[2023-03-17 09:33:09,738] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:33:09,738] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:33:09,738] [INFO] DQC Reference Directory: /var/lib/cwl/stg87580e03-06ce-4378-9c35-4210fb034015/dqc_reference
[2023-03-17 09:33:11,451] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:33:11,452] [INFO] Task started: Prodigal
[2023-03-17 09:33:11,452] [INFO] Running command: cat /var/lib/cwl/stgc32b5afd-e412-4a1c-b1d9-f66ec6d1e6d4/OceanDNA-b38301.fa | prodigal -d OceanDNA-b38301/cds.fna -a OceanDNA-b38301/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:33:30,881] [INFO] Task succeeded: Prodigal
[2023-03-17 09:33:30,881] [INFO] Task started: HMMsearch
[2023-03-17 09:33:30,881] [INFO] Running command: hmmsearch --tblout OceanDNA-b38301/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87580e03-06ce-4378-9c35-4210fb034015/dqc_reference/reference_markers.hmm OceanDNA-b38301/protein.faa > /dev/null
[2023-03-17 09:33:31,098] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:33:31,098] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc32b5afd-e412-4a1c-b1d9-f66ec6d1e6d4/OceanDNA-b38301.fa]
[2023-03-17 09:33:31,118] [INFO] Query marker FASTA was written to OceanDNA-b38301/markers.fasta
[2023-03-17 09:33:31,119] [INFO] Task started: Blastn
[2023-03-17 09:33:31,119] [INFO] Running command: blastn -query OceanDNA-b38301/markers.fasta -db /var/lib/cwl/stg87580e03-06ce-4378-9c35-4210fb034015/dqc_reference/reference_markers.fasta -out OceanDNA-b38301/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:33:31,769] [INFO] Task succeeded: Blastn
[2023-03-17 09:33:31,770] [INFO] Selected 15 target genomes.
[2023-03-17 09:33:31,770] [INFO] Target genome list was writen to OceanDNA-b38301/target_genomes.txt
[2023-03-17 09:33:31,938] [INFO] Task started: fastANI
[2023-03-17 09:33:31,938] [INFO] Running command: fastANI --query /var/lib/cwl/stgc32b5afd-e412-4a1c-b1d9-f66ec6d1e6d4/OceanDNA-b38301.fa --refList OceanDNA-b38301/target_genomes.txt --output OceanDNA-b38301/fastani_result.tsv --threads 1
[2023-03-17 09:33:43,312] [INFO] Task succeeded: fastANI
[2023-03-17 09:33:43,312] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87580e03-06ce-4378-9c35-4210fb034015/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:33:43,312] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87580e03-06ce-4378-9c35-4210fb034015/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:33:43,322] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2023-03-17 09:33:43,322] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-03-17 09:33:43,323] [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
Halomonas meridiana	strain=NBRC 15608	GCA_006540125.1	29570	29570	type	True	97.2257	869	1054	95	inconclusive
Halomonas aquamarina	strain=558	GCA_900110265.1	77097	77097	type	True	97.1778	879	1054	95	inconclusive
Halomonas meridiana	strain=ACAM 246	GCA_900129255.1	29570	29570	type	True	97.0873	917	1054	95	inconclusive
Halomonas lionensis	strain=RHS90	GCA_002087295.1	1144478	1144478	type	True	94.3722	815	1054	95	below_threshold
Halomonas piezotolerans	strain=NBT06E8	GCA_009660035.1	2609667	2609667	type	True	88.5746	856	1054	95	below_threshold
Halomonas piezotolerans	strain=NBT06E8	GCA_012427705.1	2609667	2609667	type	True	88.5182	856	1054	95	below_threshold
Halomonas lutescens	strain=CGMCC 1.15122	GCA_014640815.1	1602943	1602943	type	True	87.0956	836	1054	95	below_threshold
Halomonas glaciei	strain=DD39	GCA_013415125.1	186761	186761	type	True	80.8328	586	1054	95	below_threshold
Halomonas sedimenti	strain=QX-2	GCA_013416325.1	2729618	2729618	type	True	80.7588	570	1054	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	79.9093	476	1054	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	79.3344	428	1054	95	below_threshold
Halomonas massiliensis	strain=Marseille-P2426	GCA_900155385.1	1816686	1816686	type	True	79.2947	355	1054	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	79.2776	421	1054	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	77.9927	294	1054	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	77.9667	265	1054	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 09:33:43,323] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38301/tc_result.tsv
[2023-03-17 09:33:43,323] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:33:43,323] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:33:43,323] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87580e03-06ce-4378-9c35-4210fb034015/dqc_reference/checkm_data
[2023-03-17 09:33:43,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:33:43,328] [INFO] Task started: CheckM
[2023-03-17 09:33:43,328] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38301/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38301/checkm_input OceanDNA-b38301/checkm_result
[2023-03-17 09:34:32,776] [INFO] Task succeeded: CheckM
[2023-03-17 09:34:32,777] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:34:32,779] [INFO] ===== Completeness check finished =====
[2023-03-17 09:34:32,780] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:34:32,780] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38301/markers.fasta)
[2023-03-17 09:34:32,781] [INFO] Task started: Blastn
[2023-03-17 09:34:32,781] [INFO] Running command: blastn -query OceanDNA-b38301/markers.fasta -db /var/lib/cwl/stg87580e03-06ce-4378-9c35-4210fb034015/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38301/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:34:33,724] [INFO] Task succeeded: Blastn
[2023-03-17 09:34:33,725] [INFO] Selected 12 target genomes.
[2023-03-17 09:34:33,725] [INFO] Target genome list was writen to OceanDNA-b38301/target_genomes_gtdb.txt
[2023-03-17 09:34:34,286] [INFO] Task started: fastANI
[2023-03-17 09:34:34,286] [INFO] Running command: fastANI --query /var/lib/cwl/stgc32b5afd-e412-4a1c-b1d9-f66ec6d1e6d4/OceanDNA-b38301.fa --refList OceanDNA-b38301/target_genomes_gtdb.txt --output OceanDNA-b38301/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:34:44,101] [INFO] Task succeeded: fastANI
[2023-03-17 09:34:44,109] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 09:34:44,109] [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_900110265.1	s__Halomonas aquamarina	97.1778	879	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.65	97.09	0.84	0.80	25	conclusive
GCF_002087295.1	s__Halomonas lionensis	94.3722	815	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009846525.1	s__Halomonas sp002696125	88.6891	848	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.53	98.53	0.95	0.95	2	-
GCF_012427705.1	s__Halomonas piezotolerans	88.5218	855	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	98.70	0.97	0.94	3	-
GCF_014640815.1	s__Halomonas lutescens	87.1026	835	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000275725.1	s__Halomonas stevensii	84.1316	696	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	97.33	97.21	0.85	0.83	5	-
GCF_014651775.1	s__Halomonas hamiltonii	84.1143	698	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	98.09	97.51	0.90	0.88	5	-
GCF_002966495.1	s__Halomonas sp002966495	81.2192	591	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013415125.1	s__Halomonas glaciei	80.8145	587	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.36	97.36	0.86	0.86	2	-
GCF_013416325.1	s__Halomonas sedimenti	80.7588	570	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.54	99.54	0.90	0.90	2	-
GCA_002366715.1	s__Halomonas sp002366715	80.5211	546	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002211105.1	s__Halomonas campaniensis_A	80.0387	548	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.13	98.13	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-17 09:34:44,109] [INFO] GTDB search result was written to OceanDNA-b38301/result_gtdb.tsv
[2023-03-17 09:34:44,110] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:34:44,111] [INFO] DFAST_QC result json was written to OceanDNA-b38301/dqc_result.json
[2023-03-17 09:34:44,111] [INFO] DFAST_QC completed!
[2023-03-17 09:34:44,111] [INFO] Total running time: 0h1m34s