[2023-03-18 23:18:18,390] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:18:18,390] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:18:18,390] [INFO] DQC Reference Directory: /var/lib/cwl/stga081e0e6-e181-4ab7-9200-d028e1c30a26/dqc_reference
[2023-03-18 23:18:19,498] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:18:19,499] [INFO] Task started: Prodigal
[2023-03-18 23:18:19,499] [INFO] Running command: cat /var/lib/cwl/stgbf7d74fa-4e36-4909-836c-c70643752c1c/OceanDNA-b23521.fa | prodigal -d OceanDNA-b23521/cds.fna -a OceanDNA-b23521/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:18:39,014] [INFO] Task succeeded: Prodigal
[2023-03-18 23:18:39,015] [INFO] Task started: HMMsearch
[2023-03-18 23:18:39,015] [INFO] Running command: hmmsearch --tblout OceanDNA-b23521/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga081e0e6-e181-4ab7-9200-d028e1c30a26/dqc_reference/reference_markers.hmm OceanDNA-b23521/protein.faa > /dev/null
[2023-03-18 23:18:39,208] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:18:39,209] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbf7d74fa-4e36-4909-836c-c70643752c1c/OceanDNA-b23521.fa]
[2023-03-18 23:18:39,228] [INFO] Query marker FASTA was written to OceanDNA-b23521/markers.fasta
[2023-03-18 23:18:39,230] [INFO] Task started: Blastn
[2023-03-18 23:18:39,230] [INFO] Running command: blastn -query OceanDNA-b23521/markers.fasta -db /var/lib/cwl/stga081e0e6-e181-4ab7-9200-d028e1c30a26/dqc_reference/reference_markers.fasta -out OceanDNA-b23521/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:18:39,896] [INFO] Task succeeded: Blastn
[2023-03-18 23:18:39,897] [INFO] Selected 18 target genomes.
[2023-03-18 23:18:39,897] [INFO] Target genome list was writen to OceanDNA-b23521/target_genomes.txt
[2023-03-18 23:18:39,906] [INFO] Task started: fastANI
[2023-03-18 23:18:39,906] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf7d74fa-4e36-4909-836c-c70643752c1c/OceanDNA-b23521.fa --refList OceanDNA-b23521/target_genomes.txt --output OceanDNA-b23521/fastani_result.tsv --threads 1
[2023-03-18 23:18:51,404] [INFO] Task succeeded: fastANI
[2023-03-18 23:18:51,404] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga081e0e6-e181-4ab7-9200-d028e1c30a26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:18:51,404] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga081e0e6-e181-4ab7-9200-d028e1c30a26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:18:51,413] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:18:51,413] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:18:51,413] [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 mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	77.0182	146	1043	95	below_threshold
Henriciella pelagia	strain=CGMCC 1.15928	GCA_014644035.1	1977912	1977912	type	True	76.8034	137	1043	95	below_threshold
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	76.7163	140	1043	95	below_threshold
Henriciella marina	strain=DSM 19595	GCA_000376805.1	453851	453851	type	True	76.6934	133	1043	95	below_threshold
Henriciella litoralis	strain=DSM 22014	GCA_002088935.1	568102	568102	type	True	76.6926	125	1043	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	76.6477	160	1043	95	below_threshold
Henriciella algicola	strain=CCUG67844	GCA_003576245.1	1608422	1608422	type	True	76.6393	146	1043	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	76.5636	126	1043	95	below_threshold
Hyphomonas jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	76.5452	124	1043	95	below_threshold
Hyphomonas polymorpha	strain=PS728	GCA_000685315.1	74319	74319	type	True	76.4551	108	1043	95	below_threshold
Henriciella barbarensis	strain=CCUG66934	GCA_003576345.1	86342	86342	type	True	76.4261	127	1043	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	76.177	98	1043	95	below_threshold
Hyphomonas pacifica	strain=T16B2	GCA_000682675.1	1280941	1280941	type	True	76.1275	110	1043	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:18:51,414] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23521/tc_result.tsv
[2023-03-18 23:18:51,414] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:18:51,414] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:18:51,414] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga081e0e6-e181-4ab7-9200-d028e1c30a26/dqc_reference/checkm_data
[2023-03-18 23:18:51,415] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:18:51,419] [INFO] Task started: CheckM
[2023-03-18 23:18:51,419] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23521/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23521/checkm_input OceanDNA-b23521/checkm_result
[2023-03-18 23:19:41,457] [INFO] Task succeeded: CheckM
[2023-03-18 23:19:41,458] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:19:41,460] [INFO] ===== Completeness check finished =====
[2023-03-18 23:19:41,460] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:19:41,460] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23521/markers.fasta)
[2023-03-18 23:19:41,462] [INFO] Task started: Blastn
[2023-03-18 23:19:41,462] [INFO] Running command: blastn -query OceanDNA-b23521/markers.fasta -db /var/lib/cwl/stga081e0e6-e181-4ab7-9200-d028e1c30a26/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23521/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:19:42,630] [INFO] Task succeeded: Blastn
[2023-03-18 23:19:42,630] [INFO] Selected 11 target genomes.
[2023-03-18 23:19:42,631] [INFO] Target genome list was writen to OceanDNA-b23521/target_genomes_gtdb.txt
[2023-03-18 23:19:42,666] [INFO] Task started: fastANI
[2023-03-18 23:19:42,666] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf7d74fa-4e36-4909-836c-c70643752c1c/OceanDNA-b23521.fa --refList OceanDNA-b23521/target_genomes_gtdb.txt --output OceanDNA-b23521/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:19:50,106] [INFO] Task succeeded: fastANI
[2023-03-18 23:19:50,114] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:19:50,114] [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
GCA_013214545.1	s__Henriciella sp013214545	99.8981	989	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001854405.1	s__Henriciella sp001854405	81.566	703	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642885.1	s__Henriciella sp017642885	80.1397	595	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.99	99.99	0.96	0.96	2	-
GCA_013213785.1	s__Henriciella sp013213785	78.3162	348	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213825.1	s__Henriciella sp013213825	77.9271	349	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576285.1	s__Henriciella sp003576285	77.1021	143	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	97.82	97.80	0.89	0.89	3	-
GCA_012960415.1	s__Henriciella sp012960415	76.8327	139	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.93	99.93	0.95	0.95	2	-
GCF_002088945.1	s__Henriciella pelagia	76.766	141	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003576245.1	s__Henriciella algicola	76.6393	146	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685215.1	s__Hyphomonas jannaschiana	76.5452	124	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125515.1	s__Hyphomonas sp016125515	76.2471	95	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:19:50,114] [INFO] GTDB search result was written to OceanDNA-b23521/result_gtdb.tsv
[2023-03-18 23:19:50,114] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:19:50,115] [INFO] DFAST_QC result json was written to OceanDNA-b23521/dqc_result.json
[2023-03-18 23:19:50,116] [INFO] DFAST_QC completed!
[2023-03-18 23:19:50,116] [INFO] Total running time: 0h1m32s