[2023-03-18 20:59:43,925] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:59:43,925] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:59:43,925] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d5016aa-0716-4e34-af21-bba40586352a/dqc_reference
[2023-03-18 20:59:45,683] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:59:45,683] [INFO] Task started: Prodigal
[2023-03-18 20:59:45,683] [INFO] Running command: cat /var/lib/cwl/stg64a9026f-f877-426b-89da-c6779fc2881f/OceanDNA-b26773.fa | prodigal -d OceanDNA-b26773/cds.fna -a OceanDNA-b26773/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:59:55,726] [INFO] Task succeeded: Prodigal
[2023-03-18 20:59:55,726] [INFO] Task started: HMMsearch
[2023-03-18 20:59:55,726] [INFO] Running command: hmmsearch --tblout OceanDNA-b26773/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d5016aa-0716-4e34-af21-bba40586352a/dqc_reference/reference_markers.hmm OceanDNA-b26773/protein.faa > /dev/null
[2023-03-18 20:59:55,912] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:59:55,913] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg64a9026f-f877-426b-89da-c6779fc2881f/OceanDNA-b26773.fa]
[2023-03-18 20:59:55,930] [INFO] Query marker FASTA was written to OceanDNA-b26773/markers.fasta
[2023-03-18 20:59:55,931] [INFO] Task started: Blastn
[2023-03-18 20:59:55,931] [INFO] Running command: blastn -query OceanDNA-b26773/markers.fasta -db /var/lib/cwl/stg5d5016aa-0716-4e34-af21-bba40586352a/dqc_reference/reference_markers.fasta -out OceanDNA-b26773/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:59:56,691] [INFO] Task succeeded: Blastn
[2023-03-18 20:59:56,692] [INFO] Selected 28 target genomes.
[2023-03-18 20:59:56,692] [INFO] Target genome list was writen to OceanDNA-b26773/target_genomes.txt
[2023-03-18 20:59:56,707] [INFO] Task started: fastANI
[2023-03-18 20:59:56,707] [INFO] Running command: fastANI --query /var/lib/cwl/stg64a9026f-f877-426b-89da-c6779fc2881f/OceanDNA-b26773.fa --refList OceanDNA-b26773/target_genomes.txt --output OceanDNA-b26773/fastani_result.tsv --threads 1
[2023-03-18 21:00:19,235] [INFO] Task succeeded: fastANI
[2023-03-18 21:00:19,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d5016aa-0716-4e34-af21-bba40586352a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:00:19,236] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d5016aa-0716-4e34-af21-bba40586352a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:00:19,251] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:00:19,251] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:00:19,251] [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
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	76.7471	106	515	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	76.4135	116	515	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	76.353	94	515	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	76.2242	100	515	95	below_threshold
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	76.2057	101	515	95	below_threshold
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	76.2038	99	515	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.1999	73	515	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	76.1782	99	515	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	76.1692	94	515	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	76.1644	97	515	95	below_threshold
Aquibium oceanicum	strain=B7	GCA_001889605.1	1670800	1670800	type	True	76.0971	109	515	95	below_threshold
Aureimonas ureilytica	strain=NBRC 106430	GCA_001463945.1	401562	401562	type	True	76.0092	111	515	95	below_threshold
Aureimonas leprariae	strain=YIM 132180	GCA_008802405.1	2615207	2615207	type	True	76.0032	112	515	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	75.9972	98	515	95	below_threshold
Chelativorans xinjiangense	strain=lm93	GCA_009812055.1	2681485	2681485	type	True	75.993	104	515	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	75.9711	94	515	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	75.9584	121	515	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	75.9387	112	515	95	below_threshold
Lutibaculum baratangense	strain=AMV1	GCA_000496075.1	1358440	1358440	type	True	75.8891	90	515	95	below_threshold
Pararhizobium mangrovi	strain=BGMRC 6574	GCA_006516965.1	2590452	2590452	type	True	75.8864	86	515	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	75.8792	93	515	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	75.8615	120	515	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	75.811	98	515	95	below_threshold
Methylobacterium durans	strain=17SD2-17	GCA_003173715.1	2202825	2202825	type	True	75.6775	81	515	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	75.6675	83	515	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	75.6675	83	515	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	75.6176	84	515	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:00:19,251] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26773/tc_result.tsv
[2023-03-18 21:00:19,251] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:00:19,252] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:00:19,252] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d5016aa-0716-4e34-af21-bba40586352a/dqc_reference/checkm_data
[2023-03-18 21:00:19,252] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:00:19,256] [INFO] Task started: CheckM
[2023-03-18 21:00:19,256] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26773/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26773/checkm_input OceanDNA-b26773/checkm_result
[2023-03-18 21:00:48,605] [INFO] Task succeeded: CheckM
[2023-03-18 21:00:48,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.92%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:00:48,621] [INFO] ===== Completeness check finished =====
[2023-03-18 21:00:48,621] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:00:48,621] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26773/markers.fasta)
[2023-03-18 21:00:48,622] [INFO] Task started: Blastn
[2023-03-18 21:00:48,622] [INFO] Running command: blastn -query OceanDNA-b26773/markers.fasta -db /var/lib/cwl/stg5d5016aa-0716-4e34-af21-bba40586352a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26773/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:00:50,065] [INFO] Task succeeded: Blastn
[2023-03-18 21:00:50,073] [INFO] Selected 29 target genomes.
[2023-03-18 21:00:50,073] [INFO] Target genome list was writen to OceanDNA-b26773/target_genomes_gtdb.txt
[2023-03-18 21:00:50,116] [INFO] Task started: fastANI
[2023-03-18 21:00:50,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg64a9026f-f877-426b-89da-c6779fc2881f/OceanDNA-b26773.fa --refList OceanDNA-b26773/target_genomes_gtdb.txt --output OceanDNA-b26773/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:01:12,956] [INFO] Task succeeded: fastANI
[2023-03-18 21:01:12,973] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:01:12,973] [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_014203155.1	s__Shinella fusca	76.7451	106	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305835.1	s__RCIO01 sp017305835	76.4574	135	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177325.1	s__Mesorhizobium_A australicum_A	76.4233	93	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801285.1	s__Mesorhizobium composti	76.4135	116	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.99	96.99	0.90	0.90	2	-
GCF_009765365.1	s__VTOM01 sp009765365	76.3694	136	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__VTOM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004514435.1	s__Shinella sp004514435	76.3366	95	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	99.21	98.45	0.95	0.91	3	-
GCF_003149475.2	s__Roseitalea stylonematis	76.3123	74	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea	95.0	98.99	98.97	0.96	0.95	13	-
GCF_002088275.1	s__Jiella sp002088275	76.3099	98	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756535.1	s__Mesorhizobium sp016756535	76.3032	111	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004963905.1	s__Mesorhizobium sp004963905	76.2196	100	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500835.1	s__Aurantimonas aggregata	76.2038	99	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003863365.1	s__Mesorhizobium tamadayense	76.1782	99	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305635.1	s__Bauldia sp017305635	76.1302	78	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Bauldia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698425.1	s__Oricola sp002698425	76.1244	107	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006442965.1	s__Mesorhizobium sp006442965	76.1229	101	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_008802405.1	s__Aureimonas_A leprariae	76.0441	109	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258835.1	s__Rhodobium orientis	76.0239	89	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodobiaceae;g__Rhodobium	95.0	99.99	99.98	0.99	0.98	3	-
GCF_014843825.1	s__Mesorhizobium silamurunense	75.9972	98	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.52	99.52	0.90	0.90	2	-
GCA_002700095.1	s__Jiella sp002700095	75.9378	113	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006516965.1	s__Pararhizobium_B mangrovi	75.904	85	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716745.1	s__GCA-013693735 sp016716745	75.8807	104	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__GCA-013693735	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199455.1	s__Mesorhizobium carmichaelinearum	75.8792	93	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362745.1	s__Oharaeibacter diazotrophicus	75.8615	120	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Oharaeibacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_004103825.1	s__Hansschlegelia zhihuaiae	75.7646	69	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688075.1	s__Mesorhizobium sp000688075	75.7604	88	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173715.1	s__Methylobacterium durans	75.6926	80	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104035.1	s__Aureimonas jatrophae	75.6902	112	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	99.97	99.97	0.99	0.99	2	-
GCA_002298965.1	s__Pinisolibacter sp002298965	75.6045	84	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Pinisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002869065.1	s__Rhodobium sp002869065	75.4944	78	515	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodobiaceae;g__Rhodobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:01:12,975] [INFO] GTDB search result was written to OceanDNA-b26773/result_gtdb.tsv
[2023-03-18 21:01:12,978] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:01:12,984] [INFO] DFAST_QC result json was written to OceanDNA-b26773/dqc_result.json
[2023-03-18 21:01:12,984] [INFO] DFAST_QC completed!
[2023-03-18 21:01:12,984] [INFO] Total running time: 0h1m29s