[2023-03-16 09:16:56,161] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:16:56,162] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:16:56,162] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5c4e8eb-f71e-49f2-b6a7-55aea9242a9c/dqc_reference
[2023-03-16 09:16:58,674] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:16:58,674] [INFO] Task started: Prodigal
[2023-03-16 09:16:58,674] [INFO] Running command: cat /var/lib/cwl/stg47dd51a0-b6b4-4907-9a6f-b28384dc8aa2/OceanDNA-b30573.fa | prodigal -d OceanDNA-b30573/cds.fna -a OceanDNA-b30573/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:17:11,930] [INFO] Task succeeded: Prodigal
[2023-03-16 09:17:11,930] [INFO] Task started: HMMsearch
[2023-03-16 09:17:11,930] [INFO] Running command: hmmsearch --tblout OceanDNA-b30573/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5c4e8eb-f71e-49f2-b6a7-55aea9242a9c/dqc_reference/reference_markers.hmm OceanDNA-b30573/protein.faa > /dev/null
[2023-03-16 09:17:12,113] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:17:12,114] [INFO] Found 6/6 markers.
[2023-03-16 09:17:12,130] [INFO] Query marker FASTA was written to OceanDNA-b30573/markers.fasta
[2023-03-16 09:17:12,132] [INFO] Task started: Blastn
[2023-03-16 09:17:12,132] [INFO] Running command: blastn -query OceanDNA-b30573/markers.fasta -db /var/lib/cwl/stgb5c4e8eb-f71e-49f2-b6a7-55aea9242a9c/dqc_reference/reference_markers.fasta -out OceanDNA-b30573/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:17:12,894] [INFO] Task succeeded: Blastn
[2023-03-16 09:17:12,900] [INFO] Selected 36 target genomes.
[2023-03-16 09:17:12,900] [INFO] Target genome list was writen to OceanDNA-b30573/target_genomes.txt
[2023-03-16 09:17:12,920] [INFO] Task started: fastANI
[2023-03-16 09:17:12,920] [INFO] Running command: fastANI --query /var/lib/cwl/stg47dd51a0-b6b4-4907-9a6f-b28384dc8aa2/OceanDNA-b30573.fa --refList OceanDNA-b30573/target_genomes.txt --output OceanDNA-b30573/fastani_result.tsv --threads 1
[2023-03-16 09:17:36,228] [INFO] Task succeeded: fastANI
[2023-03-16 09:17:36,228] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5c4e8eb-f71e-49f2-b6a7-55aea9242a9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:17:36,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5c4e8eb-f71e-49f2-b6a7-55aea9242a9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:17:36,248] [INFO] Found 35 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:17:36,249] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 09:17:36,249] [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
Pelagimonas phthalicica	strain=DSM 26923	GCA_004364805.1	1037362	1037362	type	True	76.7551	142	682	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.7515	132	682	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	76.6806	128	682	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	76.6806	128	682	95	below_threshold
Roseovarius aestuarii	strain=KCTC 22174	GCA_019966515.1	475083	475083	type	True	76.6733	79	682	95	below_threshold
Roseovarius marisflavi	strain=DSM 29327	GCA_900142625.1	1054996	1054996	type	True	76.67	127	682	95	below_threshold
Salibaculum griseiflavum	strain=WDS4C29	GCA_003129565.1	1914409	1914409	type	True	76.6421	82	682	95	below_threshold
Thalassobius mediterraneus	strain=DSM 16398	GCA_900156595.1	340021	340021	type	True	76.5729	59	682	95	below_threshold
Pontibaca salina	strain=S1109L	GCA_016307205.1	2795731	2795731	type	True	76.5677	60	682	95	below_threshold
Dinoroseobacter shibae	strain=DFL 12	GCA_000018145.1	215813	215813	type	True	76.5446	90	682	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	76.5403	93	682	95	below_threshold
Poseidonocella pacifica	strain=DSM 29316	GCA_900111875.1	871651	871651	type	True	76.4987	66	682	95	below_threshold
Primorskyibacter marinus	strain=PX7	GCA_003313245.1	1977320	1977320	type	True	76.4592	121	682	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	76.4378	114	682	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	76.4272	113	682	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	76.4176	148	682	95	below_threshold
Celeribacter ethanolicus	strain=NH195	GCA_001550095.1	1758178	1758178	type	True	76.4027	68	682	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.3845	83	682	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	76.3821	84	682	95	below_threshold
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	76.3725	123	682	95	below_threshold
Roseovarius mucosus	strain=DSM 17069	GCA_000768555.3	215743	215743	type	True	76.3347	121	682	95	below_threshold
Puniceibacterium antarcticum	strain=SM1211	GCA_002760615.1	1206336	1206336	type	True	76.3103	104	682	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	76.3093	114	682	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.2772	85	682	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	76.2402	89	682	95	below_threshold
Salinihabitans flavidus	strain=DSM 27842	GCA_900110425.1	569882	569882	type	True	76.2186	91	682	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	76.2104	101	682	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	76.1105	60	682	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	76.0879	61	682	95	below_threshold
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	75.9916	101	682	95	below_threshold
Actibacterium atlanticum	strain=22II-S11-z10	GCA_000671395.1	1461693	1461693	type	True	75.9812	56	682	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	75.9219	98	682	95	below_threshold
Tritonibacter litoralis	strain=SM1979	GCA_009496005.1	2662264	2662264	type	True	75.7818	71	682	95	below_threshold
Pararhodobacter zhoushanensis	strain=ZQ420	GCA_003990445.1	2479545	2479545	type	True	75.7184	74	682	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	75.616	55	682	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:17:36,249] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30573/tc_result.tsv
[2023-03-16 09:17:36,249] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:17:36,249] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:17:36,250] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5c4e8eb-f71e-49f2-b6a7-55aea9242a9c/dqc_reference/checkm_data
[2023-03-16 09:17:36,250] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:17:36,255] [INFO] Task started: CheckM
[2023-03-16 09:17:36,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30573/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30573/checkm_input OceanDNA-b30573/checkm_result
[2023-03-16 09:18:13,190] [INFO] Task succeeded: CheckM
[2023-03-16 09:18:13,191] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 1.50%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-16 09:18:13,195] [INFO] ===== Completeness check finished =====
[2023-03-16 09:18:13,195] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:18:13,195] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30573/markers.fasta)
[2023-03-16 09:18:13,197] [INFO] Task started: Blastn
[2023-03-16 09:18:13,197] [INFO] Running command: blastn -query OceanDNA-b30573/markers.fasta -db /var/lib/cwl/stgb5c4e8eb-f71e-49f2-b6a7-55aea9242a9c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30573/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:18:14,058] [INFO] Task succeeded: Blastn
[2023-03-16 09:18:14,060] [INFO] Selected 35 target genomes.
[2023-03-16 09:18:14,060] [INFO] Target genome list was writen to OceanDNA-b30573/target_genomes_gtdb.txt
[2023-03-16 09:18:14,155] [INFO] Task started: fastANI
[2023-03-16 09:18:14,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg47dd51a0-b6b4-4907-9a6f-b28384dc8aa2/OceanDNA-b30573.fa --refList OceanDNA-b30573/target_genomes_gtdb.txt --output OceanDNA-b30573/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:18:38,677] [INFO] Task succeeded: fastANI
[2023-03-16 09:18:38,696] [INFO] Found 35 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:18:38,696] [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_003667315.2	s__Tropicibacter sp003667315	77.1049	186	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176475.1	s__Tropicibacter naphthalenivorans	77.0143	137	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001975705.1	s__Salipiger abyssi	76.8794	131	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004804335.1	s__Pelagimonas sp004804335	76.867	131	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pelagimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100085.1	s__Salipiger marinus	76.7523	131	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
GCF_017311415.1	s__Salipiger abyssi_A	76.7284	131	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101505.1	s__Mameliella alba	76.6809	127	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCF_900188425.1	s__Antarctobacter heliothermus	76.6708	143	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarctobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109145.1	s__Marinovum algicola	76.6586	129	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	99.11	98.22	0.94	0.88	3	-
GCF_900176485.1	s__Primorskyibacter flagellatus_A	76.656	96	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237555.1	s__Antarctobacter heliothermus_B	76.6533	119	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarctobacter	95.0	97.31	97.29	0.90	0.89	3	-
GCF_003129565.1	s__Salibaculum griseiflavum	76.6422	81	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302505.1	s__Pseudoprimorskyibacter insulae	76.5161	93	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoprimorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111875.1	s__Poseidonocella pacifica	76.4965	65	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Poseidonocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016019955.1	s__Shimia sp016019955	76.4949	105	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	99.56	99.56	0.93	0.93	2	-
GCA_006226775.1	s__Marinovum sp006226775	76.4713	109	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182725.1	s__Thalassobius litoralis	76.4617	98	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142665.1	s__Roseovarius pacificus	76.436	113	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_017813235.1	s__Sagittula sp017813235	76.4175	94	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019218285.1	s__DP3N28-2 sp019218285	76.4161	147	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__DP3N28-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001550095.1	s__Celeribacter ethanolicus	76.4076	68	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	98.17	98.15	0.91	0.89	3	-
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	76.3942	112	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342065.1	s__Primorskyibacter sedentarius	76.3649	121	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018066915.1	s__Roseovarius sp018066915	76.3511	98	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.88	99.88	0.93	0.93	2	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	76.2891	121	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018223085.1	s__Shimia sp018223085	76.2648	92	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344785.1	s__Puniceibacterium profundi	76.2577	100	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015665415.1	s__Pseudophaeobacter sp015665415	76.2576	108	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110425.1	s__Salinihabitans flavidus	76.2139	90	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salinihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169415.1	s__Sagittula stellata	76.2101	97	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000158135.1	s__Ruegeria sp000158135	76.1283	102	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018500075.1	s__Lentibacter sp018500075	76.1234	73	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018524345.1	s__KMM-3653 sp018524345	76.0124	77	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__KMM-3653	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002407245.1	s__Phaeobacter piscinae	76.0	99	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	97.42	96.04	0.93	0.90	10	-
GCF_003990445.1	s__Pararhodobacter zhoushanensis	75.7184	74	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:18:38,697] [INFO] GTDB search result was written to OceanDNA-b30573/result_gtdb.tsv
[2023-03-16 09:18:38,698] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:18:38,701] [INFO] DFAST_QC result json was written to OceanDNA-b30573/dqc_result.json
[2023-03-16 09:18:38,701] [INFO] DFAST_QC completed!
[2023-03-16 09:18:38,702] [INFO] Total running time: 0h1m43s