[2023-03-18 23:45:35,839] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:45:35,840] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:45:35,840] [INFO] DQC Reference Directory: /var/lib/cwl/stgd68126f5-3a8a-4f3f-8940-853c2fbcb903/dqc_reference
[2023-03-18 23:45:37,728] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:45:37,729] [INFO] Task started: Prodigal
[2023-03-18 23:45:37,729] [INFO] Running command: cat /var/lib/cwl/stg445c1736-ec2f-450d-952a-0b608877f5db/OceanDNA-b26623.fa | prodigal -d OceanDNA-b26623/cds.fna -a OceanDNA-b26623/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:46:04,818] [INFO] Task succeeded: Prodigal
[2023-03-18 23:46:04,819] [INFO] Task started: HMMsearch
[2023-03-18 23:46:04,819] [INFO] Running command: hmmsearch --tblout OceanDNA-b26623/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd68126f5-3a8a-4f3f-8940-853c2fbcb903/dqc_reference/reference_markers.hmm OceanDNA-b26623/protein.faa > /dev/null
[2023-03-18 23:46:05,040] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:46:05,040] [INFO] Found 6/6 markers.
[2023-03-18 23:46:05,066] [INFO] Query marker FASTA was written to OceanDNA-b26623/markers.fasta
[2023-03-18 23:46:05,067] [INFO] Task started: Blastn
[2023-03-18 23:46:05,068] [INFO] Running command: blastn -query OceanDNA-b26623/markers.fasta -db /var/lib/cwl/stgd68126f5-3a8a-4f3f-8940-853c2fbcb903/dqc_reference/reference_markers.fasta -out OceanDNA-b26623/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:46:06,032] [INFO] Task succeeded: Blastn
[2023-03-18 23:46:06,033] [INFO] Selected 27 target genomes.
[2023-03-18 23:46:06,033] [INFO] Target genome list was writen to OceanDNA-b26623/target_genomes.txt
[2023-03-18 23:46:06,047] [INFO] Task started: fastANI
[2023-03-18 23:46:06,048] [INFO] Running command: fastANI --query /var/lib/cwl/stg445c1736-ec2f-450d-952a-0b608877f5db/OceanDNA-b26623.fa --refList OceanDNA-b26623/target_genomes.txt --output OceanDNA-b26623/fastani_result.tsv --threads 1
[2023-03-18 23:46:30,724] [INFO] Task succeeded: fastANI
[2023-03-18 23:46:30,725] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd68126f5-3a8a-4f3f-8940-853c2fbcb903/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:46:30,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd68126f5-3a8a-4f3f-8940-853c2fbcb903/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:46:30,740] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:46:30,740] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:46:30,740] [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
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	78.1996	619	1399	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	78.0911	539	1399	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	77.993	477	1399	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	77.3957	344	1399	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	77.3004	333	1399	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	77.2526	369	1399	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	77.215	343	1399	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	77.1713	428	1399	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	77.074	273	1399	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	77.0489	401	1399	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	77.0208	267	1399	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	77.0177	326	1399	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.9325	389	1399	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.9282	438	1399	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	76.9059	343	1399	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	76.9053	239	1399	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	76.8992	340	1399	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.8654	219	1399	95	below_threshold
Skermanella aerolata	strain=5416T-32	GCA_000936425.1	393310	393310	type	True	76.8301	292	1399	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	76.6401	251	1399	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	76.5593	207	1399	95	below_threshold
Rhodospirillum rubrum	strain=ATCC 11170	GCA_000013085.1	1085	1085	type	True	76.55	208	1399	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	76.4854	279	1399	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	76.248	196	1399	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	76.2123	199	1399	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	76.1678	209	1399	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	76.1221	180	1399	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:46:30,740] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26623/tc_result.tsv
[2023-03-18 23:46:30,740] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:46:30,740] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:46:30,741] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd68126f5-3a8a-4f3f-8940-853c2fbcb903/dqc_reference/checkm_data
[2023-03-18 23:46:30,741] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:46:31,265] [INFO] Task started: CheckM
[2023-03-18 23:46:31,266] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26623/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26623/checkm_input OceanDNA-b26623/checkm_result
[2023-03-18 23:47:33,889] [INFO] Task succeeded: CheckM
[2023-03-18 23:47:33,889] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:47:33,892] [INFO] ===== Completeness check finished =====
[2023-03-18 23:47:33,892] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:47:33,893] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26623/markers.fasta)
[2023-03-18 23:47:33,894] [INFO] Task started: Blastn
[2023-03-18 23:47:33,894] [INFO] Running command: blastn -query OceanDNA-b26623/markers.fasta -db /var/lib/cwl/stgd68126f5-3a8a-4f3f-8940-853c2fbcb903/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26623/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:47:35,878] [INFO] Task succeeded: Blastn
[2023-03-18 23:47:35,879] [INFO] Selected 26 target genomes.
[2023-03-18 23:47:35,879] [INFO] Target genome list was writen to OceanDNA-b26623/target_genomes_gtdb.txt
[2023-03-18 23:47:35,897] [INFO] Task started: fastANI
[2023-03-18 23:47:35,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg445c1736-ec2f-450d-952a-0b608877f5db/OceanDNA-b26623.fa --refList OceanDNA-b26623/target_genomes_gtdb.txt --output OceanDNA-b26623/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:47:59,515] [INFO] Task succeeded: fastANI
[2023-03-18 23:47:59,531] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:47:59,531] [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_016869975.1	s__JAFAZJ01 sp016869975	78.545	545	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__JAFAZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699855.1	s__GCA-016699855 sp016699855	78.3576	613	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__GCA-016699855	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240745.1	s__Reyranella sp018240745	78.2971	462	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240695.1	s__Reyranella sp018240695	78.2165	431	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	96.90	96.90	0.84	0.84	2	-
GCA_016870055.1	s__Reyranella sp016870055	78.2068	406	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039615.1	s__SYSU-D60007 sp008039615	78.1961	620	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016467395.1	s__Reyranella sp016467395	78.1462	529	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992495.1	s__Reyranella soli	78.1206	535	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296815.1	s__Reyranella sp004296815	78.1004	388	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900110395.1	s__Reyranella sp900110395	78.0936	570	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884705.1	s__Reyranella sp005884705	78.0909	377	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019039055.1	s__Reyranella sp019039055	77.9671	493	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185145.1	s__Reyranella sp016185145	77.8884	526	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859315.1	s__SYSU-D60007 sp007859315	77.7882	540	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013290035.1	s__Reyranella sp013290035	77.6818	337	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903832005.1	s__Reyranella aerosaccus_B	77.6113	425	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.93	99.93	0.97	0.96	3	-
GCA_002781745.1	s__UBA1479 sp002781745	77.2053	216	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000342045.1	s__Phaeospirillum caucaseum	77.1034	270	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	76.9967	259	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869285.1	s__SHVZ01 sp016869285	76.8952	274	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__SHVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903941095.1	s__Magnetospirillum sp903941095	76.887	216	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	99.83	99.83	0.93	0.93	2	-
GCA_016792765.1	s__SBBV01 sp016792765	76.7449	317	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin65;f__Bin65;g__SBBV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013349665.1	s__Telmatospirillum sp013349665	76.6546	177	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654615.1	s__Telmatospirillum sp015654615	76.4527	204	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019241915.1	s__AP-15 sp019241915	76.2844	170	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__AP-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002307145.1	s__Alpha-05 sp002307145	75.9567	178	1399	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Alpha-05	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:47:59,531] [INFO] GTDB search result was written to OceanDNA-b26623/result_gtdb.tsv
[2023-03-18 23:47:59,532] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:47:59,534] [INFO] DFAST_QC result json was written to OceanDNA-b26623/dqc_result.json
[2023-03-18 23:47:59,534] [INFO] DFAST_QC completed!
[2023-03-18 23:47:59,534] [INFO] Total running time: 0h2m24s