[2023-03-15 07:25:31,271] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:25:31,278] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:25:31,278] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a45e0d1-4ae4-41ff-a2ad-ea01bed2c281/dqc_reference
[2023-03-15 07:25:32,916] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:25:32,917] [INFO] Task started: Prodigal
[2023-03-15 07:25:32,917] [INFO] Running command: cat /var/lib/cwl/stgf30ab9b5-7bf3-411c-977f-081bba747334/OceanDNA-b22893.fa | prodigal -d OceanDNA-b22893/cds.fna -a OceanDNA-b22893/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:25:58,117] [INFO] Task succeeded: Prodigal
[2023-03-15 07:25:58,117] [INFO] Task started: HMMsearch
[2023-03-15 07:25:58,117] [INFO] Running command: hmmsearch --tblout OceanDNA-b22893/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a45e0d1-4ae4-41ff-a2ad-ea01bed2c281/dqc_reference/reference_markers.hmm OceanDNA-b22893/protein.faa > /dev/null
[2023-03-15 07:25:58,370] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:25:58,371] [INFO] Found 6/6 markers.
[2023-03-15 07:25:58,447] [INFO] Query marker FASTA was written to OceanDNA-b22893/markers.fasta
[2023-03-15 07:25:58,448] [INFO] Task started: Blastn
[2023-03-15 07:25:58,448] [INFO] Running command: blastn -query OceanDNA-b22893/markers.fasta -db /var/lib/cwl/stg4a45e0d1-4ae4-41ff-a2ad-ea01bed2c281/dqc_reference/reference_markers.fasta -out OceanDNA-b22893/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:25:58,973] [INFO] Task succeeded: Blastn
[2023-03-15 07:25:58,991] [INFO] Selected 15 target genomes.
[2023-03-15 07:25:58,991] [INFO] Target genome list was writen to OceanDNA-b22893/target_genomes.txt
[2023-03-15 07:25:58,998] [INFO] Task started: fastANI
[2023-03-15 07:25:58,998] [INFO] Running command: fastANI --query /var/lib/cwl/stgf30ab9b5-7bf3-411c-977f-081bba747334/OceanDNA-b22893.fa --refList OceanDNA-b22893/target_genomes.txt --output OceanDNA-b22893/fastani_result.tsv --threads 1
[2023-03-15 07:26:15,883] [INFO] Task succeeded: fastANI
[2023-03-15 07:26:15,883] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a45e0d1-4ae4-41ff-a2ad-ea01bed2c281/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:26:15,883] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a45e0d1-4ae4-41ff-a2ad-ea01bed2c281/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:26:15,890] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:26:15,890] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:26:15,891] [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	80.313	1018	1405	95	below_threshold
Gimesia fumaroli	strain=Enr17	GCA_007754425.1	2527976	2527976	type	True	80.0583	997	1405	95	below_threshold
Gimesia algae	strain=Pan161	GCA_007746795.1	2527971	2527971	type	True	78.9158	691	1405	95	below_threshold
Gimesia maris	strain=DSM 8797	GCA_009720545.1	122	122	type	True	78.768	686	1405	95	below_threshold
Gimesia maris	strain=DSM 8797	GCA_008298035.1	122	122	type	True	78.7621	681	1405	95	below_threshold
Gimesia maris	strain=DSM 8797	GCA_000181475.1	122	122	type	True	78.7502	679	1405	95	below_threshold
Gimesia aquarii	strain=V144	GCA_007748195.1	2527964	2527964	type	True	78.2392	610	1405	95	below_threshold
Gimesia panareensis	strain=Enr10	GCA_007748155.1	2527978	2527978	type	True	78.002	610	1405	95	below_threshold
Gimesia chilikensis	strain=JC646	GCA_008329715.1	2605989	2605989	type	True	77.9324	531	1405	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:26:15,894] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22893/tc_result.tsv
[2023-03-15 07:26:15,897] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:26:15,897] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:26:15,897] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a45e0d1-4ae4-41ff-a2ad-ea01bed2c281/dqc_reference/checkm_data
[2023-03-15 07:26:15,898] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:26:15,918] [INFO] Task started: CheckM
[2023-03-15 07:26:15,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22893/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22893/checkm_input OceanDNA-b22893/checkm_result
[2023-03-15 07:27:19,903] [INFO] Task succeeded: CheckM
[2023-03-15 07:27:19,903] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.38%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:27:19,989] [INFO] ===== Completeness check finished =====
[2023-03-15 07:27:19,989] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:27:19,990] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22893/markers.fasta)
[2023-03-15 07:27:19,991] [INFO] Task started: Blastn
[2023-03-15 07:27:19,991] [INFO] Running command: blastn -query OceanDNA-b22893/markers.fasta -db /var/lib/cwl/stg4a45e0d1-4ae4-41ff-a2ad-ea01bed2c281/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22893/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:27:20,705] [INFO] Task succeeded: Blastn
[2023-03-15 07:27:20,712] [INFO] Selected 13 target genomes.
[2023-03-15 07:27:20,712] [INFO] Target genome list was writen to OceanDNA-b22893/target_genomes_gtdb.txt
[2023-03-15 07:27:20,727] [INFO] Task started: fastANI
[2023-03-15 07:27:20,727] [INFO] Running command: fastANI --query /var/lib/cwl/stgf30ab9b5-7bf3-411c-977f-081bba747334/OceanDNA-b22893.fa --refList OceanDNA-b22893/target_genomes_gtdb.txt --output OceanDNA-b22893/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:27:35,594] [INFO] Task succeeded: fastANI
[2023-03-15 07:27:35,600] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:27:35,600] [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	80.3091	1019	1405	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	80.0538	996	1405	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007746795.1	s__Gimesia algae	78.9319	688	1405	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008298035.1	s__Gimesia maris	78.7649	680	1405	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	98.48	97.03	0.94	0.89	7	-
GCA_002706765.1	s__Gimesia sp002706765	78.4889	693	1405	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	99.96	99.96	0.97	0.97	2	-
GCF_007748195.1	s__Gimesia aquarii	78.2454	609	1405	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	78.0078	609	1405	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	77.9483	529	1405	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0249	95.30	95.11	0.90	0.87	4	-
GCF_009720525.1	s__Gimesia benthica	77.9115	534	1405	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0249	95.18	95.18	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-15 07:27:35,626] [INFO] GTDB search result was written to OceanDNA-b22893/result_gtdb.tsv
[2023-03-15 07:27:35,676] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:27:35,704] [INFO] DFAST_QC result json was written to OceanDNA-b22893/dqc_result.json
[2023-03-15 07:27:35,704] [INFO] DFAST_QC completed!
[2023-03-15 07:27:35,704] [INFO] Total running time: 0h2m4s