[2023-03-18 23:50:29,205] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:50:29,205] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:50:29,205] [INFO] DQC Reference Directory: /var/lib/cwl/stg4683e81a-8569-4666-bf28-243c1e41c282/dqc_reference
[2023-03-18 23:50:30,498] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:50:30,499] [INFO] Task started: Prodigal
[2023-03-18 23:50:30,499] [INFO] Running command: cat /var/lib/cwl/stg0a1c0907-7294-4638-b748-1d42832224cb/OceanDNA-b6557.fa | prodigal -d OceanDNA-b6557/cds.fna -a OceanDNA-b6557/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:51:06,720] [INFO] Task succeeded: Prodigal
[2023-03-18 23:51:06,720] [INFO] Task started: HMMsearch
[2023-03-18 23:51:06,720] [INFO] Running command: hmmsearch --tblout OceanDNA-b6557/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4683e81a-8569-4666-bf28-243c1e41c282/dqc_reference/reference_markers.hmm OceanDNA-b6557/protein.faa > /dev/null
[2023-03-18 23:51:06,952] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:51:06,953] [INFO] Found 6/6 markers.
[2023-03-18 23:51:06,985] [INFO] Query marker FASTA was written to OceanDNA-b6557/markers.fasta
[2023-03-18 23:51:06,986] [INFO] Task started: Blastn
[2023-03-18 23:51:06,986] [INFO] Running command: blastn -query OceanDNA-b6557/markers.fasta -db /var/lib/cwl/stg4683e81a-8569-4666-bf28-243c1e41c282/dqc_reference/reference_markers.fasta -out OceanDNA-b6557/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:51:07,585] [INFO] Task succeeded: Blastn
[2023-03-18 23:51:07,586] [INFO] Selected 10 target genomes.
[2023-03-18 23:51:07,586] [INFO] Target genome list was writen to OceanDNA-b6557/target_genomes.txt
[2023-03-18 23:51:07,592] [INFO] Task started: fastANI
[2023-03-18 23:51:07,592] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a1c0907-7294-4638-b748-1d42832224cb/OceanDNA-b6557.fa --refList OceanDNA-b6557/target_genomes.txt --output OceanDNA-b6557/fastani_result.tsv --threads 1
[2023-03-18 23:51:17,077] [INFO] Task succeeded: fastANI
[2023-03-18 23:51:17,077] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4683e81a-8569-4666-bf28-243c1e41c282/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:51:17,078] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4683e81a-8569-4666-bf28-243c1e41c282/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:51:17,084] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 23:51:17,084] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 23:51:17,084] [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
Arenibacter palladensis	strain=DSM 17539	GCA_900129275.1	237373	237373	type	True	97.3803	1397	1616	95	conclusive
Arenibacter troitsensis	strain=DSM 19835	GCA_900177645.1	188872	188872	type	True	93.3226	1293	1616	95	below_threshold
Arenibacter echinorum	strain=DSM 23522	GCA_003259375.1	440515	440515	type	True	88.7613	1279	1616	95	below_threshold
Arenibacter algicola	strain=TG409	GCA_000733925.1	616991	616991	type	True	88.0427	1234	1616	95	below_threshold
Arenibacter arenosicollis	strain=BSSL-BM3	GCA_014397245.1	2762274	2762274	type	True	83.2255	1108	1616	95	below_threshold
Arenibacter hampyeongensis	strain=JCM 17788	GCA_002909255.1	1028743	1028743	type	True	82.2972	1079	1616	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.1999	53	1616	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	76.0743	95	1616	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:51:17,084] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6557/tc_result.tsv
[2023-03-18 23:51:17,084] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:51:17,085] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:51:17,085] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4683e81a-8569-4666-bf28-243c1e41c282/dqc_reference/checkm_data
[2023-03-18 23:51:17,085] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:51:17,091] [INFO] Task started: CheckM
[2023-03-18 23:51:17,091] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6557/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6557/checkm_input OceanDNA-b6557/checkm_result
[2023-03-18 23:52:42,683] [INFO] Task succeeded: CheckM
[2023-03-18 23:52:42,683] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:52:42,686] [INFO] ===== Completeness check finished =====
[2023-03-18 23:52:42,686] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:52:42,686] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6557/markers.fasta)
[2023-03-18 23:52:42,688] [INFO] Task started: Blastn
[2023-03-18 23:52:42,688] [INFO] Running command: blastn -query OceanDNA-b6557/markers.fasta -db /var/lib/cwl/stg4683e81a-8569-4666-bf28-243c1e41c282/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6557/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:52:43,522] [INFO] Task succeeded: Blastn
[2023-03-18 23:52:43,523] [INFO] Selected 6 target genomes.
[2023-03-18 23:52:43,523] [INFO] Target genome list was writen to OceanDNA-b6557/target_genomes_gtdb.txt
[2023-03-18 23:52:43,530] [INFO] Task started: fastANI
[2023-03-18 23:52:43,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a1c0907-7294-4638-b748-1d42832224cb/OceanDNA-b6557.fa --refList OceanDNA-b6557/target_genomes_gtdb.txt --output OceanDNA-b6557/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:52:51,201] [INFO] Task succeeded: fastANI
[2023-03-18 23:52:51,206] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:52:51,206] [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_900129275.1	s__Arenibacter palladensis	97.3803	1397	1616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	97.38	97.38	0.84	0.84	2	conclusive
GCF_900177645.1	s__Arenibacter troitsensis	93.3226	1293	1616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860365.1	s__Arenibacter algicola_B	89.5297	1314	1616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259375.1	s__Arenibacter echinorum	88.7654	1278	1616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733925.1	s__Arenibacter algicola	88.0422	1234	1616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	98.04	97.34	0.85	0.81	5	-
GCF_003201775.1	s__Arenibacter sp003201775	85.2742	1185	1616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:52:51,206] [INFO] GTDB search result was written to OceanDNA-b6557/result_gtdb.tsv
[2023-03-18 23:52:51,206] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:52:51,207] [INFO] DFAST_QC result json was written to OceanDNA-b6557/dqc_result.json
[2023-03-18 23:52:51,207] [INFO] DFAST_QC completed!
[2023-03-18 23:52:51,207] [INFO] Total running time: 0h2m22s