[2023-03-16 21:29:26,232] [INFO] DFAST_QC pipeline started.
[2023-03-16 21:29:26,232] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 21:29:26,232] [INFO] DQC Reference Directory: /var/lib/cwl/stg819a699a-c07d-48c7-910a-b5bf85743647/dqc_reference
[2023-03-16 21:29:29,068] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 21:29:29,068] [INFO] Task started: Prodigal
[2023-03-16 21:29:29,068] [INFO] Running command: cat /var/lib/cwl/stg6212b2da-ba9e-4c8f-ae2d-fc635c636a61/OceanDNA-b34791.fa | prodigal -d OceanDNA-b34791/cds.fna -a OceanDNA-b34791/protein.faa -g 11 -q > /dev/null
[2023-03-16 21:29:56,836] [INFO] Task succeeded: Prodigal
[2023-03-16 21:29:56,837] [INFO] Task started: HMMsearch
[2023-03-16 21:29:56,837] [INFO] Running command: hmmsearch --tblout OceanDNA-b34791/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg819a699a-c07d-48c7-910a-b5bf85743647/dqc_reference/reference_markers.hmm OceanDNA-b34791/protein.faa > /dev/null
[2023-03-16 21:29:57,081] [INFO] Task succeeded: HMMsearch
[2023-03-16 21:29:57,081] [INFO] Found 6/6 markers.
[2023-03-16 21:29:57,108] [INFO] Query marker FASTA was written to OceanDNA-b34791/markers.fasta
[2023-03-16 21:29:57,108] [INFO] Task started: Blastn
[2023-03-16 21:29:57,108] [INFO] Running command: blastn -query OceanDNA-b34791/markers.fasta -db /var/lib/cwl/stg819a699a-c07d-48c7-910a-b5bf85743647/dqc_reference/reference_markers.fasta -out OceanDNA-b34791/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:29:58,068] [INFO] Task succeeded: Blastn
[2023-03-16 21:29:58,069] [INFO] Selected 19 target genomes.
[2023-03-16 21:29:58,069] [INFO] Target genome list was writen to OceanDNA-b34791/target_genomes.txt
[2023-03-16 21:29:58,079] [INFO] Task started: fastANI
[2023-03-16 21:29:58,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg6212b2da-ba9e-4c8f-ae2d-fc635c636a61/OceanDNA-b34791.fa --refList OceanDNA-b34791/target_genomes.txt --output OceanDNA-b34791/fastani_result.tsv --threads 1
[2023-03-16 21:30:18,682] [INFO] Task succeeded: fastANI
[2023-03-16 21:30:18,682] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg819a699a-c07d-48c7-910a-b5bf85743647/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 21:30:18,682] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg819a699a-c07d-48c7-910a-b5bf85743647/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 21:30:18,689] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 21:30:18,689] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 21:30:18,689] [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
Glaciecola nitratireducens	strain=FR1064	GCA_000226565.1	300231	300231	type	True	86.6451	1060	1396	95	below_threshold
Glaciecola pallidula	strain=ACAM 615	GCA_000315035.1	56807	56807	type	True	79.6322	574	1396	95	below_threshold
Glaciecola pallidula	strain=DSM 14239	GCA_000428905.1	56807	56807	type	True	79.6188	582	1396	95	below_threshold
Ningiella ruwaisensis	strain=B66	GCA_004798935.1	2364274	2364274	type	True	77.9307	71	1396	95	below_threshold
Aliiglaciecola lipolytica	strain=E3	GCA_000314975.1	477689	477689	type	True	77.2775	71	1396	95	below_threshold
Glaciecola punicea	strain=ACAM 611	GCA_000252165.2	56804	56804	type	True	77.2095	86	1396	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	76.9211	71	1396	95	below_threshold
Paraglaciecola aquimarina	strain=GGW-M5	GCA_021532655.1	1235557	1235557	type	True	76.8004	78	1396	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 21:30:18,689] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34791/tc_result.tsv
[2023-03-16 21:30:18,689] [INFO] ===== Taxonomy check completed =====
[2023-03-16 21:30:18,689] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 21:30:18,690] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg819a699a-c07d-48c7-910a-b5bf85743647/dqc_reference/checkm_data
[2023-03-16 21:30:18,690] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 21:30:18,699] [INFO] Task started: CheckM
[2023-03-16 21:30:18,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34791/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34791/checkm_input OceanDNA-b34791/checkm_result
[2023-03-16 21:31:17,087] [INFO] Task succeeded: CheckM
[2023-03-16 21:31:17,087] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 21:31:17,090] [INFO] ===== Completeness check finished =====
[2023-03-16 21:31:17,090] [INFO] ===== Start GTDB Search =====
[2023-03-16 21:31:17,090] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34791/markers.fasta)
[2023-03-16 21:31:17,090] [INFO] Task started: Blastn
[2023-03-16 21:31:17,090] [INFO] Running command: blastn -query OceanDNA-b34791/markers.fasta -db /var/lib/cwl/stg819a699a-c07d-48c7-910a-b5bf85743647/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34791/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:31:18,120] [INFO] Task succeeded: Blastn
[2023-03-16 21:31:18,121] [INFO] Selected 16 target genomes.
[2023-03-16 21:31:18,121] [INFO] Target genome list was writen to OceanDNA-b34791/target_genomes_gtdb.txt
[2023-03-16 21:31:18,202] [INFO] Task started: fastANI
[2023-03-16 21:31:18,202] [INFO] Running command: fastANI --query /var/lib/cwl/stg6212b2da-ba9e-4c8f-ae2d-fc635c636a61/OceanDNA-b34791.fa --refList OceanDNA-b34791/target_genomes_gtdb.txt --output OceanDNA-b34791/fastani_result_gtdb.tsv --threads 1
[2023-03-16 21:31:32,197] [INFO] Task succeeded: fastANI
[2023-03-16 21:31:32,204] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 21:31:32,204] [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_000226565.1	s__Glaciecola nitratireducens	86.6567	1059	1396	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428905.1	s__Glaciecola pallidula	79.6008	584	1396	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002836745.1	s__Glaciecola sp002836745	79.5804	586	1396	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479945.1	s__Glaciecola sp905479945	78.9162	334	1396	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015595035.1	s__Glaciecola sp015595035	78.3323	192	1396	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	78.1196	104	1396	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292215.1	s__Glaciecola sp002292215	77.25	67	1396	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	99.49	98.83	0.91	0.88	4	-
GCF_000252165.1	s__Glaciecola punicea	77.2095	86	1396	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	99.53	99.53	0.94	0.94	2	-
GCF_903772925.1	s__Alteromonas macleodii_A	77.0319	70	1396	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002338515.1	s__Glaciecola sp002338515	76.4725	67	1396	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 21:31:32,204] [INFO] GTDB search result was written to OceanDNA-b34791/result_gtdb.tsv
[2023-03-16 21:31:32,205] [INFO] ===== GTDB Search completed =====
[2023-03-16 21:31:32,206] [INFO] DFAST_QC result json was written to OceanDNA-b34791/dqc_result.json
[2023-03-16 21:31:32,206] [INFO] DFAST_QC completed!
[2023-03-16 21:31:32,206] [INFO] Total running time: 0h2m6s