[2023-03-15 05:53:02,275] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:53:02,277] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:53:02,277] [INFO] DQC Reference Directory: /var/lib/cwl/stg87fad96f-bc17-4c00-9fe5-fa0a7e07818f/dqc_reference
[2023-03-15 05:53:03,395] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:53:03,395] [INFO] Task started: Prodigal
[2023-03-15 05:53:03,395] [INFO] Running command: cat /var/lib/cwl/stg7ea91ce5-020d-4ffd-97dc-e2d69b9faa16/OceanDNA-b23525.fa | prodigal -d OceanDNA-b23525/cds.fna -a OceanDNA-b23525/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:53:23,701] [INFO] Task succeeded: Prodigal
[2023-03-15 05:53:23,702] [INFO] Task started: HMMsearch
[2023-03-15 05:53:23,702] [INFO] Running command: hmmsearch --tblout OceanDNA-b23525/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87fad96f-bc17-4c00-9fe5-fa0a7e07818f/dqc_reference/reference_markers.hmm OceanDNA-b23525/protein.faa > /dev/null
[2023-03-15 05:53:23,915] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:53:23,915] [INFO] Found 6/6 markers.
[2023-03-15 05:53:23,941] [INFO] Query marker FASTA was written to OceanDNA-b23525/markers.fasta
[2023-03-15 05:53:23,943] [INFO] Task started: Blastn
[2023-03-15 05:53:23,943] [INFO] Running command: blastn -query OceanDNA-b23525/markers.fasta -db /var/lib/cwl/stg87fad96f-bc17-4c00-9fe5-fa0a7e07818f/dqc_reference/reference_markers.fasta -out OceanDNA-b23525/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:53:24,698] [INFO] Task succeeded: Blastn
[2023-03-15 05:53:24,702] [INFO] Selected 16 target genomes.
[2023-03-15 05:53:24,702] [INFO] Target genome list was writen to OceanDNA-b23525/target_genomes.txt
[2023-03-15 05:53:24,712] [INFO] Task started: fastANI
[2023-03-15 05:53:24,712] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ea91ce5-020d-4ffd-97dc-e2d69b9faa16/OceanDNA-b23525.fa --refList OceanDNA-b23525/target_genomes.txt --output OceanDNA-b23525/fastani_result.tsv --threads 1
[2023-03-15 05:53:36,799] [INFO] Task succeeded: fastANI
[2023-03-15 05:53:36,800] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87fad96f-bc17-4c00-9fe5-fa0a7e07818f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:53:36,800] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87fad96f-bc17-4c00-9fe5-fa0a7e07818f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:53:36,810] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:53:36,810] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:53:36,810] [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
Henriciella marina	strain=DSM 19595	GCA_000376805.1	453851	453851	type	True	90.4514	938	1094	95	below_threshold
Henriciella barbarensis	strain=CCUG66934	GCA_003576345.1	86342	86342	type	True	81.6205	722	1094	95	below_threshold
Henriciella algicola	strain=CCUG67844	GCA_003576245.1	1608422	1608422	type	True	81.4225	765	1094	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	79.1493	521	1094	95	below_threshold
Henriciella litoralis	strain=DSM 22014	GCA_002088935.1	568102	568102	type	True	79.1447	539	1094	95	below_threshold
Henriciella pelagia	strain=CGMCC 1.15928	GCA_014644035.1	1977912	1977912	type	True	78.8428	462	1094	95	below_threshold
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	78.8366	517	1094	95	below_threshold
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	78.8203	461	1094	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	76.6141	198	1094	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	75.4696	57	1094	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	75.4368	80	1094	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	75.371	64	1094	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	75.371	64	1094	95	below_threshold
Methylobacterium currus	strain=PR1016A	GCA_003058325.1	2051553	2051553	type	True	75.3709	60	1094	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	74.9228	53	1094	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:53:36,812] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23525/tc_result.tsv
[2023-03-15 05:53:36,813] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:53:36,813] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:53:36,813] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87fad96f-bc17-4c00-9fe5-fa0a7e07818f/dqc_reference/checkm_data
[2023-03-15 05:53:36,814] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:53:36,819] [INFO] Task started: CheckM
[2023-03-15 05:53:36,819] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23525/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23525/checkm_input OceanDNA-b23525/checkm_result
[2023-03-15 05:54:27,875] [INFO] Task succeeded: CheckM
[2023-03-15 05:54:27,875] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:54:27,887] [INFO] ===== Completeness check finished =====
[2023-03-15 05:54:27,888] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:54:27,888] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23525/markers.fasta)
[2023-03-15 05:54:27,889] [INFO] Task started: Blastn
[2023-03-15 05:54:27,889] [INFO] Running command: blastn -query OceanDNA-b23525/markers.fasta -db /var/lib/cwl/stg87fad96f-bc17-4c00-9fe5-fa0a7e07818f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23525/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:54:29,316] [INFO] Task succeeded: Blastn
[2023-03-15 05:54:29,319] [INFO] Selected 9 target genomes.
[2023-03-15 05:54:29,319] [INFO] Target genome list was writen to OceanDNA-b23525/target_genomes_gtdb.txt
[2023-03-15 05:54:29,329] [INFO] Task started: fastANI
[2023-03-15 05:54:29,329] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ea91ce5-020d-4ffd-97dc-e2d69b9faa16/OceanDNA-b23525.fa --refList OceanDNA-b23525/target_genomes_gtdb.txt --output OceanDNA-b23525/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:54:36,460] [INFO] Task succeeded: fastANI
[2023-03-15 05:54:36,466] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:54:36,466] [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_000376805.1	s__Henriciella marina	90.4437	939	1094	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576345.1	s__Henriciella barbarensis	81.6176	724	1094	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960415.1	s__Henriciella sp012960415	81.6027	734	1094	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.93	99.93	0.95	0.95	2	-
GCF_003576245.1	s__Henriciella algicola	81.4313	764	1094	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733705.1	s__Henriciella sp002733705	81.2163	681	1094	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.60	99.22	0.83	0.79	5	-
GCF_002088975.1	s__Henriciella aquimarina	79.1669	519	1094	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088935.1	s__Henriciella litoralis	79.1573	539	1094	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961795.1	s__Hyphomonas sp000961795	76.8764	224	1094	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214545.1	s__Henriciella sp013214545	76.6232	140	1094	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:54:36,470] [INFO] GTDB search result was written to OceanDNA-b23525/result_gtdb.tsv
[2023-03-15 05:54:36,474] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:54:36,477] [INFO] DFAST_QC result json was written to OceanDNA-b23525/dqc_result.json
[2023-03-15 05:54:36,477] [INFO] DFAST_QC completed!
[2023-03-15 05:54:36,477] [INFO] Total running time: 0h1m34s