[2023-03-16 14:50:24,911] [INFO] DFAST_QC pipeline started.
[2023-03-16 14:50:24,911] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 14:50:24,911] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c5b0336-e056-4486-b213-2476d9b018b9/dqc_reference
[2023-03-16 14:50:26,096] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 14:50:26,096] [INFO] Task started: Prodigal
[2023-03-16 14:50:26,096] [INFO] Running command: cat /var/lib/cwl/stg6516343b-5a8e-4468-9dc9-bcdd4a92db45/OceanDNA-b38311.fa | prodigal -d OceanDNA-b38311/cds.fna -a OceanDNA-b38311/protein.faa -g 11 -q > /dev/null
[2023-03-16 14:50:50,177] [INFO] Task succeeded: Prodigal
[2023-03-16 14:50:50,177] [INFO] Task started: HMMsearch
[2023-03-16 14:50:50,178] [INFO] Running command: hmmsearch --tblout OceanDNA-b38311/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c5b0336-e056-4486-b213-2476d9b018b9/dqc_reference/reference_markers.hmm OceanDNA-b38311/protein.faa > /dev/null
[2023-03-16 14:50:50,601] [INFO] Task succeeded: HMMsearch
[2023-03-16 14:50:50,602] [INFO] Found 6/6 markers.
[2023-03-16 14:50:50,653] [INFO] Query marker FASTA was written to OceanDNA-b38311/markers.fasta
[2023-03-16 14:50:50,653] [INFO] Task started: Blastn
[2023-03-16 14:50:50,653] [INFO] Running command: blastn -query OceanDNA-b38311/markers.fasta -db /var/lib/cwl/stg3c5b0336-e056-4486-b213-2476d9b018b9/dqc_reference/reference_markers.fasta -out OceanDNA-b38311/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 14:50:52,716] [INFO] Task succeeded: Blastn
[2023-03-16 14:50:52,716] [INFO] Selected 11 target genomes.
[2023-03-16 14:50:52,717] [INFO] Target genome list was writen to OceanDNA-b38311/target_genomes.txt
[2023-03-16 14:50:52,723] [INFO] Task started: fastANI
[2023-03-16 14:50:52,723] [INFO] Running command: fastANI --query /var/lib/cwl/stg6516343b-5a8e-4468-9dc9-bcdd4a92db45/OceanDNA-b38311.fa --refList OceanDNA-b38311/target_genomes.txt --output OceanDNA-b38311/fastani_result.tsv --threads 1
[2023-03-16 14:51:11,078] [INFO] Task succeeded: fastANI
[2023-03-16 14:51:11,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c5b0336-e056-4486-b213-2476d9b018b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 14:51:11,079] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c5b0336-e056-4486-b213-2476d9b018b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 14:51:11,086] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 14:51:11,086] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 14:51:11,086] [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 glaciei	strain=DD39	GCA_013415125.1	186761	186761	type	True	96.7294	1165	1319	95	conclusive
Halomonas maris	strain=QX-1	GCA_013371085.1	2729617	2729617	type	True	92.3278	1027	1319	95	below_threshold
Halomonas titanicae	strain=BH1	GCA_000336575.1	664683	664683	type	True	86.6737	1007	1319	95	below_threshold
Halomonas sedimenti	strain=QX-2	GCA_013416325.1	2729618	2729618	type	True	86.2877	998	1319	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_000236035.1	223527	223527	type	True	84.9288	939	1319	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_002265845.1	223527	223527	type	True	84.8273	940	1319	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	81.2197	685	1319	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	81.1574	704	1319	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	77.0243	207	1319	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	77.0178	206	1319	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	76.9092	230	1319	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 14:51:11,087] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38311/tc_result.tsv
[2023-03-16 14:51:11,087] [INFO] ===== Taxonomy check completed =====
[2023-03-16 14:51:11,087] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 14:51:11,087] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c5b0336-e056-4486-b213-2476d9b018b9/dqc_reference/checkm_data
[2023-03-16 14:51:11,088] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 14:51:11,098] [INFO] Task started: CheckM
[2023-03-16 14:51:11,098] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38311/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38311/checkm_input OceanDNA-b38311/checkm_result
[2023-03-16 14:52:23,483] [INFO] Task succeeded: CheckM
[2023-03-16 14:52:23,483] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 14:52:23,486] [INFO] ===== Completeness check finished =====
[2023-03-16 14:52:23,486] [INFO] ===== Start GTDB Search =====
[2023-03-16 14:52:23,487] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38311/markers.fasta)
[2023-03-16 14:52:23,488] [INFO] Task started: Blastn
[2023-03-16 14:52:23,488] [INFO] Running command: blastn -query OceanDNA-b38311/markers.fasta -db /var/lib/cwl/stg3c5b0336-e056-4486-b213-2476d9b018b9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38311/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 14:52:24,737] [INFO] Task succeeded: Blastn
[2023-03-16 14:52:24,738] [INFO] Selected 10 target genomes.
[2023-03-16 14:52:24,738] [INFO] Target genome list was writen to OceanDNA-b38311/target_genomes_gtdb.txt
[2023-03-16 14:52:24,781] [INFO] Task started: fastANI
[2023-03-16 14:52:24,781] [INFO] Running command: fastANI --query /var/lib/cwl/stg6516343b-5a8e-4468-9dc9-bcdd4a92db45/OceanDNA-b38311.fa --refList OceanDNA-b38311/target_genomes_gtdb.txt --output OceanDNA-b38311/fastani_result_gtdb.tsv --threads 1
[2023-03-16 14:52:35,117] [INFO] Task succeeded: fastANI
[2023-03-16 14:52:35,123] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 14:52:35,124] [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_013415125.1	s__Halomonas glaciei	96.7152	1166	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.36	97.36	0.86	0.86	2	conclusive
GCF_000235725.1	s__Halomonas sp000235725	92.9562	1035	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.32	95.32	0.80	0.80	2	-
GCF_013371085.1	s__Halomonas maris	92.3167	1028	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336575.1	s__Halomonas titanicae	86.6796	1007	1319	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	86.2909	998	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.54	99.54	0.90	0.90	2	-
GCF_001882345.1	s__Halomonas sp001882345	86.2394	957	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364445.1	s__Halomonas alkaliantarctica	86.1929	996	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.52	96.69	0.85	0.81	3	-
GCA_002366715.1	s__Halomonas sp002366715	86.1795	958	1319	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	85.9339	1041	1319	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	84.9264	939	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.96	99.96	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-16 14:52:35,124] [INFO] GTDB search result was written to OceanDNA-b38311/result_gtdb.tsv
[2023-03-16 14:52:35,124] [INFO] ===== GTDB Search completed =====
[2023-03-16 14:52:35,125] [INFO] DFAST_QC result json was written to OceanDNA-b38311/dqc_result.json
[2023-03-16 14:52:35,125] [INFO] DFAST_QC completed!
[2023-03-16 14:52:35,125] [INFO] Total running time: 0h2m10s