[2023-03-15 05:51:32,066] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:51:32,067] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:51:32,068] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9280655-dea7-49fe-9607-a5650da3ebd2/dqc_reference
[2023-03-15 05:51:33,647] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:51:33,648] [INFO] Task started: Prodigal
[2023-03-15 05:51:33,648] [INFO] Running command: cat /var/lib/cwl/stgeb2c292e-7c16-439e-b5d8-6388fe8224c2/OceanDNA-b38332.fa | prodigal -d OceanDNA-b38332/cds.fna -a OceanDNA-b38332/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:51:57,068] [INFO] Task succeeded: Prodigal
[2023-03-15 05:51:57,069] [INFO] Task started: HMMsearch
[2023-03-15 05:51:57,069] [INFO] Running command: hmmsearch --tblout OceanDNA-b38332/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9280655-dea7-49fe-9607-a5650da3ebd2/dqc_reference/reference_markers.hmm OceanDNA-b38332/protein.faa > /dev/null
[2023-03-15 05:51:57,305] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:51:57,306] [INFO] Found 6/6 markers.
[2023-03-15 05:51:57,336] [INFO] Query marker FASTA was written to OceanDNA-b38332/markers.fasta
[2023-03-15 05:51:57,337] [INFO] Task started: Blastn
[2023-03-15 05:51:57,337] [INFO] Running command: blastn -query OceanDNA-b38332/markers.fasta -db /var/lib/cwl/stgb9280655-dea7-49fe-9607-a5650da3ebd2/dqc_reference/reference_markers.fasta -out OceanDNA-b38332/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:51:58,046] [INFO] Task succeeded: Blastn
[2023-03-15 05:51:58,050] [INFO] Selected 11 target genomes.
[2023-03-15 05:51:58,050] [INFO] Target genome list was writen to OceanDNA-b38332/target_genomes.txt
[2023-03-15 05:51:58,058] [INFO] Task started: fastANI
[2023-03-15 05:51:58,058] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb2c292e-7c16-439e-b5d8-6388fe8224c2/OceanDNA-b38332.fa --refList OceanDNA-b38332/target_genomes.txt --output OceanDNA-b38332/fastani_result.tsv --threads 1
[2023-03-15 05:52:08,282] [INFO] Task succeeded: fastANI
[2023-03-15 05:52:08,283] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9280655-dea7-49fe-9607-a5650da3ebd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:52:08,283] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9280655-dea7-49fe-9607-a5650da3ebd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:52:08,291] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:52:08,292] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:52:08,292] [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	91.9584	1103	1320	95	below_threshold
Halomonas sedimenti	strain=QX-2	GCA_013416325.1	2729618	2729618	type	True	90.9584	1046	1320	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_002265845.1	223527	223527	type	True	87.6973	953	1320	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_000236035.1	223527	223527	type	True	87.6368	975	1320	95	below_threshold
Halomonas glaciei	strain=DD39	GCA_013415125.1	186761	186761	type	True	86.0676	915	1320	95	below_threshold
Halomonas maris	strain=QX-1	GCA_013371085.1	2729617	2729617	type	True	84.2663	887	1320	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	80.8238	659	1320	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	80.7517	667	1320	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	78.9758	461	1320	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	77.2203	237	1320	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	77.1047	238	1320	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:52:08,294] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38332/tc_result.tsv
[2023-03-15 05:52:08,296] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:52:08,296] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:52:08,296] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9280655-dea7-49fe-9607-a5650da3ebd2/dqc_reference/checkm_data
[2023-03-15 05:52:08,297] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:52:08,303] [INFO] Task started: CheckM
[2023-03-15 05:52:08,303] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38332/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38332/checkm_input OceanDNA-b38332/checkm_result
[2023-03-15 05:53:06,701] [INFO] Task succeeded: CheckM
[2023-03-15 05:53:06,701] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:53:06,727] [INFO] ===== Completeness check finished =====
[2023-03-15 05:53:06,727] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:53:06,728] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38332/markers.fasta)
[2023-03-15 05:53:06,729] [INFO] Task started: Blastn
[2023-03-15 05:53:06,729] [INFO] Running command: blastn -query OceanDNA-b38332/markers.fasta -db /var/lib/cwl/stgb9280655-dea7-49fe-9607-a5650da3ebd2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38332/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:53:08,002] [INFO] Task succeeded: Blastn
[2023-03-15 05:53:08,007] [INFO] Selected 10 target genomes.
[2023-03-15 05:53:08,007] [INFO] Target genome list was writen to OceanDNA-b38332/target_genomes_gtdb.txt
[2023-03-15 05:53:08,016] [INFO] Task started: fastANI
[2023-03-15 05:53:08,016] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb2c292e-7c16-439e-b5d8-6388fe8224c2/OceanDNA-b38332.fa --refList OceanDNA-b38332/target_genomes_gtdb.txt --output OceanDNA-b38332/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:53:18,657] [INFO] Task succeeded: fastANI
[2023-03-15 05:53:18,664] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 05:53:18,664] [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	98.2467	1201	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.52	96.69	0.85	0.81	3	conclusive
GCF_000336575.1	s__Halomonas titanicae	91.9584	1103	1320	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	90.9584	1046	1320	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	90.1696	1041	1320	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	89.3302	947	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004295565.1	s__Halomonas olivaria	88.6823	1099	1320	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	88.1109	1085	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.23	97.92	0.94	0.87	4	-
GCF_000236035.1	s__Halomonas boliviensis	87.6232	976	1320	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	86.0753	915	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.36	97.36	0.86	0.86	2	-
GCA_001507855.1	s__Halomonas sp001507855	83.2584	701	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-03-15 05:53:18,666] [INFO] GTDB search result was written to OceanDNA-b38332/result_gtdb.tsv
[2023-03-15 05:53:18,669] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:53:18,671] [INFO] DFAST_QC result json was written to OceanDNA-b38332/dqc_result.json
[2023-03-15 05:53:18,671] [INFO] DFAST_QC completed!
[2023-03-15 05:53:18,671] [INFO] Total running time: 0h1m47s