[2023-03-18 01:41:20,943] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:41:20,943] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:41:20,943] [INFO] DQC Reference Directory: /var/lib/cwl/stge533c7a8-679b-4615-9f4c-4bc369012279/dqc_reference
[2023-03-18 01:41:22,097] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:41:22,098] [INFO] Task started: Prodigal
[2023-03-18 01:41:22,098] [INFO] Running command: cat /var/lib/cwl/stg247ad0ad-2fde-476f-90a3-0470b0e8f607/OceanDNA-b38314.fa | prodigal -d OceanDNA-b38314/cds.fna -a OceanDNA-b38314/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:41:51,152] [INFO] Task succeeded: Prodigal
[2023-03-18 01:41:51,152] [INFO] Task started: HMMsearch
[2023-03-18 01:41:51,153] [INFO] Running command: hmmsearch --tblout OceanDNA-b38314/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge533c7a8-679b-4615-9f4c-4bc369012279/dqc_reference/reference_markers.hmm OceanDNA-b38314/protein.faa > /dev/null
[2023-03-18 01:41:51,397] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:41:51,397] [INFO] Found 6/6 markers.
[2023-03-18 01:41:51,427] [INFO] Query marker FASTA was written to OceanDNA-b38314/markers.fasta
[2023-03-18 01:41:51,428] [INFO] Task started: Blastn
[2023-03-18 01:41:51,428] [INFO] Running command: blastn -query OceanDNA-b38314/markers.fasta -db /var/lib/cwl/stge533c7a8-679b-4615-9f4c-4bc369012279/dqc_reference/reference_markers.fasta -out OceanDNA-b38314/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:41:52,309] [INFO] Task succeeded: Blastn
[2023-03-18 01:41:52,310] [INFO] Selected 11 target genomes.
[2023-03-18 01:41:52,310] [INFO] Target genome list was writen to OceanDNA-b38314/target_genomes.txt
[2023-03-18 01:41:52,316] [INFO] Task started: fastANI
[2023-03-18 01:41:52,316] [INFO] Running command: fastANI --query /var/lib/cwl/stg247ad0ad-2fde-476f-90a3-0470b0e8f607/OceanDNA-b38314.fa --refList OceanDNA-b38314/target_genomes.txt --output OceanDNA-b38314/fastani_result.tsv --threads 1
[2023-03-18 01:42:02,638] [INFO] Task succeeded: fastANI
[2023-03-18 01:42:02,638] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge533c7a8-679b-4615-9f4c-4bc369012279/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:42:02,638] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge533c7a8-679b-4615-9f4c-4bc369012279/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:42:02,646] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 01:42:02,646] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 01:42:02,646] [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 sedimenti	strain=QX-2	GCA_013416325.1	2729618	2729618	type	True	99.4972	1460	1615	95	conclusive
Halomonas titanicae	strain=BH1	GCA_000336575.1	664683	664683	type	True	94.156	1305	1615	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_002265845.1	223527	223527	type	True	87.6151	1081	1615	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_000236035.1	223527	223527	type	True	87.5889	1087	1615	95	below_threshold
Halomonas glaciei	strain=DD39	GCA_013415125.1	186761	186761	type	True	86.5027	1088	1615	95	below_threshold
Halomonas maris	strain=QX-1	GCA_013371085.1	2729617	2729617	type	True	85.0046	996	1615	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	81.099	771	1615	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	81.0755	767	1615	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	79.3641	513	1615	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	77.4879	274	1615	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	77.3379	206	1615	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:42:02,646] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38314/tc_result.tsv
[2023-03-18 01:42:02,647] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:42:02,647] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:42:02,647] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge533c7a8-679b-4615-9f4c-4bc369012279/dqc_reference/checkm_data
[2023-03-18 01:42:02,647] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:42:02,653] [INFO] Task started: CheckM
[2023-03-18 01:42:02,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38314/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38314/checkm_input OceanDNA-b38314/checkm_result
[2023-03-18 01:43:13,726] [INFO] Task succeeded: CheckM
[2023-03-18 01:43:13,726] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:43:13,729] [INFO] ===== Completeness check finished =====
[2023-03-18 01:43:13,729] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:43:13,729] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38314/markers.fasta)
[2023-03-18 01:43:13,731] [INFO] Task started: Blastn
[2023-03-18 01:43:13,731] [INFO] Running command: blastn -query OceanDNA-b38314/markers.fasta -db /var/lib/cwl/stge533c7a8-679b-4615-9f4c-4bc369012279/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38314/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:43:14,937] [INFO] Task succeeded: Blastn
[2023-03-18 01:43:14,938] [INFO] Selected 9 target genomes.
[2023-03-18 01:43:14,938] [INFO] Target genome list was writen to OceanDNA-b38314/target_genomes_gtdb.txt
[2023-03-18 01:43:14,943] [INFO] Task started: fastANI
[2023-03-18 01:43:14,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg247ad0ad-2fde-476f-90a3-0470b0e8f607/OceanDNA-b38314.fa --refList OceanDNA-b38314/target_genomes_gtdb.txt --output OceanDNA-b38314/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:43:25,698] [INFO] Task succeeded: fastANI
[2023-03-18 01:43:25,704] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:43:25,704] [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_013416325.1	s__Halomonas sedimenti	99.4839	1461	1615	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.54	99.54	0.90	0.90	2	conclusive
GCF_000336575.1	s__Halomonas titanicae	94.156	1305	1615	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.70	97.17	0.86	0.84	22	-
GCF_004364445.1	s__Halomonas alkaliantarctica	91.1145	1220	1615	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.52	96.69	0.85	0.81	3	-
GCF_001882345.1	s__Halomonas sp001882345	89.2875	1079	1615	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	88.9597	1164	1615	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.13	98.13	0.90	0.90	2	-
GCF_002257525.1	s__Halomonas ventosae_B	88.2679	1280	1615	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	88.2177	1195	1615	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	87.5889	1087	1615	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	86.5027	1088	1615	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.36	97.36	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-18 01:43:25,704] [INFO] GTDB search result was written to OceanDNA-b38314/result_gtdb.tsv
[2023-03-18 01:43:25,705] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:43:25,706] [INFO] DFAST_QC result json was written to OceanDNA-b38314/dqc_result.json
[2023-03-18 01:43:25,706] [INFO] DFAST_QC completed!
[2023-03-18 01:43:25,706] [INFO] Total running time: 0h2m5s