[2023-03-15 21:48:06,709] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:48:06,710] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:48:06,710] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c4b5a75-945f-415e-a5e1-8ebd5b1f8ab9/dqc_reference
[2023-03-15 21:48:07,846] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:48:07,846] [INFO] Task started: Prodigal
[2023-03-15 21:48:07,846] [INFO] Running command: cat /var/lib/cwl/stg1def79ff-837d-4579-9b8f-eaae76e57944/OceanDNA-b24136.fa | prodigal -d OceanDNA-b24136/cds.fna -a OceanDNA-b24136/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:48:37,522] [INFO] Task succeeded: Prodigal
[2023-03-15 21:48:37,523] [INFO] Task started: HMMsearch
[2023-03-15 21:48:37,523] [INFO] Running command: hmmsearch --tblout OceanDNA-b24136/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c4b5a75-945f-415e-a5e1-8ebd5b1f8ab9/dqc_reference/reference_markers.hmm OceanDNA-b24136/protein.faa > /dev/null
[2023-03-15 21:48:37,751] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:48:37,751] [INFO] Found 6/6 markers.
[2023-03-15 21:48:37,780] [INFO] Query marker FASTA was written to OceanDNA-b24136/markers.fasta
[2023-03-15 21:48:37,782] [INFO] Task started: Blastn
[2023-03-15 21:48:37,782] [INFO] Running command: blastn -query OceanDNA-b24136/markers.fasta -db /var/lib/cwl/stg5c4b5a75-945f-415e-a5e1-8ebd5b1f8ab9/dqc_reference/reference_markers.fasta -out OceanDNA-b24136/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:48:38,780] [INFO] Task succeeded: Blastn
[2023-03-15 21:48:38,782] [INFO] Selected 28 target genomes.
[2023-03-15 21:48:38,783] [INFO] Target genome list was writen to OceanDNA-b24136/target_genomes.txt
[2023-03-15 21:48:38,829] [INFO] Task started: fastANI
[2023-03-15 21:48:38,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg1def79ff-837d-4579-9b8f-eaae76e57944/OceanDNA-b24136.fa --refList OceanDNA-b24136/target_genomes.txt --output OceanDNA-b24136/fastani_result.tsv --threads 1
[2023-03-15 21:49:01,111] [INFO] Task succeeded: fastANI
[2023-03-15 21:49:01,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c4b5a75-945f-415e-a5e1-8ebd5b1f8ab9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:49:01,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c4b5a75-945f-415e-a5e1-8ebd5b1f8ab9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:49:01,126] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:49:01,126] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:49:01,126] [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
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.8337	162	1611	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.4925	177	1611	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.412	180	1611	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.4103	180	1611	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.3224	138	1611	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.3208	148	1611	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.2891	149	1611	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	76.2788	103	1611	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	76.2385	157	1611	95	below_threshold
Hankyongella ginsenosidimutans	strain=W1-2-3	GCA_005144965.1	1763828	1763828	type	True	76.2156	82	1611	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	76.1832	165	1611	95	below_threshold
Oceanibacterium hippocampi	strain=CECT 7691	GCA_900172325.1	745714	745714	type	True	76.1785	174	1611	95	below_threshold
Skermanella aerolata	strain=5416T-32	GCA_000936425.1	393310	393310	type	True	76.0787	169	1611	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.0679	88	1611	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	76.0586	172	1611	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.0138	177	1611	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	75.987	168	1611	95	below_threshold
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	75.9194	127	1611	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	75.9045	100	1611	95	below_threshold
Elstera cyanobacteriorum	strain=CGMCC 1.15802	GCA_014643715.1	2022747	2022747	type	True	75.9003	71	1611	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	75.8441	119	1611	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	75.7917	170	1611	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.6643	164	1611	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	75.6504	158	1611	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.6429	205	1611	95	below_threshold
Streptomyces microflavus	strain=JCM 4496	GCA_014650075.1	1919	1919	type	True	74.9367	54	1611	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:49:01,129] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24136/tc_result.tsv
[2023-03-15 21:49:01,134] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:49:01,134] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:49:01,134] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c4b5a75-945f-415e-a5e1-8ebd5b1f8ab9/dqc_reference/checkm_data
[2023-03-15 21:49:01,135] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:49:01,217] [INFO] Task started: CheckM
[2023-03-15 21:49:01,217] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24136/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24136/checkm_input OceanDNA-b24136/checkm_result
[2023-03-15 21:50:11,145] [INFO] Task succeeded: CheckM
[2023-03-15 21:50:11,146] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:50:11,169] [INFO] ===== Completeness check finished =====
[2023-03-15 21:50:11,169] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:50:11,169] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24136/markers.fasta)
[2023-03-15 21:50:11,170] [INFO] Task started: Blastn
[2023-03-15 21:50:11,170] [INFO] Running command: blastn -query OceanDNA-b24136/markers.fasta -db /var/lib/cwl/stg5c4b5a75-945f-415e-a5e1-8ebd5b1f8ab9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24136/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:50:12,620] [INFO] Task succeeded: Blastn
[2023-03-15 21:50:12,623] [INFO] Selected 24 target genomes.
[2023-03-15 21:50:12,623] [INFO] Target genome list was writen to OceanDNA-b24136/target_genomes_gtdb.txt
[2023-03-15 21:50:12,670] [INFO] Task started: fastANI
[2023-03-15 21:50:12,671] [INFO] Running command: fastANI --query /var/lib/cwl/stg1def79ff-837d-4579-9b8f-eaae76e57944/OceanDNA-b24136.fa --refList OceanDNA-b24136/target_genomes_gtdb.txt --output OceanDNA-b24136/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:50:30,523] [INFO] Task succeeded: fastANI
[2023-03-15 21:50:30,536] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:50:30,536] [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	79.7521	631	1611	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	79.6262	609	1611	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	77.8568	392	1611	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	77.4869	144	1611	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377375.1	s__WHUE01 sp009377375	76.8546	278	1611	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640745.1	s__Nisaea sp017640745	76.7238	135	1611	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869145.1	s__VGEU01 sp016869145	76.5483	221	1611	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__VGEU01;g__VGEU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018660305.1	s__JABJKO01 sp018660305	76.5009	146	1611	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__JABJKO01	95.0	99.60	99.60	0.81	0.81	2	-
GCA_903856295.1	s__CAIZDL01 sp903856295	76.3983	104	1611	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__CAIZDL01	95.0	99.95	99.95	0.95	0.95	2	-
GCA_009840595.1	s__Bin65 sp009840595	76.3389	165	1611	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin65;f__Bin65;g__Bin65	95.0	98.91	96.90	0.94	0.92	4	-
GCF_014904705.1	s__Nisaea sp014904705	76.3206	148	1611	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102465.1	s__Thalassobaculum litoreum	76.2429	170	1611	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	-
GCA_018240695.1	s__Reyranella sp018240695	76.1749	133	1611	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	96.90	96.90	0.84	0.84	2	-
GCF_017876095.1	s__Azospirillum agricola	76.0239	176	1611	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	96.88	96.88	0.87	0.87	2	-
GCF_004923315.1	s__Azospirillum sp003116065	76.0119	197	1611	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.27	96.11	0.89	0.85	4	-
GCF_016595245.1	s__Azospirillum sp016595245	75.943	202	1611	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016201015.1	s__JACQDQ01 sp016201015	75.9376	143	1611	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__JACQDQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710335.1	s__JADJXQ01 sp016710335	75.9225	100	1611	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__JADJXQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519335.1	s__Jiella endophytica	75.9194	127	1611	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015291645.1	s__Bradyrhizobium sp015291645	75.886	128	1611	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903822185.1	s__CAIKMD01 sp903822185	75.8197	126	1611	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__CAIKMD01	95.0	99.70	99.51	0.99	0.98	4	-
GCF_008039615.1	s__SYSU-D60007 sp008039615	75.6482	204	1611	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016202695.1	s__JACQOE01 sp016202695	75.6314	98	1611	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JACQOE01;f__JACQOE01;g__JACQOE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:50:30,537] [INFO] GTDB search result was written to OceanDNA-b24136/result_gtdb.tsv
[2023-03-15 21:50:30,539] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:50:30,543] [INFO] DFAST_QC result json was written to OceanDNA-b24136/dqc_result.json
[2023-03-15 21:50:30,543] [INFO] DFAST_QC completed!
[2023-03-15 21:50:30,543] [INFO] Total running time: 0h2m24s