[2023-03-18 21:29:07,896] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:29:07,896] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:29:07,896] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa18ea4d-1670-45d5-a091-3ef6feb75b70/dqc_reference
[2023-03-18 21:29:09,004] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:29:09,004] [INFO] Task started: Prodigal
[2023-03-18 21:29:09,005] [INFO] Running command: cat /var/lib/cwl/stg45fd7cd0-cd26-413c-b4f7-4122a94b1733/OceanDNA-b23680.fa | prodigal -d OceanDNA-b23680/cds.fna -a OceanDNA-b23680/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:29:23,658] [INFO] Task succeeded: Prodigal
[2023-03-18 21:29:23,658] [INFO] Task started: HMMsearch
[2023-03-18 21:29:23,658] [INFO] Running command: hmmsearch --tblout OceanDNA-b23680/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa18ea4d-1670-45d5-a091-3ef6feb75b70/dqc_reference/reference_markers.hmm OceanDNA-b23680/protein.faa > /dev/null
[2023-03-18 21:29:23,858] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:29:23,859] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg45fd7cd0-cd26-413c-b4f7-4122a94b1733/OceanDNA-b23680.fa]
[2023-03-18 21:29:23,887] [INFO] Query marker FASTA was written to OceanDNA-b23680/markers.fasta
[2023-03-18 21:29:23,888] [INFO] Task started: Blastn
[2023-03-18 21:29:23,888] [INFO] Running command: blastn -query OceanDNA-b23680/markers.fasta -db /var/lib/cwl/stgfa18ea4d-1670-45d5-a091-3ef6feb75b70/dqc_reference/reference_markers.fasta -out OceanDNA-b23680/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:29:24,560] [INFO] Task succeeded: Blastn
[2023-03-18 21:29:24,561] [INFO] Selected 13 target genomes.
[2023-03-18 21:29:24,561] [INFO] Target genome list was writen to OceanDNA-b23680/target_genomes.txt
[2023-03-18 21:29:24,571] [INFO] Task started: fastANI
[2023-03-18 21:29:24,571] [INFO] Running command: fastANI --query /var/lib/cwl/stg45fd7cd0-cd26-413c-b4f7-4122a94b1733/OceanDNA-b23680.fa --refList OceanDNA-b23680/target_genomes.txt --output OceanDNA-b23680/fastani_result.tsv --threads 1
[2023-03-18 21:29:33,331] [INFO] Task succeeded: fastANI
[2023-03-18 21:29:33,331] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa18ea4d-1670-45d5-a091-3ef6feb75b70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:29:33,332] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa18ea4d-1670-45d5-a091-3ef6feb75b70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:29:33,339] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 21:29:33,339] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 21:29:33,339] [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 pacifica	strain=T16B2	GCA_000682675.1	1280941	1280941	type	True	99.8428	736	771	95	conclusive
Hyphomonas beringensis	strain=25B14_1	GCA_000682755.1	1280946	1280946	type	True	87.4265	675	771	95	below_threshold
Hyphomonas atlantica	strain=22II1-22F38	GCA_000682715.1	1280948	1280948	type	True	79.1293	358	771	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	78.4269	296	771	95	below_threshold
Hyphomonas jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	78.205	312	771	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	77.7585	269	771	95	below_threshold
Hyphomonas polymorpha	strain=PS728	GCA_000685315.1	74319	74319	type	True	77.5145	184	771	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	76.9803	145	771	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	76.8274	196	771	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:29:33,340] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23680/tc_result.tsv
[2023-03-18 21:29:33,341] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:29:33,341] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:29:33,341] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa18ea4d-1670-45d5-a091-3ef6feb75b70/dqc_reference/checkm_data
[2023-03-18 21:29:33,342] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:29:33,386] [INFO] Task started: CheckM
[2023-03-18 21:29:33,386] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23680/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23680/checkm_input OceanDNA-b23680/checkm_result
[2023-03-18 21:30:13,299] [INFO] Task succeeded: CheckM
[2023-03-18 21:30:13,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.00%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 21:30:13,303] [INFO] ===== Completeness check finished =====
[2023-03-18 21:30:13,303] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:30:13,303] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23680/markers.fasta)
[2023-03-18 21:30:13,304] [INFO] Task started: Blastn
[2023-03-18 21:30:13,304] [INFO] Running command: blastn -query OceanDNA-b23680/markers.fasta -db /var/lib/cwl/stgfa18ea4d-1670-45d5-a091-3ef6feb75b70/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23680/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:30:14,482] [INFO] Task succeeded: Blastn
[2023-03-18 21:30:14,483] [INFO] Selected 11 target genomes.
[2023-03-18 21:30:14,483] [INFO] Target genome list was writen to OceanDNA-b23680/target_genomes_gtdb.txt
[2023-03-18 21:30:14,490] [INFO] Task started: fastANI
[2023-03-18 21:30:14,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg45fd7cd0-cd26-413c-b4f7-4122a94b1733/OceanDNA-b23680.fa --refList OceanDNA-b23680/target_genomes_gtdb.txt --output OceanDNA-b23680/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:30:21,770] [INFO] Task succeeded: fastANI
[2023-03-18 21:30:21,778] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:30:21,778] [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_000682675.1	s__Hyphomonas pacifica	99.8428	736	771	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.59	99.19	0.95	0.91	3	conclusive
GCA_018222605.1	s__Hyphomonas sp002695785	92.5952	713	771	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.58	99.58	0.85	0.85	2	-
GCF_000682755.1	s__Hyphomonas beringensis	87.4265	675	771	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792385.1	s__Hyphomonas sp017792385	79.7581	428	771	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	79.1293	358	771	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	98.47	98.11	0.91	0.87	6	-
GCA_002414505.1	s__Hyphomonas sp002414505	79.0803	362	771	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	78.806	369	771	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	95.72	95.47	0.88	0.83	38	-
GCF_000685235.1	s__Hyphomonas adhaerens	78.4005	298	771	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	97.03	96.92	0.83	0.82	4	-
GCA_000961695.1	s__Hyphomonas sp000961695	78.3612	300	771	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	78.3317	315	771	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	78.1022	307	771	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.48	99.29	0.92	0.85	3	-
--------------------------------------------------------------------------------
[2023-03-18 21:30:21,778] [INFO] GTDB search result was written to OceanDNA-b23680/result_gtdb.tsv
[2023-03-18 21:30:21,778] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:30:21,780] [INFO] DFAST_QC result json was written to OceanDNA-b23680/dqc_result.json
[2023-03-18 21:30:21,780] [INFO] DFAST_QC completed!
[2023-03-18 21:30:21,780] [INFO] Total running time: 0h1m14s