[2023-03-17 05:59:11,102] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:59:11,103] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:59:11,103] [INFO] DQC Reference Directory: /var/lib/cwl/stg94350e27-80ec-43d1-94cb-82d97ecb54bb/dqc_reference
[2023-03-17 05:59:12,203] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:59:12,203] [INFO] Task started: Prodigal
[2023-03-17 05:59:12,203] [INFO] Running command: cat /var/lib/cwl/stgffeec512-ed3e-46ca-a204-4e926b9950b4/OceanDNA-b26893.fa | prodigal -d OceanDNA-b26893/cds.fna -a OceanDNA-b26893/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:59:48,981] [INFO] Task succeeded: Prodigal
[2023-03-17 05:59:48,982] [INFO] Task started: HMMsearch
[2023-03-17 05:59:48,982] [INFO] Running command: hmmsearch --tblout OceanDNA-b26893/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94350e27-80ec-43d1-94cb-82d97ecb54bb/dqc_reference/reference_markers.hmm OceanDNA-b26893/protein.faa > /dev/null
[2023-03-17 05:59:49,223] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:59:49,223] [INFO] Found 6/6 markers.
[2023-03-17 05:59:49,256] [INFO] Query marker FASTA was written to OceanDNA-b26893/markers.fasta
[2023-03-17 05:59:49,257] [INFO] Task started: Blastn
[2023-03-17 05:59:49,257] [INFO] Running command: blastn -query OceanDNA-b26893/markers.fasta -db /var/lib/cwl/stg94350e27-80ec-43d1-94cb-82d97ecb54bb/dqc_reference/reference_markers.fasta -out OceanDNA-b26893/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:59:49,940] [INFO] Task succeeded: Blastn
[2023-03-17 05:59:49,941] [INFO] Selected 35 target genomes.
[2023-03-17 05:59:49,941] [INFO] Target genome list was writen to OceanDNA-b26893/target_genomes.txt
[2023-03-17 05:59:49,956] [INFO] Task started: fastANI
[2023-03-17 05:59:49,956] [INFO] Running command: fastANI --query /var/lib/cwl/stgffeec512-ed3e-46ca-a204-4e926b9950b4/OceanDNA-b26893.fa --refList OceanDNA-b26893/target_genomes.txt --output OceanDNA-b26893/fastani_result.tsv --threads 1
[2023-03-17 06:00:20,462] [INFO] Task succeeded: fastANI
[2023-03-17 06:00:20,462] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94350e27-80ec-43d1-94cb-82d97ecb54bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 06:00:20,463] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94350e27-80ec-43d1-94cb-82d97ecb54bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 06:00:20,479] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 06:00:20,479] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 06:00:20,479] [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
Phyllobacterium phragmitis	strain=1N-3	GCA_002980495.1	2670329	2670329	type	True	76.6149	125	1863	95	below_threshold
Rhizobium jaguaris	strain=CCGE525	GCA_003627755.1	1312183	1312183	type	True	76.5787	126	1863	95	below_threshold
Hoeflea alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	76.4991	186	1863	95	below_threshold
Hoeflea halophila	strain=KCTC 23107	GCA_900220985.1	714899	714899	type	True	76.4924	172	1863	95	below_threshold
Shinella daejeonensis	strain=JCM 16236	GCA_024281235.1	659017	659017	type	True	76.4628	120	1863	95	below_threshold
Rhizobium changzhiense	strain=WYCCWR 11279	GCA_013087625.1	2692317	2692317	type	True	76.4584	117	1863	95	below_threshold
Sinorhizobium fredii	strain=USDA 205	GCA_001461695.1	380	380	type	True	76.4346	143	1863	95	below_threshold
Shinella kummerowiae	strain=CCBAU 25048	GCA_009827055.1	417745	417745	type	True	76.4233	143	1863	95	below_threshold
Rhizobium vallis	strain=CCBAU 65647	GCA_003985155.1	634290	634290	type	True	76.423	124	1863	95	below_threshold
Agrobacterium rubi	strain=NBRC 13261	GCA_000739935.1	28099	28099	type	True	76.386	100	1863	95	below_threshold
Ensifer sojae	strain=CCBAU 05684	GCA_000261485.1	716925	716925	type	True	76.3708	124	1863	95	below_threshold
Hoeflea phototrophica	strain=DFL-43	GCA_000154705.2	244596	244596	type	True	76.3687	176	1863	95	below_threshold
Agrobacterium rubi	strain=DSM 6772	GCA_017873055.1	28099	28099	type	True	76.3643	102	1863	95	below_threshold
Ensifer sojae	strain=CCBAU 05684	GCA_002288525.1	716925	716925	type	True	76.3525	124	1863	95	below_threshold
Agrobacterium tumefaciens	strain=B6	GCA_001541315.1	358	358	suspected-type	True	76.3306	126	1863	95	below_threshold
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	76.3243	118	1863	95	below_threshold
Agrobacterium bohemicum	strain=R90	GCA_002896715.1	2052828	2052828	type	True	76.3142	93	1863	95	below_threshold
Brucella haematophila	strain=CCUG 38531	GCA_005938105.1	419474	419474	type	True	76.2532	118	1863	95	below_threshold
Rhizobium pisi	strain=DSM 30132	GCA_003938655.1	574561	574561	type	True	76.2464	128	1863	95	below_threshold
Rhizobium sophorae	strain=CCBAU 03386	GCA_013087515.1	1535242	1535242	type	True	76.2404	130	1863	95	below_threshold
Mesorhizobium sangaii	strain=DSM 100039	GCA_014207355.1	505389	505389	type	True	76.2359	133	1863	95	below_threshold
Agrobacterium larrymoorei	strain=CFBP5473	GCA_005145045.1	160699	160699	type	True	76.2072	112	1863	95	below_threshold
Agrobacterium larrymoorei	strain=ATCC 51759	GCA_000518585.1	160699	160699	type	True	76.2058	112	1863	95	below_threshold
Mesorhizobium japonicum	strain=MAFF 303099	GCA_000009625.1	2066070	2066070	type	True	76.1358	145	1863	95	below_threshold
Ciceribacter lividus	strain=DSM 25528	GCA_003337715.1	1197950	1197950	type	True	76.1077	106	1863	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	76.1059	141	1863	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	76.0374	139	1863	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	75.6182	55	1863	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	75.5913	54	1863	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	75.1897	62	1863	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 06:00:20,479] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26893/tc_result.tsv
[2023-03-17 06:00:20,479] [INFO] ===== Taxonomy check completed =====
[2023-03-17 06:00:20,479] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 06:00:20,479] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94350e27-80ec-43d1-94cb-82d97ecb54bb/dqc_reference/checkm_data
[2023-03-17 06:00:20,480] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 06:00:20,549] [INFO] Task started: CheckM
[2023-03-17 06:00:20,550] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26893/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26893/checkm_input OceanDNA-b26893/checkm_result
[2023-03-17 06:01:56,762] [INFO] Task succeeded: CheckM
[2023-03-17 06:01:56,762] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 06:01:56,766] [INFO] ===== Completeness check finished =====
[2023-03-17 06:01:56,766] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:01:56,767] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26893/markers.fasta)
[2023-03-17 06:01:56,767] [INFO] Task started: Blastn
[2023-03-17 06:01:56,767] [INFO] Running command: blastn -query OceanDNA-b26893/markers.fasta -db /var/lib/cwl/stg94350e27-80ec-43d1-94cb-82d97ecb54bb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26893/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:01:57,960] [INFO] Task succeeded: Blastn
[2023-03-17 06:01:57,961] [INFO] Selected 33 target genomes.
[2023-03-17 06:01:57,961] [INFO] Target genome list was writen to OceanDNA-b26893/target_genomes_gtdb.txt
[2023-03-17 06:01:58,383] [INFO] Task started: fastANI
[2023-03-17 06:01:58,383] [INFO] Running command: fastANI --query /var/lib/cwl/stgffeec512-ed3e-46ca-a204-4e926b9950b4/OceanDNA-b26893.fa --refList OceanDNA-b26893/target_genomes_gtdb.txt --output OceanDNA-b26893/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:02:26,734] [INFO] Task succeeded: fastANI
[2023-03-17 06:02:26,751] [INFO] Found 32 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 06:02:26,752] [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_004959855.1	s__SPNT01 sp004959855	77.0422	351	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__SPNT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017794825.1	s__SPNT01 sp017794825	76.8956	223	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__SPNT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733955.1	s__Hoeflea sp002733955	76.7602	205	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900220985.1	s__Hoeflea halophila	76.4924	172	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952725.1	s__Georhizobium profundi	76.4898	118	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Georhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019084245.1	s__Hoeflea sp019084245	76.4892	194	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	100.00	100.00	0.99	0.99	6	-
GCF_902498795.1	s__Hoeflea sp902498795	76.4745	184	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	97.67	97.67	0.92	0.92	2	-
GCF_001854865.1	s__Neorhizobium sp001854865	76.4294	115	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017352135.1	s__Rhizobium lentis	76.4018	120	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007002745.1	s__Agrobacterium rhizogenes_B	76.3887	143	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154705.2	s__Hoeflea phototrophica	76.3687	176	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004912165.1	s__Allorhizobium ipomoeae	76.3668	110	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739935.1	s__Agrobacterium rubi	76.3664	101	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	96.45	95.90	0.89	0.87	10	-
GCF_014193025.1	s__Rhizobium sp014193025	76.3617	141	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092025.1	s__Agrobacterium fabrum	76.3397	151	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.52	95.41	0.93	0.85	28	-
GCF_902498825.1	s__Georhizobium sp902498825	76.33	115	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Georhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688075.1	s__Mesorhizobium sp000688075	76.3265	135	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001938945.1	s__Pararhizobium rhizosphaerae	76.284	143	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	97.96	97.96	0.94	0.94	2	-
GCF_002968635.1	s__Neorhizobium alkalisoli	76.2777	99	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422245.1	s__Agrobacterium sp001422245	76.2584	106	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003938655.1	s__Rhizobium pisi	76.2464	128	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.78	97.55	0.94	0.90	5	-
GCF_017874015.1	s__Pseudaminobacter sp017874015	76.2285	103	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829525.1	s__VLJP01 sp007829525	76.1923	113	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__VLJP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006442685.1	s__Mesorhizobium sp006442685	76.1907	116	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.73	95.49	0.95	0.85	44	-
GCF_003597675.1	s__Neorhizobium sp003597675	76.1671	130	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900472295.1	s__Mesorhizobium sp900472295	76.1392	132	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.35	97.33	0.92	0.92	3	-
GCF_003337715.1	s__Allorhizobium lividum	76.1077	106	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000350085.1	s__Mesorhizobium metallidurans	76.0465	138	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000359125.1	s__Mesorhizobium sp000359125	76.0343	132	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001686985.1	s__Mesorhizobium amorphae_B	76.0066	137	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0866	99.99	99.99	1.00	1.00	2	-
GCF_000949865.1	s__Agrobacterium nepotum	75.9954	133	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016742175.1	s__Aliihoeflea sp016742175	75.9536	113	1863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aliihoeflea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 06:02:26,752] [INFO] GTDB search result was written to OceanDNA-b26893/result_gtdb.tsv
[2023-03-17 06:02:26,752] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:02:26,755] [INFO] DFAST_QC result json was written to OceanDNA-b26893/dqc_result.json
[2023-03-17 06:02:26,755] [INFO] DFAST_QC completed!
[2023-03-17 06:02:26,755] [INFO] Total running time: 0h3m16s