[2023-03-15 05:29:12,371] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:29:12,371] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:29:12,371] [INFO] DQC Reference Directory: /var/lib/cwl/stg01261660-7458-4fff-bd99-4c424f8ad127/dqc_reference
[2023-03-15 05:29:13,555] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:29:13,555] [INFO] Task started: Prodigal
[2023-03-15 05:29:13,555] [INFO] Running command: cat /var/lib/cwl/stg6e95737e-0fdd-4044-9dd9-249964b0e1d7/OceanDNA-b28564.fa | prodigal -d OceanDNA-b28564/cds.fna -a OceanDNA-b28564/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:29:31,552] [INFO] Task succeeded: Prodigal
[2023-03-15 05:29:31,552] [INFO] Task started: HMMsearch
[2023-03-15 05:29:31,552] [INFO] Running command: hmmsearch --tblout OceanDNA-b28564/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01261660-7458-4fff-bd99-4c424f8ad127/dqc_reference/reference_markers.hmm OceanDNA-b28564/protein.faa > /dev/null
[2023-03-15 05:29:31,805] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:29:31,806] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6e95737e-0fdd-4044-9dd9-249964b0e1d7/OceanDNA-b28564.fa]
[2023-03-15 05:29:31,832] [INFO] Query marker FASTA was written to OceanDNA-b28564/markers.fasta
[2023-03-15 05:29:31,833] [INFO] Task started: Blastn
[2023-03-15 05:29:31,833] [INFO] Running command: blastn -query OceanDNA-b28564/markers.fasta -db /var/lib/cwl/stg01261660-7458-4fff-bd99-4c424f8ad127/dqc_reference/reference_markers.fasta -out OceanDNA-b28564/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:29:32,618] [INFO] Task succeeded: Blastn
[2023-03-15 05:29:32,619] [INFO] Selected 34 target genomes.
[2023-03-15 05:29:32,619] [INFO] Target genome list was writen to OceanDNA-b28564/target_genomes.txt
[2023-03-15 05:29:32,637] [INFO] Task started: fastANI
[2023-03-15 05:29:32,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e95737e-0fdd-4044-9dd9-249964b0e1d7/OceanDNA-b28564.fa --refList OceanDNA-b28564/target_genomes.txt --output OceanDNA-b28564/fastani_result.tsv --threads 1
[2023-03-15 05:29:55,412] [INFO] Task succeeded: fastANI
[2023-03-15 05:29:55,412] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01261660-7458-4fff-bd99-4c424f8ad127/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:29:55,412] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01261660-7458-4fff-bd99-4c424f8ad127/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:29:55,430] [INFO] Found 34 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:29:55,430] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:29:55,431] [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
Salibaculum griseiflavum	strain=WDS4C29	GCA_003129565.1	1914409	1914409	type	True	77.1926	224	937	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	77.1077	220	937	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.1071	209	937	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	77.0593	214	937	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	77.0488	174	937	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	77.0364	204	937	95	below_threshold
Roseivivax marinus	strain=DSM 27511	GCA_900109705.1	1379903	1379903	type	True	77.0046	190	937	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	76.9744	167	937	95	below_threshold
Roseivivax halodurans	strain=JCM 10272	GCA_000521785.1	93683	93683	type	True	76.9741	181	937	95	below_threshold
Allosediminivita pacifica	strain=DSM 29329	GCA_003054175.1	1267769	1267769	type	True	76.9557	180	937	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	76.9329	182	937	95	below_threshold
Jannaschia marina	strain=SHC163	GCA_013404595.1	2741674	2741674	type	True	76.8993	148	937	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	76.8925	206	937	95	below_threshold
Roseovarius atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	76.8705	184	937	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	76.8704	173	937	95	below_threshold
Roseivivax halotolerans	strain=JCM 10271	GCA_900115815.1	93684	93684	type	True	76.8645	164	937	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.86	180	937	95	below_threshold
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	76.7378	163	937	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	76.7156	163	937	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	76.681	213	937	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	76.6695	166	937	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	76.6609	213	937	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.6286	160	937	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_003149265.1	475081	475081	type	True	76.5945	183	937	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_900116765.1	475081	475081	type	True	76.5945	183	937	95	below_threshold
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	76.5842	143	937	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_000152805.1	404236	404236	type	True	76.5633	193	937	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	76.5625	159	937	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	76.5276	175	937	95	below_threshold
Silicimonas algicola	strain=KC90	GCA_003970735.1	1826607	1826607	type	True	76.5261	145	937	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	76.5117	175	937	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	76.4786	162	937	95	below_threshold
Pseudodonghicola xiamenensis	strain=CGMCC 1.7081	GCA_014653505.1	337702	337702	type	True	76.4467	158	937	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	76.3389	141	937	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:29:55,431] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28564/tc_result.tsv
[2023-03-15 05:29:55,431] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:29:55,431] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:29:55,431] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01261660-7458-4fff-bd99-4c424f8ad127/dqc_reference/checkm_data
[2023-03-15 05:29:55,432] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:29:55,439] [INFO] Task started: CheckM
[2023-03-15 05:29:55,439] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28564/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28564/checkm_input OceanDNA-b28564/checkm_result
[2023-03-15 05:30:42,950] [INFO] Task succeeded: CheckM
[2023-03-15 05:30:42,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 05:30:42,953] [INFO] ===== Completeness check finished =====
[2023-03-15 05:30:42,953] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:30:42,953] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28564/markers.fasta)
[2023-03-15 05:30:42,954] [INFO] Task started: Blastn
[2023-03-15 05:30:42,954] [INFO] Running command: blastn -query OceanDNA-b28564/markers.fasta -db /var/lib/cwl/stg01261660-7458-4fff-bd99-4c424f8ad127/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28564/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:30:44,470] [INFO] Task succeeded: Blastn
[2023-03-15 05:30:44,471] [INFO] Selected 32 target genomes.
[2023-03-15 05:30:44,471] [INFO] Target genome list was writen to OceanDNA-b28564/target_genomes_gtdb.txt
[2023-03-15 05:30:44,495] [INFO] Task started: fastANI
[2023-03-15 05:30:44,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e95737e-0fdd-4044-9dd9-249964b0e1d7/OceanDNA-b28564.fa --refList OceanDNA-b28564/target_genomes_gtdb.txt --output OceanDNA-b28564/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:31:05,992] [INFO] Task succeeded: fastANI
[2023-03-15 05:31:06,010] [INFO] Found 32 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:31:06,010] [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_001314655.1	s__Salibaculum sp001314655	77.5187	250	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003789055.1	s__Oceanicola lentulus	77.4179	223	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908505.1	s__Salibaculum sp009908505	77.2942	211	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129565.1	s__Salibaculum griseiflavum	77.1926	224	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	77.1591	206	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002094885.1	s__Salibaculum halophilum	77.1199	219	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142295.1	s__Vannielia litorea	77.0831	190	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Vannielia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156805.1	s__Roseivivax lentus	77.0764	220	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656415.1	s__Seohaeicola zhoushanensis	77.0646	206	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Seohaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172235.1	s__Pseudoruegeria aquimaris	77.05	224	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226775.1	s__Marinovum sp006226775	77.0388	235	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109705.1	s__Roseivivax marinus	77.0179	189	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	97.84	97.84	0.91	0.91	2	-
GCF_900108275.1	s__Jhaorihella thermophila	77.0058	180	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521785.1	s__Roseivivax halodurans	76.9741	181	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363555.1	s__Sulfitobacter sp009363555	76.963	182	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458395.1	s__Leisingera aquaemixtae	76.9612	188	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	97.55	97.51	0.94	0.92	3	-
GCF_001975705.1	s__Salipiger abyssi	76.9512	228	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169415.1	s__Sagittula stellata	76.9088	191	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434965.1	s__Marimonas lutisalis	76.9028	179	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001441615.1	s__Roseovarius atlanticus	76.8841	183	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115815.1	s__Roseivivax halotolerans	76.8644	164	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	97.75	97.75	0.88	0.88	2	-
GCF_900109145.1	s__Marinovum algicola	76.8499	223	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	99.11	98.22	0.94	0.88	3	-
GCF_009363655.1	s__Roseovarius sp009363655	76.8368	187	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.13	98.13	0.93	0.93	2	-
GCA_006227805.1	s__Aestuariivita sp006227805	76.8045	167	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115595.1	s__Tranquillimonas alkanivorans	76.7713	201	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152725.1	s__Pseudooceanicola batsensis	76.7616	206	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116005.1	s__Poseidonocella sedimentorum	76.7098	177	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Poseidonocella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002291955.1	s__UBA996 sp002291955	76.7065	130	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA996	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142765.1	s__Roseovarius litoreus	76.7025	164	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	95.85	95.85	0.86	0.86	2	-
GCF_003111685.1	s__Salipiger pacificus_A	76.6389	194	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.69	97.64	0.90	0.89	3	-
GCF_009789075.1	s__Pseudooceanicola pacificus	76.6158	159	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001408515.1	s__Jannaschia seosinensis	76.5161	118	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:31:06,011] [INFO] GTDB search result was written to OceanDNA-b28564/result_gtdb.tsv
[2023-03-15 05:31:06,011] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:31:06,014] [INFO] DFAST_QC result json was written to OceanDNA-b28564/dqc_result.json
[2023-03-15 05:31:06,014] [INFO] DFAST_QC completed!
[2023-03-15 05:31:06,014] [INFO] Total running time: 0h1m54s