciecola aquimarina	strain=GGW-M5	GCA_021532655.1	1235557	1235557	type	True	77.2798	66	866	95	below_threshold
Alteromonas profundi	strain=345S023	GCA_010500865.1	2696062	2696062	type	True	77.2312	55	866	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	77.2062	59	866	95	below_threshold
Paraglaciecola arctica	strain=BSs20135	GCA_000314995.1	1128911	1128911	type	True	77.1867	73	866	95	below_threshold
Glaciecola pallidula	strain=ACAM 615	GCA_000315035.1	56807	56807	type	True	77.1171	59	866	95	below_threshold
Glaciecola pallidula	strain=DSM 14239	GCA_000428905.1	56807	56807	type	True	77.0308	58	866	95	below_threshold
Paraglaciecola hydrolytica	strain=S66	GCA_001565895.1	1799789	1799789	type	True	76.7626	67	866	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	76.6297	51	866	95	below_threshold
Neptunicella marina	strain=S27-2	GCA_014270035.1	2125989	2125989	type	True	76.6022	54	866	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 16:44:06,575] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34798/tc_result.tsv
[2023-03-16 16:44:06,575] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:44:06,575] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:44:06,576] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8008b25c-b3d5-441f-bf13-006c04bcf76a/dqc_reference/checkm_data
[2023-03-16 16:44:06,576] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:44:06,603] [INFO] Task started: CheckM
[2023-03-16 16:44:06,603] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34798/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34798/checkm_input OceanDNA-b34798/checkm_result
[2023-03-16 16:44:45,389] [INFO] Task succeeded: CheckM
[2023-03-16 16:44:45,390] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 16:44:45,392] [INFO] ===== Completeness check finished =====
[2023-03-16 16:44:45,392] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:44:45,392] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34798/markers.fasta)
[2023-03-16 16:44:45,393] [INFO] Task started: Blastn
[2023-03-16 16:44:45,393] [INFO] Running command: blastn -query OceanDNA-b34798/markers.fasta -db /var/lib/cwl/stg8008b25c-b3d5-441f-bf13-006c04bcf76a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34798/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:44:46,437] [INFO] Task succeeded: Blastn
[2023-03-16 16:44:46,438] [INFO] Selected 23 target genomes.
[2023-03-16 16:44:46,438] [INFO] Target genome list was writen to OceanDNA-b34798/target_genomes_gtdb.txt
[2023-03-16 16:44:46,488] [INFO] Task started: fastANI
[2023-03-16 16:44:46,488] [INFO] Running command: fastANI --query /var/lib/cwl/stgb614548b-dc73-4c33-b22b-22cb834a6494/OceanDNA-b34798.fa --refList OceanDNA-b34798/target_genomes_gtdb.txt --output OceanDNA-b34798/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:45:01,196] [INFO] Task succeeded: fastANI
[2023-03-16 16:45:01,204] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 16:45:01,205] [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_002292215.1	s__Glaciecola sp002292215	99.7207	764	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	99.49	98.83	0.91	0.88	4	conclusive
GCF_000155775.1	s__Glaciecola sp000155775	78.6733	275	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003203515.1	s__Glaciecola sp003203515	77.8961	64	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000213655.1	s__Alteromonas naphthalenivorans	77.6037	68	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.31	95.95	0.86	0.84	6	-
GCA_001562115.1	s__Alteromonas stellipolaris	77.59	67	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.45	98.97	0.97	0.94	8	-
GCF_902506055.1	s__Alteromonas lipotrueae	77.5756	60	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.66	99.49	0.97	0.95	4	-
GCF_017368475.1	s__Alteromonas_F sp017368475	77.561	55	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861065.1	s__Paraglaciecola arctica_B	77.4239	58	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018100795.1	s__Alteromonas sp018100795	77.3262	70	866	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	77.2312	55	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860635.1	s__Aliiglaciecola lipolytica_A	77.1912	63	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliiglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796765.1	s__Paraglaciecola sp009796765	77.0882	74	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428905.1	s__Glaciecola pallidula	77.0308	58	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	100.00	100.00	0.99	0.99	2	-
GCA_014872805.1	s__Glaciecola sp014872805	76.9624	96	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002835935.1	s__Paraglaciecola sp002835935	76.7642	73	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 16:45:01,205] [INFO] GTDB search result was written to OceanDNA-b34798/result_gtdb.tsv
[2023-03-16 16:45:01,205] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:45:01,206] [INFO] DFAST_QC result json was written to OceanDNA-b34798/dqc_result.json
[2023-03-16 16:45:01,207] [INFO] DFAST_QC completed!
[2023-03-16 16:45:01,207] [INFO] Total running time: 0h1m40s