[2023-03-17 03:24:50,887] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:24:50,890] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:24:50,890] [INFO] DQC Reference Directory: /var/lib/cwl/stg08db1bc5-e359-484c-944a-f46571594dc8/dqc_reference
[2023-03-17 03:24:52,032] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:24:52,033] [INFO] Task started: Prodigal
[2023-03-17 03:24:52,033] [INFO] Running command: cat /var/lib/cwl/stgee5d947d-c54f-4634-85b9-9317a1704d76/OceanDNA-b34930.fa | prodigal -d OceanDNA-b34930/cds.fna -a OceanDNA-b34930/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:25:19,789] [INFO] Task succeeded: Prodigal
[2023-03-17 03:25:19,789] [INFO] Task started: HMMsearch
[2023-03-17 03:25:19,789] [INFO] Running command: hmmsearch --tblout OceanDNA-b34930/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08db1bc5-e359-484c-944a-f46571594dc8/dqc_reference/reference_markers.hmm OceanDNA-b34930/protein.faa > /dev/null
[2023-03-17 03:25:20,046] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:25:20,046] [INFO] Found 6/6 markers.
[2023-03-17 03:25:20,079] [INFO] Query marker FASTA was written to OceanDNA-b34930/markers.fasta
[2023-03-17 03:25:20,080] [INFO] Task started: Blastn
[2023-03-17 03:25:20,081] [INFO] Running command: blastn -query OceanDNA-b34930/markers.fasta -db /var/lib/cwl/stg08db1bc5-e359-484c-944a-f46571594dc8/dqc_reference/reference_markers.fasta -out OceanDNA-b34930/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:25:20,724] [INFO] Task succeeded: Blastn
[2023-03-17 03:25:20,728] [INFO] Selected 25 target genomes.
[2023-03-17 03:25:20,729] [INFO] Target genome list was writen to OceanDNA-b34930/target_genomes.txt
[2023-03-17 03:25:20,744] [INFO] Task started: fastANI
[2023-03-17 03:25:20,744] [INFO] Running command: fastANI --query /var/lib/cwl/stgee5d947d-c54f-4634-85b9-9317a1704d76/OceanDNA-b34930.fa --refList OceanDNA-b34930/target_genomes.txt --output OceanDNA-b34930/fastani_result.tsv --threads 1
[2023-03-17 03:25:38,722] [INFO] Task succeeded: fastANI
[2023-03-17 03:25:38,722] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08db1bc5-e359-484c-944a-f46571594dc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:25:38,722] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08db1bc5-e359-484c-944a-f46571594dc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:25:38,730] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 03:25:38,730] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 03:25:38,730] [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
Paraglaciecola polaris	strain=LMG 21857	GCA_000315055.1	222814	222814	type	True	99.2406	1468	1628	95	conclusive
Paraglaciecola mesophila	strain=KMM 241	GCA_000315015.1	197222	197222	type	True	80.6792	727	1628	95	below_threshold
Paraglaciecola arctica	strain=BSs20135	GCA_000314995.1	1128911	1128911	type	True	78.2352	203	1628	95	below_threshold
Paraglaciecola psychrophila	strain=170	GCA_000315075.1	326544	326544	type	True	77.8587	153	1628	95	below_threshold
Paraglaciecola marina	strain=D3211	GCA_004360155.1	2500157	2500157	type	True	77.7523	138	1628	95	below_threshold
Paraglaciecola aquimarina	strain=GGW-M5	GCA_021532655.1	1235557	1235557	type	True	77.7248	150	1628	95	below_threshold
Paraglaciecola hydrolytica	strain=S66	GCA_001565895.1	1799789	1799789	type	True	77.6975	156	1628	95	below_threshold
Neptunicella marina	strain=S27-2	GCA_014270035.1	2125989	2125989	type	True	77.2529	71	1628	95	below_threshold
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	77.0267	80	1628	95	below_threshold
Bowmanella pacifica	strain=CGMCC 1.7086	GCA_014645355.1	502051	502051	type	True	76.8369	59	1628	95	below_threshold
Paraneptunicella aestuarii	strain=NBU2194	GCA_019900845.1	2831148	2831148	type	True	76.8117	58	1628	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:25:38,730] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34930/tc_result.tsv
[2023-03-17 03:25:38,730] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:25:38,730] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:25:38,730] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08db1bc5-e359-484c-944a-f46571594dc8/dqc_reference/checkm_data
[2023-03-17 03:25:38,731] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:25:38,737] [INFO] Task started: CheckM
[2023-03-17 03:25:38,737] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34930/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34930/checkm_input OceanDNA-b34930/checkm_result
[2023-03-17 03:26:46,429] [INFO] Task succeeded: CheckM
[2023-03-17 03:26:46,430] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:26:46,433] [INFO] ===== Completeness check finished =====
[2023-03-17 03:26:46,433] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:26:46,433] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34930/markers.fasta)
[2023-03-17 03:26:46,434] [INFO] Task started: Blastn
[2023-03-17 03:26:46,434] [INFO] Running command: blastn -query OceanDNA-b34930/markers.fasta -db /var/lib/cwl/stg08db1bc5-e359-484c-944a-f46571594dc8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34930/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:26:47,472] [INFO] Task succeeded: Blastn
[2023-03-17 03:26:47,473] [INFO] Selected 13 target genomes.
[2023-03-17 03:26:47,473] [INFO] Target genome list was writen to OceanDNA-b34930/target_genomes_gtdb.txt
[2023-03-17 03:26:47,525] [INFO] Task started: fastANI
[2023-03-17 03:26:47,525] [INFO] Running command: fastANI --query /var/lib/cwl/stgee5d947d-c54f-4634-85b9-9317a1704d76/OceanDNA-b34930.fa --refList OceanDNA-b34930/target_genomes_gtdb.txt --output OceanDNA-b34930/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:26:59,364] [INFO] Task succeeded: fastANI
[2023-03-17 03:26:59,371] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 03:26:59,371] [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_000315055.1	s__Paraglaciecola polaris	99.2406	1468	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009796745.1	s__Paraglaciecola sp009796745	81.7478	906	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011378905.1	s__Paraglaciecola sp011378905	81.4209	909	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315015.1	s__Paraglaciecola mesophila	80.6738	728	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	98.29	98.05	0.87	0.80	4	-
GCF_000014225.1	s__Paraglaciecola atlantica_A	80.3821	754	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000314955.1	s__Paraglaciecola chathamensis	80.2533	686	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	98.24	97.58	0.90	0.88	8	-
GCF_009906955.1	s__Paraglaciecola mesophila_A	80.0844	694	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000314995.1	s__Paraglaciecola arctica	78.2352	203	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003232445.1	s__Paraglaciecola arctica_A	77.9482	102	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009993955.1	s__Paraglaciecola sp009993955	77.4969	117	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	99.98	99.98	0.98	0.98	2	-
GCF_014645355.1	s__Bowmanella pacifica	76.8369	59	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Bowmanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:26:59,371] [INFO] GTDB search result was written to OceanDNA-b34930/result_gtdb.tsv
[2023-03-17 03:26:59,372] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:26:59,373] [INFO] DFAST_QC result json was written to OceanDNA-b34930/dqc_result.json
[2023-03-17 03:26:59,373] [INFO] DFAST_QC completed!
[2023-03-17 03:26:59,373] [INFO] Total running time: 0h2m8s