[2023-03-15 17:28:53,476] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:28:53,477] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:28:53,477] [INFO] DQC Reference Directory: /var/lib/cwl/stge56c8ea9-2504-4063-b905-1502a380282c/dqc_reference
[2023-03-15 17:28:54,561] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:28:54,562] [INFO] Task started: Prodigal
[2023-03-15 17:28:54,562] [INFO] Running command: cat /var/lib/cwl/stgdc6ca17a-92f3-4732-9fe6-84f16999f959/OceanDNA-b23644.fa | prodigal -d OceanDNA-b23644/cds.fna -a OceanDNA-b23644/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:29:17,105] [INFO] Task succeeded: Prodigal
[2023-03-15 17:29:17,105] [INFO] Task started: HMMsearch
[2023-03-15 17:29:17,105] [INFO] Running command: hmmsearch --tblout OceanDNA-b23644/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge56c8ea9-2504-4063-b905-1502a380282c/dqc_reference/reference_markers.hmm OceanDNA-b23644/protein.faa > /dev/null
[2023-03-15 17:29:17,313] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:29:17,313] [INFO] Found 6/6 markers.
[2023-03-15 17:29:17,341] [INFO] Query marker FASTA was written to OceanDNA-b23644/markers.fasta
[2023-03-15 17:29:17,343] [INFO] Task started: Blastn
[2023-03-15 17:29:17,343] [INFO] Running command: blastn -query OceanDNA-b23644/markers.fasta -db /var/lib/cwl/stge56c8ea9-2504-4063-b905-1502a380282c/dqc_reference/reference_markers.fasta -out OceanDNA-b23644/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:29:18,151] [INFO] Task succeeded: Blastn
[2023-03-15 17:29:18,152] [INFO] Selected 18 target genomes.
[2023-03-15 17:29:18,152] [INFO] Target genome list was writen to OceanDNA-b23644/target_genomes.txt
[2023-03-15 17:29:18,177] [INFO] Task started: fastANI
[2023-03-15 17:29:18,177] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc6ca17a-92f3-4732-9fe6-84f16999f959/OceanDNA-b23644.fa --refList OceanDNA-b23644/target_genomes.txt --output OceanDNA-b23644/fastani_result.tsv --threads 1
[2023-03-15 17:29:32,161] [INFO] Task succeeded: fastANI
[2023-03-15 17:29:32,161] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge56c8ea9-2504-4063-b905-1502a380282c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:29:32,161] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge56c8ea9-2504-4063-b905-1502a380282c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:29:32,179] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 17:29:32,179] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 17:29:32,179] [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 adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	97.0385	1010	1212	95	conclusive
Hyphomonas jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	85.7522	907	1212	95	below_threshold
Hyphomonas beringensis	strain=25B14_1	GCA_000682755.1	1280946	1280946	type	True	79.3674	466	1212	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	79.0394	473	1212	95	below_threshold
Hyphomonas atlantica	strain=22II1-22F38	GCA_000682715.1	1280948	1280948	type	True	78.909	394	1212	95	below_threshold
Hyphomonas pacifica	strain=T16B2	GCA_000682675.1	1280941	1280941	type	True	78.9008	407	1212	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	78.8903	472	1212	95	below_threshold
Hyphomonas johnsonii	strain=MHS-2	GCA_000685275.1	81031	81031	type	True	78.4845	432	1212	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	78.2955	368	1212	95	below_threshold
Hyphomonas polymorpha	strain=PS728	GCA_000685315.1	74319	74319	type	True	78.2419	396	1212	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	78.0999	324	1212	95	below_threshold
Henriciella barbarensis	strain=CCUG66934	GCA_003576345.1	86342	86342	type	True	77.289	178	1212	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	76.1127	121	1212	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	75.9026	89	1212	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	75.7904	72	1212	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	75.6417	100	1212	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	75.5792	96	1212	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:29:32,180] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23644/tc_result.tsv
[2023-03-15 17:29:32,182] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:29:32,182] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:29:32,182] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge56c8ea9-2504-4063-b905-1502a380282c/dqc_reference/checkm_data
[2023-03-15 17:29:32,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:29:32,204] [INFO] Task started: CheckM
[2023-03-15 17:29:32,204] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23644/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23644/checkm_input OceanDNA-b23644/checkm_result
[2023-03-15 17:30:29,504] [INFO] Task succeeded: CheckM
[2023-03-15 17:30:29,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:30:29,516] [INFO] ===== Completeness check finished =====
[2023-03-15 17:30:29,516] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:30:29,516] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23644/markers.fasta)
[2023-03-15 17:30:29,526] [INFO] Task started: Blastn
[2023-03-15 17:30:29,526] [INFO] Running command: blastn -query OceanDNA-b23644/markers.fasta -db /var/lib/cwl/stge56c8ea9-2504-4063-b905-1502a380282c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23644/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:30:31,241] [INFO] Task succeeded: Blastn
[2023-03-15 17:30:31,245] [INFO] Selected 10 target genomes.
[2023-03-15 17:30:31,245] [INFO] Target genome list was writen to OceanDNA-b23644/target_genomes_gtdb.txt
[2023-03-15 17:30:31,252] [INFO] Task started: fastANI
[2023-03-15 17:30:31,252] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc6ca17a-92f3-4732-9fe6-84f16999f959/OceanDNA-b23644.fa --refList OceanDNA-b23644/target_genomes_gtdb.txt --output OceanDNA-b23644/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:30:38,871] [INFO] Task succeeded: fastANI
[2023-03-15 17:30:38,877] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 17:30:38,878] [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_000685235.1	s__Hyphomonas adhaerens	97.0385	1010	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	97.03	96.92	0.83	0.82	4	conclusive
GCA_002700305.1	s__Hyphomonas sp002700305	86.9494	901	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.48	99.29	0.92	0.85	3	-
GCF_000682735.1	s__Hyphomonas sp000682735	86.1718	933	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.43	99.16	0.91	0.90	3	-
GCF_000685215.1	s__Hyphomonas jannaschiana	85.7588	906	1212	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	84.4187	825	1212	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	82.8974	757	1212	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	79.1648	416	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.04	98.84	0.81	0.74	4	-
GCF_000685315.1	s__Hyphomonas polymorpha	78.2419	396	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	98.45	98.45	0.90	0.90	2	-
GCA_002408125.1	s__UBA5336 sp002408125	77.578	276	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__UBA5336	95.0	99.93	99.87	0.96	0.95	4	-
GCF_003576345.1	s__Henriciella barbarensis	77.3032	177	1212	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 17:30:38,880] [INFO] GTDB search result was written to OceanDNA-b23644/result_gtdb.tsv
[2023-03-15 17:30:38,884] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:30:38,888] [INFO] DFAST_QC result json was written to OceanDNA-b23644/dqc_result.json
[2023-03-15 17:30:38,888] [INFO] DFAST_QC completed!
[2023-03-15 17:30:38,888] [INFO] Total running time: 0h1m45s