[2023-03-16 07:28:29,993] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:28:29,993] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:28:29,993] [INFO] DQC Reference Directory: /var/lib/cwl/stg38cb8741-4ce5-438a-b3f2-6a253504b4ba/dqc_reference
[2023-03-16 07:28:31,085] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:28:31,085] [INFO] Task started: Prodigal
[2023-03-16 07:28:31,086] [INFO] Running command: cat /var/lib/cwl/stgd84b794c-7652-4f80-b772-3eeb5cefa498/OceanDNA-b23796.fa | prodigal -d OceanDNA-b23796/cds.fna -a OceanDNA-b23796/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:28:52,242] [INFO] Task succeeded: Prodigal
[2023-03-16 07:28:52,242] [INFO] Task started: HMMsearch
[2023-03-16 07:28:52,242] [INFO] Running command: hmmsearch --tblout OceanDNA-b23796/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38cb8741-4ce5-438a-b3f2-6a253504b4ba/dqc_reference/reference_markers.hmm OceanDNA-b23796/protein.faa > /dev/null
[2023-03-16 07:28:52,463] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:28:52,464] [INFO] Found 6/6 markers.
[2023-03-16 07:28:52,489] [INFO] Query marker FASTA was written to OceanDNA-b23796/markers.fasta
[2023-03-16 07:28:52,489] [INFO] Task started: Blastn
[2023-03-16 07:28:52,490] [INFO] Running command: blastn -query OceanDNA-b23796/markers.fasta -db /var/lib/cwl/stg38cb8741-4ce5-438a-b3f2-6a253504b4ba/dqc_reference/reference_markers.fasta -out OceanDNA-b23796/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:28:53,300] [INFO] Task succeeded: Blastn
[2023-03-16 07:28:53,302] [INFO] Selected 14 target genomes.
[2023-03-16 07:28:53,303] [INFO] Target genome list was writen to OceanDNA-b23796/target_genomes.txt
[2023-03-16 07:28:53,311] [INFO] Task started: fastANI
[2023-03-16 07:28:53,312] [INFO] Running command: fastANI --query /var/lib/cwl/stgd84b794c-7652-4f80-b772-3eeb5cefa498/OceanDNA-b23796.fa --refList OceanDNA-b23796/target_genomes.txt --output OceanDNA-b23796/fastani_result.tsv --threads 1
[2023-03-16 07:29:03,978] [INFO] Task succeeded: fastANI
[2023-03-16 07:29:03,979] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38cb8741-4ce5-438a-b3f2-6a253504b4ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:29:03,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38cb8741-4ce5-438a-b3f2-6a253504b4ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:29:03,988] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:29:03,988] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:29:03,988] [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	82.3858	741	1111	95	below_threshold
Hyphomonas pacifica	strain=T16B2	GCA_000682675.1	1280941	1280941	type	True	80.7168	597	1111	95	below_threshold
Hyphomonas beringensis	strain=25B14_1	GCA_000682755.1	1280946	1280946	type	True	80.6773	649	1111	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	79.1717	488	1111	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	79.0404	495	1111	95	below_threshold
Hyphomonas jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	79.0191	516	1111	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	79.0088	474	1111	95	below_threshold
Hyphomonas johnsonii	strain=MHS-2	GCA_000685275.1	81031	81031	type	True	78.8789	438	1111	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	78.015	336	1111	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	76.1914	100	1111	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	76.1193	68	1111	95	below_threshold
Phyllobacterium myrsinacearum	strain=DSM 5892	GCA_002980555.1	28101	28101	type	True	76.0411	60	1111	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	75.7196	68	1111	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	75.5656	52	1111	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:29:03,989] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23796/tc_result.tsv
[2023-03-16 07:29:03,990] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:29:03,990] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:29:03,990] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38cb8741-4ce5-438a-b3f2-6a253504b4ba/dqc_reference/checkm_data
[2023-03-16 07:29:03,991] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:29:04,017] [INFO] Task started: CheckM
[2023-03-16 07:29:04,017] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23796/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23796/checkm_input OceanDNA-b23796/checkm_result
[2023-03-16 07:29:57,086] [INFO] Task succeeded: CheckM
[2023-03-16 07:29:57,086] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:29:57,090] [INFO] ===== Completeness check finished =====
[2023-03-16 07:29:57,090] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:29:57,090] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23796/markers.fasta)
[2023-03-16 07:29:57,090] [INFO] Task started: Blastn
[2023-03-16 07:29:57,091] [INFO] Running command: blastn -query OceanDNA-b23796/markers.fasta -db /var/lib/cwl/stg38cb8741-4ce5-438a-b3f2-6a253504b4ba/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23796/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:29:58,672] [INFO] Task succeeded: Blastn
[2023-03-16 07:29:58,673] [INFO] Selected 13 target genomes.
[2023-03-16 07:29:58,673] [INFO] Target genome list was writen to OceanDNA-b23796/target_genomes_gtdb.txt
[2023-03-16 07:29:58,779] [INFO] Task started: fastANI
[2023-03-16 07:29:58,779] [INFO] Running command: fastANI --query /var/lib/cwl/stgd84b794c-7652-4f80-b772-3eeb5cefa498/OceanDNA-b23796.fa --refList OceanDNA-b23796/target_genomes_gtdb.txt --output OceanDNA-b23796/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:30:08,425] [INFO] Task succeeded: fastANI
[2023-03-16 07:30:08,433] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 07:30:08,433] [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_002414505.1	s__Hyphomonas sp002414505	96.3316	836	1111	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.04	98.84	0.81	0.74	4	conclusive
GCF_000682775.1	s__Hyphomonas sp000682775	85.6796	856	1111	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	95.72	95.47	0.88	0.83	38	-
GCA_017792385.1	s__Hyphomonas sp017792385	83.1707	809	1111	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000682715.1	s__Hyphomonas atlantica	82.3858	741	1111	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	98.47	98.11	0.91	0.87	6	-
GCA_018222605.1	s__Hyphomonas sp002695785	81.4179	669	1111	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	80.7168	597	1111	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	80.6996	646	1111	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000682735.1	s__Hyphomonas sp000682735	79.4755	504	1111	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.43	99.16	0.91	0.90	3	-
GCA_002700305.1	s__Hyphomonas sp002700305	79.4689	526	1111	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.48	99.29	0.92	0.85	3	-
GCF_000685235.1	s__Hyphomonas adhaerens	79.1673	489	1111	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	97.03	96.92	0.83	0.82	4	-
GCF_000682695.1	s__Hyphomonas chukchiensis	79.054	493	1111	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685295.1	s__Hyphomonas oceanitis	79.004	475	1111	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685275.1	s__Hyphomonas johnsonii	78.8789	438	1111	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:30:08,434] [INFO] GTDB search result was written to OceanDNA-b23796/result_gtdb.tsv
[2023-03-16 07:30:08,434] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:30:08,435] [INFO] DFAST_QC result json was written to OceanDNA-b23796/dqc_result.json
[2023-03-16 07:30:08,435] [INFO] DFAST_QC completed!
[2023-03-16 07:30:08,436] [INFO] Total running time: 0h1m38s