[2023-03-17 09:41:39,966] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:41:39,970] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:41:39,970] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbe5e913-2e90-4e97-9dd9-10523238a31c/dqc_reference
[2023-03-17 09:41:41,757] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:41:41,757] [INFO] Task started: Prodigal
[2023-03-17 09:41:41,757] [INFO] Running command: cat /var/lib/cwl/stgfdaa5dc4-0cb1-43f7-94ed-92fa00fd52be/OceanDNA-b24137.fa | prodigal -d OceanDNA-b24137/cds.fna -a OceanDNA-b24137/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:41:59,943] [INFO] Task succeeded: Prodigal
[2023-03-17 09:41:59,944] [INFO] Task started: HMMsearch
[2023-03-17 09:41:59,944] [INFO] Running command: hmmsearch --tblout OceanDNA-b24137/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbe5e913-2e90-4e97-9dd9-10523238a31c/dqc_reference/reference_markers.hmm OceanDNA-b24137/protein.faa > /dev/null
[2023-03-17 09:42:00,149] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:42:00,149] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfdaa5dc4-0cb1-43f7-94ed-92fa00fd52be/OceanDNA-b24137.fa]
[2023-03-17 09:42:00,198] [INFO] Query marker FASTA was written to OceanDNA-b24137/markers.fasta
[2023-03-17 09:42:00,200] [INFO] Task started: Blastn
[2023-03-17 09:42:00,200] [INFO] Running command: blastn -query OceanDNA-b24137/markers.fasta -db /var/lib/cwl/stgbbe5e913-2e90-4e97-9dd9-10523238a31c/dqc_reference/reference_markers.fasta -out OceanDNA-b24137/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:42:00,864] [INFO] Task succeeded: Blastn
[2023-03-17 09:42:00,874] [INFO] Selected 30 target genomes.
[2023-03-17 09:42:00,874] [INFO] Target genome list was writen to OceanDNA-b24137/target_genomes.txt
[2023-03-17 09:42:01,033] [INFO] Task started: fastANI
[2023-03-17 09:42:01,034] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdaa5dc4-0cb1-43f7-94ed-92fa00fd52be/OceanDNA-b24137.fa --refList OceanDNA-b24137/target_genomes.txt --output OceanDNA-b24137/fastani_result.tsv --threads 1
[2023-03-17 09:42:26,670] [INFO] Task succeeded: fastANI
[2023-03-17 09:42:26,671] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbe5e913-2e90-4e97-9dd9-10523238a31c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:42:26,671] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbe5e913-2e90-4e97-9dd9-10523238a31c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:42:26,683] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:42:26,684] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 09:42:26,684] [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
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.1601	76	951	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.0115	56	951	95	below_threshold
Nisaea denitrificans	strain=DSM 18348	GCA_000426505.1	390877	390877	type	True	75.9933	55	951	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	75.9241	70	951	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	75.9013	51	951	95	below_threshold
Oceanibacterium hippocampi	strain=CECT 7691	GCA_900172325.1	745714	745714	type	True	75.871	77	951	95	below_threshold
Pelagibius litoralis	strain=DSM 21314	GCA_011683915.1	374515	374515	type	True	75.8284	62	951	95	below_threshold
Dongia mobilis	strain=CGMCC 1.7660	GCA_004363235.1	578943	578943	type	True	75.8248	71	951	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	75.772	51	951	95	below_threshold
Bradyrhizobium uaiense	strain=UFLA03-164	GCA_010811875.1	2594946	2594946	type	True	75.7348	58	951	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_014197785.1	34017	34017	type	True	75.6919	52	951	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	75.674	65	951	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	75.6683	53	951	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_016653375.1	34017	34017	type	True	75.6683	53	951	95	below_threshold
Bradyrhizobium guangzhouense	strain=CCBAU 51670	GCA_004114955.1	1325095	1325095	type	True	75.6652	52	951	95	below_threshold
Bradyrhizobium sacchari	strain=p9-20	GCA_002068095.1	1399419	1399419	type	True	75.5853	62	951	95	below_threshold
Bosea psychrotolerans	strain=1131	GCA_002917105.1	1871628	1871628	type	True	75.5613	62	951	95	below_threshold
Bradyrhizobium lablabi	strain=CCBAU 23086	GCA_001440475.1	722472	722472	suspected-type	True	75.5331	68	951	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	75.277	59	951	95	below_threshold
Falsiroseomonas frigidaquae	strain=JCM 15073	GCA_012163145.1	487318	487318	type	True	75.242	72	951	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	75.1003	50	951	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 09:42:26,686] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24137/tc_result.tsv
[2023-03-17 09:42:26,687] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:42:26,688] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:42:26,688] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbe5e913-2e90-4e97-9dd9-10523238a31c/dqc_reference/checkm_data
[2023-03-17 09:42:26,688] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:42:26,733] [INFO] Task started: CheckM
[2023-03-17 09:42:26,733] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24137/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24137/checkm_input OceanDNA-b24137/checkm_result
[2023-03-17 09:43:13,784] [INFO] Task succeeded: CheckM
[2023-03-17 09:43:13,784] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.82%
Contamintation: 1.85%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:43:13,872] [INFO] ===== Completeness check finished =====
[2023-03-17 09:43:13,873] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:43:13,873] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24137/markers.fasta)
[2023-03-17 09:43:13,874] [INFO] Task started: Blastn
[2023-03-17 09:43:13,874] [INFO] Running command: blastn -query OceanDNA-b24137/markers.fasta -db /var/lib/cwl/stgbbe5e913-2e90-4e97-9dd9-10523238a31c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24137/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:43:14,947] [INFO] Task succeeded: Blastn
[2023-03-17 09:43:14,963] [INFO] Selected 25 target genomes.
[2023-03-17 09:43:14,963] [INFO] Target genome list was writen to OceanDNA-b24137/target_genomes_gtdb.txt
[2023-03-17 09:43:15,384] [INFO] Task started: fastANI
[2023-03-17 09:43:15,384] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdaa5dc4-0cb1-43f7-94ed-92fa00fd52be/OceanDNA-b24137.fa --refList OceanDNA-b24137/target_genomes_gtdb.txt --output OceanDNA-b24137/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:43:32,319] [INFO] Task succeeded: fastANI
[2023-03-17 09:43:32,327] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 09:43:32,327] [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_905181725.1	s__UBA830 sp905181725	79.6062	432	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479125.1	s__UBA830 sp905479125	79.3465	426	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	98.22	98.19	0.84	0.83	3	-
GCA_002471575.1	s__UBA830 sp002471575	77.4294	230	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	97.90	95.90	0.91	0.84	7	-
GCA_002689465.1	s__UBA830 sp002689465	77.0948	92	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869645.1	s__SHVW01 sp016869645	76.349	66	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002325375.1	s__UBA1479 sp002325375	76.2952	59	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.20	96.43	0.95	0.85	6	-
GCF_900102465.1	s__Thalassobaculum litoreum	76.1711	78	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	-
GCA_009840595.1	s__Bin65 sp009840595	75.9605	77	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin65;f__Bin65;g__Bin65	95.0	98.91	96.90	0.94	0.92	4	-
GCF_014904795.1	s__Nisaea nitritireducens	75.9013	51	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172325.1	s__Oceanibacterium hippocampi	75.871	77	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Oceanibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014925385.1	s__WHTV01 sp014925385	75.674	65	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114955.1	s__Bradyrhizobium guangzhouense	75.6652	52	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.35	98.94	0.94	0.93	3	-
GCA_018240685.1	s__Reyranella sp018240685	75.6079	57	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653355.1	s__Rhodoplanes elegans	75.2656	60	951	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	99.89	99.89	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-17 09:43:32,336] [INFO] GTDB search result was written to OceanDNA-b24137/result_gtdb.tsv
[2023-03-17 09:43:32,347] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:43:32,353] [INFO] DFAST_QC result json was written to OceanDNA-b24137/dqc_result.json
[2023-03-17 09:43:32,353] [INFO] DFAST_QC completed!
[2023-03-17 09:43:32,353] [INFO] Total running time: 0h1m52s