[2023-03-17 00:17:04,289] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:17:04,289] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:17:04,289] [INFO] DQC Reference Directory: /var/lib/cwl/stg73615be7-ca4c-448e-824f-01b9107be729/dqc_reference
[2023-03-17 00:17:05,425] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:17:05,425] [INFO] Task started: Prodigal
[2023-03-17 00:17:05,425] [INFO] Running command: cat /var/lib/cwl/stg2cf50a9b-5891-4b7d-8547-9d6602d09d25/OceanDNA-b23491.fa | prodigal -d OceanDNA-b23491/cds.fna -a OceanDNA-b23491/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:17:26,499] [INFO] Task succeeded: Prodigal
[2023-03-17 00:17:26,500] [INFO] Task started: HMMsearch
[2023-03-17 00:17:26,500] [INFO] Running command: hmmsearch --tblout OceanDNA-b23491/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73615be7-ca4c-448e-824f-01b9107be729/dqc_reference/reference_markers.hmm OceanDNA-b23491/protein.faa > /dev/null
[2023-03-17 00:17:26,697] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:17:26,698] [INFO] Found 6/6 markers.
[2023-03-17 00:17:26,719] [INFO] Query marker FASTA was written to OceanDNA-b23491/markers.fasta
[2023-03-17 00:17:26,720] [INFO] Task started: Blastn
[2023-03-17 00:17:26,720] [INFO] Running command: blastn -query OceanDNA-b23491/markers.fasta -db /var/lib/cwl/stg73615be7-ca4c-448e-824f-01b9107be729/dqc_reference/reference_markers.fasta -out OceanDNA-b23491/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:17:27,348] [INFO] Task succeeded: Blastn
[2023-03-17 00:17:27,349] [INFO] Selected 28 target genomes.
[2023-03-17 00:17:27,349] [INFO] Target genome list was writen to OceanDNA-b23491/target_genomes.txt
[2023-03-17 00:17:27,364] [INFO] Task started: fastANI
[2023-03-17 00:17:27,364] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cf50a9b-5891-4b7d-8547-9d6602d09d25/OceanDNA-b23491.fa --refList OceanDNA-b23491/target_genomes.txt --output OceanDNA-b23491/fastani_result.tsv --threads 1
[2023-03-17 00:17:44,272] [INFO] Task succeeded: fastANI
[2023-03-17 00:17:44,273] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73615be7-ca4c-448e-824f-01b9107be729/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:17:44,273] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73615be7-ca4c-448e-824f-01b9107be729/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:17:44,279] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:17:44,279] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 00:17:44,280] [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 litoralis	strain=DSM 22014	GCA_002088935.1	568102	568102	type	True	76.3402	66	1108	95	below_threshold
Henriciella algicola	strain=CCUG67844	GCA_003576245.1	1608422	1608422	type	True	76.1156	72	1108	95	below_threshold
Henriciella pelagia	strain=CGMCC 1.15928	GCA_014644035.1	1977912	1977912	type	True	75.9632	79	1108	95	below_threshold
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	75.9632	79	1108	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	75.948	72	1108	95	below_threshold
Hyphomonas atlantica	strain=22II1-22F38	GCA_000682715.1	1280948	1280948	type	True	75.8907	51	1108	95	below_threshold
Henriciella barbarensis	strain=CCUG66934	GCA_003576345.1	86342	86342	type	True	75.698	59	1108	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	75.5931	53	1108	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 00:17:44,280] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23491/tc_result.tsv
[2023-03-17 00:17:44,280] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:17:44,280] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:17:44,280] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73615be7-ca4c-448e-824f-01b9107be729/dqc_reference/checkm_data
[2023-03-17 00:17:44,281] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:17:44,294] [INFO] Task started: CheckM
[2023-03-17 00:17:44,294] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23491/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23491/checkm_input OceanDNA-b23491/checkm_result
[2023-03-17 00:18:39,216] [INFO] Task succeeded: CheckM
[2023-03-17 00:18:39,216] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:18:39,218] [INFO] ===== Completeness check finished =====
[2023-03-17 00:18:39,219] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:18:39,219] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23491/markers.fasta)
[2023-03-17 00:18:39,220] [INFO] Task started: Blastn
[2023-03-17 00:18:39,220] [INFO] Running command: blastn -query OceanDNA-b23491/markers.fasta -db /var/lib/cwl/stg73615be7-ca4c-448e-824f-01b9107be729/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23491/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:18:40,288] [INFO] Task succeeded: Blastn
[2023-03-17 00:18:40,298] [INFO] Selected 33 target genomes.
[2023-03-17 00:18:40,298] [INFO] Target genome list was writen to OceanDNA-b23491/target_genomes_gtdb.txt
[2023-03-17 00:18:40,334] [INFO] Task started: fastANI
[2023-03-17 00:18:40,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cf50a9b-5891-4b7d-8547-9d6602d09d25/OceanDNA-b23491.fa --refList OceanDNA-b23491/target_genomes_gtdb.txt --output OceanDNA-b23491/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:18:57,153] [INFO] Task succeeded: fastANI
[2023-03-17 00:18:57,162] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:18:57,162] [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_001854405.1	s__Henriciella sp001854405	76.7224	124	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213785.1	s__Henriciella sp013213785	76.7071	99	1108	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	76.3759	92	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214545.1	s__Henriciella sp013214545	76.3686	111	1108	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	76.2717	68	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.93	99.93	0.95	0.95	2	-
GCA_017642885.1	s__Henriciella sp017642885	76.1644	124	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.99	99.99	0.96	0.96	2	-
GCF_002088945.1	s__Henriciella pelagia	75.9632	79	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002088975.1	s__Henriciella aquimarina	75.948	72	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000682775.1	s__Hyphomonas sp000682775	75.9356	55	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	95.72	95.47	0.88	0.83	38	-
GCF_000682715.1	s__Hyphomonas atlantica	75.8907	51	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	98.47	98.11	0.91	0.87	6	-
GCA_017792385.1	s__Hyphomonas sp017792385	75.8894	63	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002408125.1	s__UBA5336 sp002408125	75.8799	57	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__UBA5336	95.0	99.93	99.87	0.96	0.95	4	-
GCF_000682735.1	s__Hyphomonas sp000682735	75.8192	66	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.43	99.16	0.91	0.90	3	-
GCA_002733705.1	s__Henriciella sp002733705	75.7777	74	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.60	99.22	0.83	0.79	5	-
GCF_003576345.1	s__Henriciella barbarensis	75.698	59	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685235.1	s__Hyphomonas adhaerens	75.5931	53	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	97.03	96.92	0.83	0.82	4	-
--------------------------------------------------------------------------------
[2023-03-17 00:18:57,163] [INFO] GTDB search result was written to OceanDNA-b23491/result_gtdb.tsv
[2023-03-17 00:18:57,163] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:18:57,166] [INFO] DFAST_QC result json was written to OceanDNA-b23491/dqc_result.json
[2023-03-17 00:18:57,166] [INFO] DFAST_QC completed!
[2023-03-17 00:18:57,167] [INFO] Total running time: 0h1m53s