[2023-03-15 07:25:31,263] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:25:31,265] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:25:31,265] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a88d0b4-f191-4a05-b0f4-ff40437db8f3/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/stg313d5277-1de8-4d5b-924e-5f435f87abf5/OceanDNA-b38210.fa | prodigal -d OceanDNA-b38210/cds.fna -a OceanDNA-b38210/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:25:53,274] [INFO] Task succeeded: Prodigal
[2023-03-15 07:25:53,274] [INFO] Task started: HMMsearch
[2023-03-15 07:25:53,274] [INFO] Running command: hmmsearch --tblout OceanDNA-b38210/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a88d0b4-f191-4a05-b0f4-ff40437db8f3/dqc_reference/reference_markers.hmm OceanDNA-b38210/protein.faa > /dev/null
[2023-03-15 07:25:53,491] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:25:53,492] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg313d5277-1de8-4d5b-924e-5f435f87abf5/OceanDNA-b38210.fa]
[2023-03-15 07:25:53,536] [INFO] Query marker FASTA was written to OceanDNA-b38210/markers.fasta
[2023-03-15 07:25:53,536] [INFO] Task started: Blastn
[2023-03-15 07:25:53,536] [INFO] Running command: blastn -query OceanDNA-b38210/markers.fasta -db /var/lib/cwl/stg3a88d0b4-f191-4a05-b0f4-ff40437db8f3/dqc_reference/reference_markers.fasta -out OceanDNA-b38210/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:25:54,194] [INFO] Task succeeded: Blastn
[2023-03-15 07:25:54,201] [INFO] Selected 15 target genomes.
[2023-03-15 07:25:54,201] [INFO] Target genome list was writen to OceanDNA-b38210/target_genomes.txt
[2023-03-15 07:25:54,208] [INFO] Task started: fastANI
[2023-03-15 07:25:54,208] [INFO] Running command: fastANI --query /var/lib/cwl/stg313d5277-1de8-4d5b-924e-5f435f87abf5/OceanDNA-b38210.fa --refList OceanDNA-b38210/target_genomes.txt --output OceanDNA-b38210/fastani_result.tsv --threads 1
[2023-03-15 07:26:05,841] [INFO] Task succeeded: fastANI
[2023-03-15 07:26:05,842] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a88d0b4-f191-4a05-b0f4-ff40437db8f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:26:05,842] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a88d0b4-f191-4a05-b0f4-ff40437db8f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:26:05,851] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:26:05,851] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:26:05,851] [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 titanicae	strain=BH1	GCA_000336575.1	664683	664683	type	True	91.5196	983	1151	95	below_threshold
Halomonas sedimenti	strain=QX-2	GCA_013416325.1	2729618	2729618	type	True	90.7683	960	1151	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_002265845.1	223527	223527	type	True	87.7741	866	1151	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_000236035.1	223527	223527	type	True	87.7502	869	1151	95	below_threshold
Halomonas glaciei	strain=DD39	GCA_013415125.1	186761	186761	type	True	85.8301	806	1151	95	below_threshold
Halomonas maris	strain=QX-1	GCA_013371085.1	2729617	2729617	type	True	83.915	771	1151	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	80.4632	608	1151	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	80.4127	619	1151	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	78.5242	395	1151	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	77.0377	188	1151	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	77.0184	136	1151	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	76.9652	178	1151	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	76.8907	190	1151	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	76.8807	162	1151	95	below_threshold
Chromohalobacter beijerinckii	strain=DSM 7218	GCA_023061185.1	86179	86179	type	True	76.2279	68	1151	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:26:05,855] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38210/tc_result.tsv
[2023-03-15 07:26:05,859] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:26:05,859] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:26:05,860] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a88d0b4-f191-4a05-b0f4-ff40437db8f3/dqc_reference/checkm_data
[2023-03-15 07:26:05,860] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:26:05,934] [INFO] Task started: CheckM
[2023-03-15 07:26:05,934] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38210/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38210/checkm_input OceanDNA-b38210/checkm_result
[2023-03-15 07:26:57,667] [INFO] Task succeeded: CheckM
[2023-03-15 07:26:57,667] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 39.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:26:57,714] [INFO] ===== Completeness check finished =====
[2023-03-15 07:26:57,715] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:26:57,715] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38210/markers.fasta)
[2023-03-15 07:26:57,716] [INFO] Task started: Blastn
[2023-03-15 07:26:57,716] [INFO] Running command: blastn -query OceanDNA-b38210/markers.fasta -db /var/lib/cwl/stg3a88d0b4-f191-4a05-b0f4-ff40437db8f3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38210/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:26:58,854] [INFO] Task succeeded: Blastn
[2023-03-15 07:26:58,860] [INFO] Selected 9 target genomes.
[2023-03-15 07:26:58,861] [INFO] Target genome list was writen to OceanDNA-b38210/target_genomes_gtdb.txt
[2023-03-15 07:26:58,868] [INFO] Task started: fastANI
[2023-03-15 07:26:58,869] [INFO] Running command: fastANI --query /var/lib/cwl/stg313d5277-1de8-4d5b-924e-5f435f87abf5/OceanDNA-b38210.fa --refList OceanDNA-b38210/target_genomes_gtdb.txt --output OceanDNA-b38210/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:27:08,015] [INFO] Task succeeded: fastANI
[2023-03-15 07:27:08,021] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:27:08,022] [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_004364445.1	s__Halomonas alkaliantarctica	92.3347	959	1151	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.52	96.69	0.85	0.81	3	-
GCF_000336575.1	s__Halomonas titanicae	91.5196	983	1151	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.70	97.17	0.86	0.84	22	-
GCF_013416325.1	s__Halomonas sedimenti	90.7811	960	1151	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.54	99.54	0.90	0.90	2	-
GCF_002211105.1	s__Halomonas campaniensis_A	89.5324	924	1151	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.13	98.13	0.90	0.90	2	-
GCF_001882345.1	s__Halomonas sp001882345	89.2973	858	1151	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002257525.1	s__Halomonas ventosae_B	88.6651	974	1151	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.23	97.92	0.94	0.87	4	-
GCA_004295565.1	s__Halomonas olivaria	88.2911	958	1151	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000236035.1	s__Halomonas boliviensis	87.7476	870	1151	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.96	99.96	0.99	0.99	2	-
GCF_013415125.1	s__Halomonas glaciei	85.816	807	1151	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.36	97.36	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-15 07:27:08,028] [INFO] GTDB search result was written to OceanDNA-b38210/result_gtdb.tsv
[2023-03-15 07:27:08,045] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:27:08,056] [INFO] DFAST_QC result json was written to OceanDNA-b38210/dqc_result.json
[2023-03-15 07:27:08,056] [INFO] DFAST_QC completed!
[2023-03-15 07:27:08,056] [INFO] Total running time: 0h1m37s