[2023-03-18 02:53:05,583] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:53:05,583] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:53:05,583] [INFO] DQC Reference Directory: /var/lib/cwl/stg44b9f130-ac1f-4492-8d9a-2134168a9844/dqc_reference
[2023-03-18 02:53:07,191] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:53:07,191] [INFO] Task started: Prodigal
[2023-03-18 02:53:07,191] [INFO] Running command: cat /var/lib/cwl/stg750a9923-2113-41e0-8037-e83129906909/OceanDNA-b23503.fa | prodigal -d OceanDNA-b23503/cds.fna -a OceanDNA-b23503/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:53:26,246] [INFO] Task succeeded: Prodigal
[2023-03-18 02:53:26,246] [INFO] Task started: HMMsearch
[2023-03-18 02:53:26,247] [INFO] Running command: hmmsearch --tblout OceanDNA-b23503/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44b9f130-ac1f-4492-8d9a-2134168a9844/dqc_reference/reference_markers.hmm OceanDNA-b23503/protein.faa > /dev/null
[2023-03-18 02:53:26,448] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:53:26,449] [INFO] Found 6/6 markers.
[2023-03-18 02:53:26,469] [INFO] Query marker FASTA was written to OceanDNA-b23503/markers.fasta
[2023-03-18 02:53:26,470] [INFO] Task started: Blastn
[2023-03-18 02:53:26,470] [INFO] Running command: blastn -query OceanDNA-b23503/markers.fasta -db /var/lib/cwl/stg44b9f130-ac1f-4492-8d9a-2134168a9844/dqc_reference/reference_markers.fasta -out OceanDNA-b23503/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:53:27,090] [INFO] Task succeeded: Blastn
[2023-03-18 02:53:27,091] [INFO] Selected 26 target genomes.
[2023-03-18 02:53:27,091] [INFO] Target genome list was writen to OceanDNA-b23503/target_genomes.txt
[2023-03-18 02:53:27,104] [INFO] Task started: fastANI
[2023-03-18 02:53:27,104] [INFO] Running command: fastANI --query /var/lib/cwl/stg750a9923-2113-41e0-8037-e83129906909/OceanDNA-b23503.fa --refList OceanDNA-b23503/target_genomes.txt --output OceanDNA-b23503/fastani_result.tsv --threads 1
[2023-03-18 02:53:42,297] [INFO] Task succeeded: fastANI
[2023-03-18 02:53:42,297] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44b9f130-ac1f-4492-8d9a-2134168a9844/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:53:42,298] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44b9f130-ac1f-4492-8d9a-2134168a9844/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:53:42,305] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:53:42,305] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:53:42,305] [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
Henriciella pelagia	strain=CGMCC 1.15928	GCA_014644035.1	1977912	1977912	type	True	76.4083	80	1022	95	below_threshold
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	76.2914	84	1022	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	76.239	83	1022	95	below_threshold
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	76.1911	76	1022	95	below_threshold
Henriciella marina	strain=DSM 19595	GCA_000376805.1	453851	453851	type	True	76.1534	77	1022	95	below_threshold
Henriciella litoralis	strain=DSM 22014	GCA_002088935.1	568102	568102	type	True	76.1065	72	1022	95	below_threshold
Henriciella algicola	strain=CCUG67844	GCA_003576245.1	1608422	1608422	type	True	75.9865	77	1022	95	below_threshold
Hyphomonas atlantica	strain=22II1-22F38	GCA_000682715.1	1280948	1280948	type	True	75.7734	82	1022	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	75.7602	79	1022	95	below_threshold
Hyphomonas pacifica	strain=T16B2	GCA_000682675.1	1280941	1280941	type	True	75.749	71	1022	95	below_threshold
Hyphomonas polymorpha	strain=PS728	GCA_000685315.1	74319	74319	type	True	75.473	62	1022	95	below_threshold
Hyphomonas johnsonii	strain=MHS-2	GCA_000685275.1	81031	81031	type	True	75.2997	53	1022	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:53:42,305] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23503/tc_result.tsv
[2023-03-18 02:53:42,306] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:53:42,306] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:53:42,306] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44b9f130-ac1f-4492-8d9a-2134168a9844/dqc_reference/checkm_data
[2023-03-18 02:53:42,306] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:53:42,388] [INFO] Task started: CheckM
[2023-03-18 02:53:42,388] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23503/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23503/checkm_input OceanDNA-b23503/checkm_result
[2023-03-18 02:54:31,087] [INFO] Task succeeded: CheckM
[2023-03-18 02:54:31,088] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.05%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:54:31,090] [INFO] ===== Completeness check finished =====
[2023-03-18 02:54:31,091] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:54:31,091] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23503/markers.fasta)
[2023-03-18 02:54:31,091] [INFO] Task started: Blastn
[2023-03-18 02:54:31,091] [INFO] Running command: blastn -query OceanDNA-b23503/markers.fasta -db /var/lib/cwl/stg44b9f130-ac1f-4492-8d9a-2134168a9844/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23503/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:54:32,158] [INFO] Task succeeded: Blastn
[2023-03-18 02:54:32,159] [INFO] Selected 14 target genomes.
[2023-03-18 02:54:32,159] [INFO] Target genome list was writen to OceanDNA-b23503/target_genomes_gtdb.txt
[2023-03-18 02:54:32,317] [INFO] Task started: fastANI
[2023-03-18 02:54:32,317] [INFO] Running command: fastANI --query /var/lib/cwl/stg750a9923-2113-41e0-8037-e83129906909/OceanDNA-b23503.fa --refList OceanDNA-b23503/target_genomes_gtdb.txt --output OceanDNA-b23503/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:54:40,355] [INFO] Task succeeded: fastANI
[2023-03-18 02:54:40,362] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:54:40,362] [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_013213785.1	s__Henriciella sp013213785	78.3853	356	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214545.1	s__Henriciella sp013214545	78.2368	352	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001854405.1	s__Henriciella sp001854405	78.1308	359	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213825.1	s__Henriciella sp013213825	77.8662	291	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642885.1	s__Henriciella sp017642885	77.8359	323	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.99	99.99	0.96	0.96	2	-
GCF_002088945.1	s__Henriciella pelagia	76.2819	82	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000961695.1	s__Hyphomonas sp000961695	76.2596	62	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685235.1	s__Hyphomonas adhaerens	75.7528	76	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	97.03	96.92	0.83	0.82	4	-
GCF_000682675.1	s__Hyphomonas pacifica	75.7221	69	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.59	99.19	0.95	0.91	3	-
GCA_002700305.1	s__Hyphomonas sp002700305	75.7039	67	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.48	99.29	0.92	0.85	3	-
--------------------------------------------------------------------------------
[2023-03-18 02:54:40,362] [INFO] GTDB search result was written to OceanDNA-b23503/result_gtdb.tsv
[2023-03-18 02:54:40,362] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:54:40,364] [INFO] DFAST_QC result json was written to OceanDNA-b23503/dqc_result.json
[2023-03-18 02:54:40,364] [INFO] DFAST_QC completed!
[2023-03-18 02:54:40,364] [INFO] Total running time: 0h1m35s