[2023-03-17 00:45:47,264] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:45:47,264] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:45:47,264] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d076429-92de-4b35-8670-d4e19774a266/dqc_reference
[2023-03-17 00:45:48,352] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:45:48,352] [INFO] Task started: Prodigal
[2023-03-17 00:45:48,353] [INFO] Running command: cat /var/lib/cwl/stgd84cc2df-ffb7-4e45-aca6-a48673b182c4/OceanDNA-b38220.fa | prodigal -d OceanDNA-b38220/cds.fna -a OceanDNA-b38220/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:46:08,428] [INFO] Task succeeded: Prodigal
[2023-03-17 00:46:08,428] [INFO] Task started: HMMsearch
[2023-03-17 00:46:08,428] [INFO] Running command: hmmsearch --tblout OceanDNA-b38220/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d076429-92de-4b35-8670-d4e19774a266/dqc_reference/reference_markers.hmm OceanDNA-b38220/protein.faa > /dev/null
[2023-03-17 00:46:08,633] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:46:08,633] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd84cc2df-ffb7-4e45-aca6-a48673b182c4/OceanDNA-b38220.fa]
[2023-03-17 00:46:08,654] [INFO] Query marker FASTA was written to OceanDNA-b38220/markers.fasta
[2023-03-17 00:46:08,655] [INFO] Task started: Blastn
[2023-03-17 00:46:08,655] [INFO] Running command: blastn -query OceanDNA-b38220/markers.fasta -db /var/lib/cwl/stg9d076429-92de-4b35-8670-d4e19774a266/dqc_reference/reference_markers.fasta -out OceanDNA-b38220/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:09,290] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:09,291] [INFO] Selected 11 target genomes.
[2023-03-17 00:46:09,291] [INFO] Target genome list was writen to OceanDNA-b38220/target_genomes.txt
[2023-03-17 00:46:09,298] [INFO] Task started: fastANI
[2023-03-17 00:46:09,298] [INFO] Running command: fastANI --query /var/lib/cwl/stgd84cc2df-ffb7-4e45-aca6-a48673b182c4/OceanDNA-b38220.fa --refList OceanDNA-b38220/target_genomes.txt --output OceanDNA-b38220/fastani_result.tsv --threads 1
[2023-03-17 00:46:17,921] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:17,922] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d076429-92de-4b35-8670-d4e19774a266/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:46:17,922] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d076429-92de-4b35-8670-d4e19774a266/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:46:17,929] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:46:17,929] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 00:46:17,930] [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	81.2329	699	1127	95	below_threshold
Halomonas glaciei	strain=DD39	GCA_013415125.1	186761	186761	type	True	81.0936	679	1127	95	below_threshold
Halomonas sedimenti	strain=QX-2	GCA_013416325.1	2729618	2729618	type	True	80.9175	708	1127	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_000236035.1	223527	223527	type	True	80.829	694	1127	95	below_threshold
Halomonas maris	strain=QX-1	GCA_013371085.1	2729617	2729617	type	True	80.782	698	1127	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_002265845.1	223527	223527	type	True	80.7676	696	1127	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	79.7505	498	1127	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	79.7009	507	1127	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	78.4681	408	1127	95	below_threshold
Halomonas alkalisoli	strain=M5N1S17	GCA_021412585.1	2907158	2907158	type	True	76.9647	159	1127	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	76.4789	158	1127	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 00:46:17,930] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38220/tc_result.tsv
[2023-03-17 00:46:17,930] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:46:17,930] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:46:17,930] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d076429-92de-4b35-8670-d4e19774a266/dqc_reference/checkm_data
[2023-03-17 00:46:17,931] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:46:17,935] [INFO] Task started: CheckM
[2023-03-17 00:46:17,936] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38220/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38220/checkm_input OceanDNA-b38220/checkm_result
[2023-03-17 00:47:08,828] [INFO] Task succeeded: CheckM
[2023-03-17 00:47:08,828] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:47:08,831] [INFO] ===== Completeness check finished =====
[2023-03-17 00:47:08,831] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:47:08,831] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38220/markers.fasta)
[2023-03-17 00:47:08,832] [INFO] Task started: Blastn
[2023-03-17 00:47:08,832] [INFO] Running command: blastn -query OceanDNA-b38220/markers.fasta -db /var/lib/cwl/stg9d076429-92de-4b35-8670-d4e19774a266/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38220/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:47:09,857] [INFO] Task succeeded: Blastn
[2023-03-17 00:47:09,858] [INFO] Selected 14 target genomes.
[2023-03-17 00:47:09,858] [INFO] Target genome list was writen to OceanDNA-b38220/target_genomes_gtdb.txt
[2023-03-17 00:47:09,916] [INFO] Task started: fastANI
[2023-03-17 00:47:09,916] [INFO] Running command: fastANI --query /var/lib/cwl/stgd84cc2df-ffb7-4e45-aca6-a48673b182c4/OceanDNA-b38220.fa --refList OceanDNA-b38220/target_genomes_gtdb.txt --output OceanDNA-b38220/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:47:21,621] [INFO] Task succeeded: fastANI
[2023-03-17 00:47:21,630] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:47:21,630] [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_000336575.1	s__Halomonas titanicae	81.242	698	1127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.70	97.17	0.86	0.84	22	-
GCF_013415125.1	s__Halomonas glaciei	81.0964	679	1127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.36	97.36	0.86	0.86	2	-
GCF_002257525.1	s__Halomonas ventosae_B	81.0882	721	1127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.23	97.92	0.94	0.87	4	-
GCF_004364445.1	s__Halomonas alkaliantarctica	81.08	712	1127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.52	96.69	0.85	0.81	3	-
GCF_000235725.1	s__Halomonas sp000235725	80.9837	663	1127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.32	95.32	0.80	0.80	2	-
GCF_013416325.1	s__Halomonas sedimenti	80.9205	707	1127	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	80.8816	707	1127	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	80.8587	714	1127	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	80.8556	691	1127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.96	99.96	0.99	0.99	2	-
GCF_013371085.1	s__Halomonas maris	80.7941	696	1127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001651035.1	s__Halomonas sp001651035	80.6322	664	1127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.79	97.57	0.91	0.81	5	-
GCA_002366715.1	s__Halomonas sp002366715	80.5593	644	1127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991175.1	s__Halomonas variabilis	80.4281	606	1127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001507855.1	s__Halomonas sp001507855	80.0632	528	1127	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-03-17 00:47:21,630] [INFO] GTDB search result was written to OceanDNA-b38220/result_gtdb.tsv
[2023-03-17 00:47:21,630] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:47:21,632] [INFO] DFAST_QC result json was written to OceanDNA-b38220/dqc_result.json
[2023-03-17 00:47:21,632] [INFO] DFAST_QC completed!
[2023-03-17 00:47:21,632] [INFO] Total running time: 0h1m34s