[2023-03-15 09:48:16,401] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:48:16,401] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:48:16,401] [INFO] DQC Reference Directory: /var/lib/cwl/stga7995de0-14fa-4065-980c-821a4f0e41b6/dqc_reference
[2023-03-15 09:48:18,052] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:48:18,054] [INFO] Task started: Prodigal
[2023-03-15 09:48:18,054] [INFO] Running command: cat /var/lib/cwl/stgf57fe05b-de02-4b83-9c04-be5b18ae1b33/OceanDNA-b23549.fa | prodigal -d OceanDNA-b23549/cds.fna -a OceanDNA-b23549/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:48:31,030] [INFO] Task succeeded: Prodigal
[2023-03-15 09:48:31,030] [INFO] Task started: HMMsearch
[2023-03-15 09:48:31,030] [INFO] Running command: hmmsearch --tblout OceanDNA-b23549/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7995de0-14fa-4065-980c-821a4f0e41b6/dqc_reference/reference_markers.hmm OceanDNA-b23549/protein.faa > /dev/null
[2023-03-15 09:48:31,256] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:48:31,257] [INFO] Found 6/6 markers.
[2023-03-15 09:48:31,277] [INFO] Query marker FASTA was written to OceanDNA-b23549/markers.fasta
[2023-03-15 09:48:31,277] [INFO] Task started: Blastn
[2023-03-15 09:48:31,277] [INFO] Running command: blastn -query OceanDNA-b23549/markers.fasta -db /var/lib/cwl/stga7995de0-14fa-4065-980c-821a4f0e41b6/dqc_reference/reference_markers.fasta -out OceanDNA-b23549/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:31,971] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:31,972] [INFO] Selected 20 target genomes.
[2023-03-15 09:48:31,972] [INFO] Target genome list was writen to OceanDNA-b23549/target_genomes.txt
[2023-03-15 09:48:31,983] [INFO] Task started: fastANI
[2023-03-15 09:48:31,983] [INFO] Running command: fastANI --query /var/lib/cwl/stgf57fe05b-de02-4b83-9c04-be5b18ae1b33/OceanDNA-b23549.fa --refList OceanDNA-b23549/target_genomes.txt --output OceanDNA-b23549/fastani_result.tsv --threads 1
[2023-03-15 09:48:45,783] [INFO] Task succeeded: fastANI
[2023-03-15 09:48:45,784] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7995de0-14fa-4065-980c-821a4f0e41b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:48:45,784] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7995de0-14fa-4065-980c-821a4f0e41b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:48:45,791] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:48:45,791] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 09:48:45,791] [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
Hyphomonas atlantica	strain=22II1-22F38	GCA_000682715.1	1280948	1280948	type	True	87.1796	563	660	95	below_threshold
Hyphomonas pacifica	strain=T16B2	GCA_000682675.1	1280941	1280941	type	True	79.5688	362	660	95	below_threshold
Hyphomonas beringensis	strain=25B14_1	GCA_000682755.1	1280946	1280946	type	True	79.5569	391	660	95	below_threshold
Hyphomonas jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	78.42	284	660	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	78.3754	281	660	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	78.1042	231	660	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	77.5466	178	660	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	77.0626	126	660	95	below_threshold
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	76.8806	135	660	95	below_threshold
Henriciella marina	strain=DSM 19595	GCA_000376805.1	453851	453851	type	True	76.6989	100	660	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 09:48:45,791] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23549/tc_result.tsv
[2023-03-15 09:48:45,791] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:48:45,792] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:48:45,792] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7995de0-14fa-4065-980c-821a4f0e41b6/dqc_reference/checkm_data
[2023-03-15 09:48:45,792] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:48:45,797] [INFO] Task started: CheckM
[2023-03-15 09:48:45,797] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23549/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23549/checkm_input OceanDNA-b23549/checkm_result
[2023-03-15 09:49:22,166] [INFO] Task succeeded: CheckM
[2023-03-15 09:49:22,167] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.95%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:49:22,169] [INFO] ===== Completeness check finished =====
[2023-03-15 09:49:22,169] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:49:22,169] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23549/markers.fasta)
[2023-03-15 09:49:22,169] [INFO] Task started: Blastn
[2023-03-15 09:49:22,169] [INFO] Running command: blastn -query OceanDNA-b23549/markers.fasta -db /var/lib/cwl/stga7995de0-14fa-4065-980c-821a4f0e41b6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23549/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:49:23,231] [INFO] Task succeeded: Blastn
[2023-03-15 09:49:23,232] [INFO] Selected 14 target genomes.
[2023-03-15 09:49:23,232] [INFO] Target genome list was writen to OceanDNA-b23549/target_genomes_gtdb.txt
[2023-03-15 09:49:23,511] [INFO] Task started: fastANI
[2023-03-15 09:49:23,511] [INFO] Running command: fastANI --query /var/lib/cwl/stgf57fe05b-de02-4b83-9c04-be5b18ae1b33/OceanDNA-b23549.fa --refList OceanDNA-b23549/target_genomes_gtdb.txt --output OceanDNA-b23549/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:49:32,089] [INFO] Task succeeded: fastANI
[2023-03-15 09:49:32,097] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 09:49:32,097] [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_000682715.1	s__Hyphomonas atlantica	87.1796	563	660	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	82.54	492	660	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002414505.1	s__Hyphomonas sp002414505	81.3175	407	660	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.04	98.84	0.81	0.74	4	-
GCF_000682775.1	s__Hyphomonas sp000682775	80.9121	455	660	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	95.72	95.47	0.88	0.83	38	-
GCA_018222605.1	s__Hyphomonas sp002695785	79.8344	402	660	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.58	99.58	0.85	0.85	2	-
GCF_000682675.1	s__Hyphomonas pacifica	79.5831	361	660	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.59	99.19	0.95	0.91	3	-
GCF_000682755.1	s__Hyphomonas beringensis	79.5569	391	660	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763715.1	s__Hyphomonas sp014763715	78.6246	274	660	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700305.1	s__Hyphomonas sp002700305	78.5384	274	660	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.48	99.29	0.92	0.85	3	-
GCF_000685215.1	s__Hyphomonas jannaschiana	78.42	284	660	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961695.1	s__Hyphomonas sp000961695	78.2429	271	660	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	77.413	175	660	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712445.1	s__Hyphomonas sp016712445	77.1764	179	660	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376805.1	s__Henriciella marina	76.6989	100	660	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 09:49:32,098] [INFO] GTDB search result was written to OceanDNA-b23549/result_gtdb.tsv
[2023-03-15 09:49:32,098] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:49:32,099] [INFO] DFAST_QC result json was written to OceanDNA-b23549/dqc_result.json
[2023-03-15 09:49:32,099] [INFO] DFAST_QC completed!
[2023-03-15 09:49:32,099] [INFO] Total running time: 0h1m16s