[2023-03-17 10:19:15,263] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:19:15,264] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:19:15,264] [INFO] DQC Reference Directory: /var/lib/cwl/stg1034ae38-30a4-4010-924f-b4010f7aabe3/dqc_reference
[2023-03-17 10:19:16,987] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:19:16,989] [INFO] Task started: Prodigal
[2023-03-17 10:19:16,989] [INFO] Running command: cat /var/lib/cwl/stg265e6ef0-c77d-48bc-85d0-012b94908894/OceanDNA-b26888.fa | prodigal -d OceanDNA-b26888/cds.fna -a OceanDNA-b26888/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:19:34,479] [INFO] Task succeeded: Prodigal
[2023-03-17 10:19:34,479] [INFO] Task started: HMMsearch
[2023-03-17 10:19:34,479] [INFO] Running command: hmmsearch --tblout OceanDNA-b26888/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1034ae38-30a4-4010-924f-b4010f7aabe3/dqc_reference/reference_markers.hmm OceanDNA-b26888/protein.faa > /dev/null
[2023-03-17 10:19:34,666] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:19:34,666] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg265e6ef0-c77d-48bc-85d0-012b94908894/OceanDNA-b26888.fa]
[2023-03-17 10:19:34,685] [INFO] Query marker FASTA was written to OceanDNA-b26888/markers.fasta
[2023-03-17 10:19:34,686] [INFO] Task started: Blastn
[2023-03-17 10:19:34,687] [INFO] Running command: blastn -query OceanDNA-b26888/markers.fasta -db /var/lib/cwl/stg1034ae38-30a4-4010-924f-b4010f7aabe3/dqc_reference/reference_markers.fasta -out OceanDNA-b26888/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:19:35,325] [INFO] Task succeeded: Blastn
[2023-03-17 10:19:35,326] [INFO] Selected 24 target genomes.
[2023-03-17 10:19:35,326] [INFO] Target genome list was writen to OceanDNA-b26888/target_genomes.txt
[2023-03-17 10:19:35,339] [INFO] Task started: fastANI
[2023-03-17 10:19:35,339] [INFO] Running command: fastANI --query /var/lib/cwl/stg265e6ef0-c77d-48bc-85d0-012b94908894/OceanDNA-b26888.fa --refList OceanDNA-b26888/target_genomes.txt --output OceanDNA-b26888/fastani_result.tsv --threads 1
[2023-03-17 10:19:57,252] [INFO] Task succeeded: fastANI
[2023-03-17 10:19:57,253] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1034ae38-30a4-4010-924f-b4010f7aabe3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:19:57,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1034ae38-30a4-4010-924f-b4010f7aabe3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:19:57,266] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:19:57,266] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 10:19:57,266] [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
Notoacmeibacter ruber	strain=M2BS9Y-3-1	GCA_003668555.1	2670375	2670375	type	True	78.7053	384	947	95	below_threshold
Notoacmeibacter marinus	strain=XMTR2A4	GCA_002238045.1	1876515	1876515	type	True	78.6858	427	947	95	below_threshold
Zhengella mangrovi	strain=X9-2-2	GCA_002727065.1	1982044	1982044	type	True	77.1552	201	947	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	77.146	197	947	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	77.0649	179	947	95	below_threshold
Mesorhizobium camelthorni	strain=CCNWXJ 40-4	GCA_011045125.1	475069	475069	type	True	76.968	198	947	95	below_threshold
Oricola thermophila	strain=MEBiC13590	GCA_013358405.1	2742145	2742145	type	True	76.9389	156	947	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	76.8637	203	947	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	76.8588	191	947	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	76.8309	179	947	95	below_threshold
Aquibium carbonis	strain=B2.3	GCA_003970795.1	2495581	2495581	type	True	76.8158	167	947	95	below_threshold
Mesorhizobium temperatum	strain=SDW018	GCA_002284575.1	241416	241416	type	True	76.7815	185	947	95	below_threshold
Mesorhizobium qingshengii	strain=CGMCC 1.12097	GCA_900103325.1	1165689	1165689	type	True	76.7735	183	947	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	76.7274	200	947	95	below_threshold
Mesorhizobium sangaii	strain=DSM 100039	GCA_014207355.1	505389	505389	type	True	76.7239	190	947	95	below_threshold
Aquamicrobium defluvii	strain=DSM 11603	GCA_004363725.1	69279	69279	type	True	76.7104	171	947	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	76.6679	150	947	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	76.6679	150	947	95	below_threshold
Aminobacter niigataensis	strain=DSM 7050	GCA_014200015.1	83265	83265	type	True	76.6556	187	947	95	below_threshold
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	76.6262	156	947	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	76.5728	179	947	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	76.3672	130	947	95	below_threshold
Rhizobium tubonense	strain=CCBAU 85046	GCA_003240585.1	484088	484088	type	True	76.1724	125	947	95	below_threshold
Afipia felis	strain=ATCC 53690	GCA_000314735.2	1035	1035	type	True	76.1579	81	947	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 10:19:57,267] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26888/tc_result.tsv
[2023-03-17 10:19:57,269] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:19:57,269] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:19:57,269] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1034ae38-30a4-4010-924f-b4010f7aabe3/dqc_reference/checkm_data
[2023-03-17 10:19:57,270] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:19:57,285] [INFO] Task started: CheckM
[2023-03-17 10:19:57,285] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26888/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26888/checkm_input OceanDNA-b26888/checkm_result
[2023-03-17 10:20:42,461] [INFO] Task succeeded: CheckM
[2023-03-17 10:20:42,462] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:20:42,526] [INFO] ===== Completeness check finished =====
[2023-03-17 10:20:42,526] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:20:42,526] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26888/markers.fasta)
[2023-03-17 10:20:42,527] [INFO] Task started: Blastn
[2023-03-17 10:20:42,527] [INFO] Running command: blastn -query OceanDNA-b26888/markers.fasta -db /var/lib/cwl/stg1034ae38-30a4-4010-924f-b4010f7aabe3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26888/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:20:43,583] [INFO] Task succeeded: Blastn
[2023-03-17 10:20:43,591] [INFO] Selected 23 target genomes.
[2023-03-17 10:20:43,591] [INFO] Target genome list was writen to OceanDNA-b26888/target_genomes_gtdb.txt
[2023-03-17 10:20:44,087] [INFO] Task started: fastANI
[2023-03-17 10:20:44,087] [INFO] Running command: fastANI --query /var/lib/cwl/stg265e6ef0-c77d-48bc-85d0-012b94908894/OceanDNA-b26888.fa --refList OceanDNA-b26888/target_genomes_gtdb.txt --output OceanDNA-b26888/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:21:02,990] [INFO] Task succeeded: fastANI
[2023-03-17 10:21:03,003] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 10:21:03,003] [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_003668555.1	s__Notoacmeibacter ruber	78.7053	384	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Notoacmeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002238045.1	s__Notoacmeibacter marinus	78.6762	428	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Notoacmeibacter	95.0	97.91	97.88	0.92	0.92	3	-
GCA_002708825.1	s__Zhengella sp002708825	77.49	214	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Zhengella	95.0	99.96	99.96	0.93	0.93	2	-
GCF_002727065.1	s__Zhengella mangrovi	77.1552	201	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Zhengella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300335.1	s__Nitratireductor pacificus	77.146	197	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014615.2	s__Aquamicrobium_A sp001014615	77.0697	206	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009749525.1	s__Im94 sp009749525	76.9951	179	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Im94	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904745.1	s__Oricola sp014904745	76.9897	195	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013358405.1	s__Oricola thermophila	76.9549	155	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007922615.2	s__Nitratireductor_D sp007922615	76.9089	188	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000359125.1	s__Mesorhizobium sp000359125	76.9046	178	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014495845.1	s__Mesorhizobium_E sp014495845	76.8756	202	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000350085.1	s__Mesorhizobium metallidurans	76.8309	179	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829525.1	s__VLJP01 sp007829525	76.8172	142	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__VLJP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970795.1	s__Mesorhizobium_E carbonis	76.8158	167	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012745.1	s__Mesorhizobium_D ephedrae	76.8105	201	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115245.1	s__Mesorhizobium sp900115245	76.7907	176	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253745.1	s__Mesorhizobium kowhaii	76.7471	197	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003601975.1	s__Mesorhizobium waimense	76.716	201	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207355.1	s__Mesorhizobium sangaii	76.7122	191	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200015.1	s__Aminobacter niigataensis	76.656	187	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.01	98.00	0.90	0.90	3	-
GCA_002700095.1	s__Jiella sp002700095	76.5782	172	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002968635.1	s__Neorhizobium alkalisoli	76.3672	130	947	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 10:21:03,005] [INFO] GTDB search result was written to OceanDNA-b26888/result_gtdb.tsv
[2023-03-17 10:21:03,010] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:21:03,014] [INFO] DFAST_QC result json was written to OceanDNA-b26888/dqc_result.json
[2023-03-17 10:21:03,014] [INFO] DFAST_QC completed!
[2023-03-17 10:21:03,014] [INFO] Total running time: 0h1m48s