[2023-03-15 11:10:12,367] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:10:12,367] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:10:12,367] [INFO] DQC Reference Directory: /var/lib/cwl/stgb12f79ea-3a6c-4105-b177-b9f0c1ac98cc/dqc_reference
[2023-03-15 11:10:13,469] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:10:13,470] [INFO] Task started: Prodigal
[2023-03-15 11:10:13,470] [INFO] Running command: cat /var/lib/cwl/stgb2e7f1e0-cb0d-441b-b1df-d6d3d82fd46d/OceanDNA-b46874.fa | prodigal -d OceanDNA-b46874/cds.fna -a OceanDNA-b46874/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:10:28,138] [INFO] Task succeeded: Prodigal
[2023-03-15 11:10:28,139] [INFO] Task started: HMMsearch
[2023-03-15 11:10:28,139] [INFO] Running command: hmmsearch --tblout OceanDNA-b46874/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb12f79ea-3a6c-4105-b177-b9f0c1ac98cc/dqc_reference/reference_markers.hmm OceanDNA-b46874/protein.faa > /dev/null
[2023-03-15 11:10:28,301] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:10:28,301] [INFO] Found 6/6 markers.
[2023-03-15 11:10:28,334] [INFO] Query marker FASTA was written to OceanDNA-b46874/markers.fasta
[2023-03-15 11:10:28,336] [INFO] Task started: Blastn
[2023-03-15 11:10:28,336] [INFO] Running command: blastn -query OceanDNA-b46874/markers.fasta -db /var/lib/cwl/stgb12f79ea-3a6c-4105-b177-b9f0c1ac98cc/dqc_reference/reference_markers.fasta -out OceanDNA-b46874/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:10:28,930] [INFO] Task succeeded: Blastn
[2023-03-15 11:10:28,938] [INFO] Selected 22 target genomes.
[2023-03-15 11:10:28,939] [INFO] Target genome list was writen to OceanDNA-b46874/target_genomes.txt
[2023-03-15 11:10:28,952] [INFO] Task started: fastANI
[2023-03-15 11:10:28,952] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2e7f1e0-cb0d-441b-b1df-d6d3d82fd46d/OceanDNA-b46874.fa --refList OceanDNA-b46874/target_genomes.txt --output OceanDNA-b46874/fastani_result.tsv --threads 1
[2023-03-15 11:10:44,671] [INFO] Task succeeded: fastANI
[2023-03-15 11:10:44,671] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb12f79ea-3a6c-4105-b177-b9f0c1ac98cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:10:44,671] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb12f79ea-3a6c-4105-b177-b9f0c1ac98cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:10:44,677] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:10:44,677] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:10:44,677] [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
Luteolibacter yonseiensis	strain=JCM 18052	GCA_016595465.1	1144680	1144680	type	True	77.8241	138	446	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	77.3476	116	446	95	below_threshold
Luteolibacter luteus	strain=G-1-1-1	GCA_012913485.1	2728835	2728835	type	True	77.1867	81	446	95	below_threshold
Haloferula rosea	strain=KCTC 22201	GCA_016595525.1	490093	490093	type	True	76.6908	56	446	95	below_threshold
Luteolibacter pohnpeiensis	strain=KCTC 22041	GCA_016595435.1	454153	454153	type	True	76.6537	61	446	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:10:44,681] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46874/tc_result.tsv
[2023-03-15 11:10:44,681] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:10:44,681] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:10:44,681] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb12f79ea-3a6c-4105-b177-b9f0c1ac98cc/dqc_reference/checkm_data
[2023-03-15 11:10:44,682] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:10:44,691] [INFO] Task started: CheckM
[2023-03-15 11:10:44,691] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46874/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46874/checkm_input OceanDNA-b46874/checkm_result
[2023-03-15 11:11:25,102] [INFO] Task succeeded: CheckM
[2023-03-15 11:11:25,103] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:11:25,180] [INFO] ===== Completeness check finished =====
[2023-03-15 11:11:25,180] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:11:25,181] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46874/markers.fasta)
[2023-03-15 11:11:25,182] [INFO] Task started: Blastn
[2023-03-15 11:11:25,182] [INFO] Running command: blastn -query OceanDNA-b46874/markers.fasta -db /var/lib/cwl/stgb12f79ea-3a6c-4105-b177-b9f0c1ac98cc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46874/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:11:26,139] [INFO] Task succeeded: Blastn
[2023-03-15 11:11:26,140] [INFO] Selected 12 target genomes.
[2023-03-15 11:11:26,140] [INFO] Target genome list was writen to OceanDNA-b46874/target_genomes_gtdb.txt
[2023-03-15 11:11:26,154] [INFO] Task started: fastANI
[2023-03-15 11:11:26,154] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2e7f1e0-cb0d-441b-b1df-d6d3d82fd46d/OceanDNA-b46874.fa --refList OceanDNA-b46874/target_genomes_gtdb.txt --output OceanDNA-b46874/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:11:34,610] [INFO] Task succeeded: fastANI
[2023-03-15 11:11:34,619] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:11:34,620] [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
GCA_018402445.1	s__Luteolibacter sp018402445	85.7234	342	446	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017798145.1	s__Luteolibacter sp017798145	80.472	272	446	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478925.1	s__Luteolibacter sp905478925	79.3245	211	446	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	97.95	97.95	0.92	0.92	2	-
GCA_003820635.1	s__Luteolibacter sp003820635	78.4487	139	446	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182475.1	s__Luteolibacter sp905182475	78.3033	178	446	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.83	99.83	0.94	0.94	2	-
GCA_903919975.1	s__Luteolibacter sp903919975	78.1078	104	446	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.90	99.84	0.96	0.96	3	-
GCF_016595465.1	s__Luteolibacter yonseiensis	77.8241	138	446	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007126655.1	s__Luteolibacter sp007126655	77.7389	115	446	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.62	99.62	0.82	0.82	2	-
GCA_018969605.1	s__Luteolibacter sp018969605	77.7348	84	446	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017301995.1	s__Luteolibacter sp017301995	77.4149	90	446	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903906515.1	s__Luteolibacter sp903906515	77.2615	84	446	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.85	99.81	0.93	0.92	3	-
GCA_903908495.1	s__Luteolibacter sp903908495	76.8981	80	446	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:11:34,620] [INFO] GTDB search result was written to OceanDNA-b46874/result_gtdb.tsv
[2023-03-15 11:11:34,620] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:11:34,621] [INFO] DFAST_QC result json was written to OceanDNA-b46874/dqc_result.json
[2023-03-15 11:11:34,621] [INFO] DFAST_QC completed!
[2023-03-15 11:11:34,621] [INFO] Total running time: 0h1m22s