[2023-03-15 23:07:02,632] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:07:02,632] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:07:02,632] [INFO] DQC Reference Directory: /var/lib/cwl/stg822c864e-2094-4064-aab5-8a69caae5202/dqc_reference
[2023-03-15 23:07:03,965] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:07:03,966] [INFO] Task started: Prodigal
[2023-03-15 23:07:03,966] [INFO] Running command: cat /var/lib/cwl/stg5126f9c4-41fa-439b-ba81-79b677a406da/OceanDNA-b22891.fa | prodigal -d OceanDNA-b22891/cds.fna -a OceanDNA-b22891/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:07:44,821] [INFO] Task succeeded: Prodigal
[2023-03-15 23:07:44,821] [INFO] Task started: HMMsearch
[2023-03-15 23:07:44,821] [INFO] Running command: hmmsearch --tblout OceanDNA-b22891/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg822c864e-2094-4064-aab5-8a69caae5202/dqc_reference/reference_markers.hmm OceanDNA-b22891/protein.faa > /dev/null
[2023-03-15 23:07:45,097] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:07:45,097] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5126f9c4-41fa-439b-ba81-79b677a406da/OceanDNA-b22891.fa]
[2023-03-15 23:07:45,142] [INFO] Query marker FASTA was written to OceanDNA-b22891/markers.fasta
[2023-03-15 23:07:45,143] [INFO] Task started: Blastn
[2023-03-15 23:07:45,143] [INFO] Running command: blastn -query OceanDNA-b22891/markers.fasta -db /var/lib/cwl/stg822c864e-2094-4064-aab5-8a69caae5202/dqc_reference/reference_markers.fasta -out OceanDNA-b22891/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:07:45,676] [INFO] Task succeeded: Blastn
[2023-03-15 23:07:45,678] [INFO] Selected 13 target genomes.
[2023-03-15 23:07:45,678] [INFO] Target genome list was writen to OceanDNA-b22891/target_genomes.txt
[2023-03-15 23:07:45,713] [INFO] Task started: fastANI
[2023-03-15 23:07:45,713] [INFO] Running command: fastANI --query /var/lib/cwl/stg5126f9c4-41fa-439b-ba81-79b677a406da/OceanDNA-b22891.fa --refList OceanDNA-b22891/target_genomes.txt --output OceanDNA-b22891/fastani_result.tsv --threads 1
[2023-03-15 23:08:02,424] [INFO] Task succeeded: fastANI
[2023-03-15 23:08:02,425] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg822c864e-2094-4064-aab5-8a69caae5202/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:08:02,425] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg822c864e-2094-4064-aab5-8a69caae5202/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:08:02,431] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:08:02,431] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:08:02,431] [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
Gimesia alba	strain=Pan241w	GCA_007744675.1	2527973	2527973	type	True	80.1384	1415	2267	95	below_threshold
Gimesia fumaroli	strain=Enr17	GCA_007754425.1	2527976	2527976	type	True	80.0503	1326	2267	95	below_threshold
Gimesia maris	strain=DSM 8797	GCA_000181475.1	122	122	type	True	79.0631	964	2267	95	below_threshold
Gimesia maris	strain=DSM 8797	GCA_008298035.1	122	122	type	True	79.006	990	2267	95	below_threshold
Gimesia maris	strain=DSM 8797	GCA_009720545.1	122	122	type	True	78.9946	984	2267	95	below_threshold
Gimesia algae	strain=Pan161	GCA_007746795.1	2527971	2527971	type	True	78.8769	1011	2267	95	below_threshold
Gimesia benthica	strain=E7	GCA_009720525.1	2608982	2608982	type	True	78.7993	800	2267	95	below_threshold
Gimesia aquarii	strain=V144	GCA_007748195.1	2527964	2527964	type	True	78.3557	857	2267	95	below_threshold
Gimesia panareensis	strain=Enr10	GCA_007748155.1	2527978	2527978	type	True	77.968	810	2267	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:08:02,440] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22891/tc_result.tsv
[2023-03-15 23:08:02,452] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:08:02,452] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:08:02,452] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg822c864e-2094-4064-aab5-8a69caae5202/dqc_reference/checkm_data
[2023-03-15 23:08:02,453] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:08:02,465] [INFO] Task started: CheckM
[2023-03-15 23:08:02,465] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22891/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22891/checkm_input OceanDNA-b22891/checkm_result
[2023-03-15 23:09:41,173] [INFO] Task succeeded: CheckM
[2023-03-15 23:09:41,173] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:09:41,290] [INFO] ===== Completeness check finished =====
[2023-03-15 23:09:41,290] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:09:41,291] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22891/markers.fasta)
[2023-03-15 23:09:41,292] [INFO] Task started: Blastn
[2023-03-15 23:09:41,292] [INFO] Running command: blastn -query OceanDNA-b22891/markers.fasta -db /var/lib/cwl/stg822c864e-2094-4064-aab5-8a69caae5202/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22891/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:09:42,023] [INFO] Task succeeded: Blastn
[2023-03-15 23:09:42,028] [INFO] Selected 17 target genomes.
[2023-03-15 23:09:42,029] [INFO] Target genome list was writen to OceanDNA-b22891/target_genomes_gtdb.txt
[2023-03-15 23:09:42,094] [INFO] Task started: fastANI
[2023-03-15 23:09:42,094] [INFO] Running command: fastANI --query /var/lib/cwl/stg5126f9c4-41fa-439b-ba81-79b677a406da/OceanDNA-b22891.fa --refList OceanDNA-b22891/target_genomes_gtdb.txt --output OceanDNA-b22891/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:10:00,250] [INFO] Task succeeded: fastANI
[2023-03-15 23:10:00,255] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:10:00,256] [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_007744675.1	s__Gimesia alba	80.135	1415	2267	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007754425.1	s__Gimesia fumaroli	80.0481	1327	2267	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706765.1	s__Gimesia sp002706765	79.1607	984	2267	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	99.96	99.96	0.97	0.97	2	-
GCF_008298035.1	s__Gimesia maris	79.0072	991	2267	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	98.48	97.03	0.94	0.89	7	-
GCF_007746795.1	s__Gimesia algae	78.8709	1013	2267	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720525.1	s__Gimesia benthica	78.8161	802	2267	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0249	95.18	95.18	0.86	0.86	2	-
GCF_007748195.1	s__Gimesia aquarii	78.351	858	2267	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	95.04	95.04	0.88	0.88	2	-
GCF_007748155.1	s__Gimesia panareensis	77.9656	809	2267	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	96.61	95.86	0.91	0.90	3	-
GCF_008329715.1	s__Gimesia chilikensis	77.7618	738	2267	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0249	95.30	95.11	0.90	0.87	4	-
--------------------------------------------------------------------------------
[2023-03-15 23:10:00,256] [INFO] GTDB search result was written to OceanDNA-b22891/result_gtdb.tsv
[2023-03-15 23:10:00,256] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:10:00,257] [INFO] DFAST_QC result json was written to OceanDNA-b22891/dqc_result.json
[2023-03-15 23:10:00,257] [INFO] DFAST_QC completed!
[2023-03-15 23:10:00,257] [INFO] Total running time: 0h2m58s