[root@4527fed4ab00 16:49:56 /work/my_reseq/ref]# sh $scriptdir/index.sh Oryza_sativa.IRGSP-1.0.dna.toplevel.fa Oryza_sativa.IRGSP-1.0.61.gff3
REF: Oryza_sativa.IRGSP-1.0.dna.toplevel.fa
GFF: Oryza_sativa.IRGSP-1.0.61.gff3
GTF:
build Index start:
RNN CMD:samtools faidx Oryza_sativa.IRGSP-1.0.dna.toplevel.fa
RNN CMD: picard CreateSequenceDictionary R=Oryza_sativa.IRGSP-1.0.dna.toplevel.fa O=Oryza_sativa.IRGSP-1.0.dna.toplevel.dict
INFO 2025-05-30 16:52:07 CreateSequenceDictionary
********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
**********
https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
**********
********** The command line looks like this in the new syntax:
**********
********** CreateSequenceDictionary -R Oryza_sativa.IRGSP-1.0.dna.toplevel.fa -O Oryza_sativa.IRGSP-1.0.dna.toplevel.dict
**********
16:52:08.028 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/share/work/biosoft/picard/picard-3.0.0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Fri May 30 16:52:08 CST 2025] CreateSequenceDictionary OUTPUT=Oryza_sativa.IRGSP-1.0.dna.toplevel.dict REFERENCE=Oryza_sativa.IRGSP-1.0.dna.toplevel.fa TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Fri May 30 16:52:08 CST 2025] Executing as root@4527fed4ab00 on Linux 5.15.133.1-microsoft-standard-WSL2 amd64; Java HotSpot(TM) 64-Bit Server VM 19.0.1+10-21; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 3.0.0
[Fri May 30 16:52:08 CST 2025] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=518979584
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" picard.PicardException: /work/my_reseq/ref/Oryza_sativa.IRGSP-1.0.dna.toplevel.dict already exists. Delete this file and try again, or specify a different output file.
at picard.sam.CreateSequenceDictionary.doWork(CreateSequenceDictionary.java:220)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:289)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:104)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:114)
RNN CMD: bwa index Oryza_sativa.IRGSP-1.0.dna.toplevel.fa
[bwa_index] Pack FASTA... 3.05 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=750098570, availableWord=64779716
[BWTIncConstructFromPacked] 10 iterations done. 99578618 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 190947162 characters processed.
[BWTIncConstructFromPacked] 30 iterations done. 272151770 characters processed.
[BWTIncConstructFromPacked] 40 iterations done. 344322602 characters processed.
[BWTIncConstructFromPacked] 50 iterations done. 408464234 characters processed.
[BWTIncConstructFromPacked] 60 iterations done. 465469450 characters processed.
[BWTIncConstructFromPacked] 70 iterations done. 516131818 characters processed.
[BWTIncConstructFromPacked] 80 iterations done. 561156666 characters processed.
[BWTIncConstructFromPacked] 90 iterations done. 601170810 characters processed.
[BWTIncConstructFromPacked] 100 iterations done. 636731466 characters processed.
[BWTIncConstructFromPacked] 110 iterations done. 668333834 characters processed.
[BWTIncConstructFromPacked] 120 iterations done. 696418042 characters processed.
[BWTIncConstructFromPacked] 130 iterations done. 721375386 characters processed.
[BWTIncConstructFromPacked] 140 iterations done. 743553498 characters processed.
[bwt_gen] Finished constructing BWT in 144 iterations.
[bwa_index] 204.44 seconds elapse.
[bwa_index] Update BWT... 2.87 sec
[bwa_index] Pack forward-only FASTA... 2.11 sec
[bwa_index] Construct SA from BWT and Occ... 112.57 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index Oryza_sativa.IRGSP-1.0.dna.toplevel.fa
[main] Real time: 345.354 sec; CPU: 325.053 sec
gtf file not provide, try get gtf from gff:
RUN CMD: gffread Oryza_sativa.IRGSP-1.0.61.gff3 -T -o Oryza_sativa.IRGSP-1.0.61.gtf
Error: discarding overlapping duplicate tRNA feature (9778-9852) with ID=EPlORYSAT000373673
Error: discarding overlapping duplicate pseudogenic_transcript feature (25585-25708) with ID=EPlORYSAT000373610
Error: discarding overlapping duplicate tRNA feature (26189-26261) with ID=EPlORYSAT000373616
Error: discarding overlapping duplicate tRNA feature (32203-32276) with ID=EPlORYSAT000373652
Error: discarding overlapping duplicate pseudogenic_transcript feature (35219-35292) with ID=EPlORYSAT000373643
Error: discarding overlapping duplicate tRNA feature (45135-45206) with ID=EPlORYSAT000373669
Error: discarding overlapping duplicate tRNA feature (54284-54356) with ID=EPlORYSAT000373614
Error: discarding overlapping duplicate pseudogenic_transcript feature (60344-60373) with ID=EPlORYSAT000373621
Error: discarding overlapping duplicate tRNA feature (64083-64156) with ID=EPlORYSAT000373613
Error: discarding overlapping duplicate tRNA feature (64882-64955) with ID=EPlORYSAT000373619
Error: discarding overlapping duplicate tRNA feature (65154-65225) with ID=EPlORYSAT000373629
Error: discarding overlapping duplicate tRNA feature (69323-69395) with ID=EPlORYSAT000373640
Error: discarding overlapping duplicate tRNA feature (188545-188618) with ID=EPlORYSAT000373624
Error: discarding overlapping duplicate tRNA feature (261618-261704) with ID=EPlORYSAT000373653
Error: discarding overlapping duplicate rRNA feature (282532-282653) with ID=EPlORYSAT000373611
Error: discarding overlapping duplicate rRNA feature (282767-284461) with ID=EPlORYSAT000373647
Error: discarding overlapping duplicate tRNA feature (336728-336815) with ID=EPlORYSAT000373650
Error: discarding overlapping duplicate tRNA feature (357852-357938) with ID=EPlORYSAT000373657
Error: discarding overlapping duplicate tRNA feature (359447-359549) with ID=EPlORYSAT000373612
Error: discarding overlapping duplicate tRNA feature (363110-363192) with ID=EPlORYSAT000373635
Error: discarding overlapping duplicate rRNA feature (380118-383624) with ID=EPlORYSAT000373608
Error: discarding overlapping duplicate tRNA feature (390806-390876) with ID=EPlORYSAT000373620
Error: discarding overlapping duplicate tRNA feature (407229-407300) with ID=EPlORYSAT000373615
Error: discarding overlapping duplicate tRNA feature (1363-3938) with ID=EPlORYSAT000373869
Error: discarding overlapping duplicate tRNA feature (6615-6687) with ID=EPlORYSAT000373784
Error: discarding overlapping duplicate tRNA feature (7829-7916) with ID=EPlORYSAT000373814
Error: discarding overlapping duplicate tRNA feature (11503-11590) with ID=EPlORYSAT000373785
Error: discarding overlapping duplicate tRNA feature (12331-12401) with ID=EPlORYSAT000373825
Error: discarding overlapping duplicate pseudogenic_transcript feature (12528-12601) with ID=EPlORYSAT000373851
Error: discarding overlapping duplicate tRNA feature (12839-12912) with ID=EPlORYSAT000373815
Error: discarding overlapping duplicate tRNA feature (13010-13752) with ID=EPlORYSAT000373846
Error: discarding overlapping duplicate tRNA feature (15060-15131) with ID=EPlORYSAT000373818
Error: discarding overlapping duplicate pseudogenic_transcript feature (15128-15200) with ID=EPlORYSAT000373795
Error: discarding overlapping duplicate tRNA feature (15650-15722) with ID=EPlORYSAT000373797
Error: discarding overlapping duplicate tRNA feature (15784-15867) with ID=EPlORYSAT000373810
Error: discarding overlapping duplicate tRNA feature (16231-16304) with ID=EPlORYSAT000373840
Error: discarding overlapping duplicate tRNA feature (18059-18129) with ID=EPlORYSAT000373854
Error: discarding overlapping duplicate tRNA feature (35866-35937) with ID=EPlORYSAT000373835
Error: discarding overlapping duplicate pseudogenic_transcript feature (36073-36147) with ID=EPlORYSAT000373871
Error: discarding overlapping duplicate tRNA feature (44438-44524) with ID=EPlORYSAT000373859
Error: discarding overlapping duplicate tRNA feature (46558-47182) with ID=EPlORYSAT000373822
Error: discarding overlapping duplicate tRNA feature (47425-47497) with ID=EPlORYSAT000373831
Error: discarding overlapping duplicate tRNA feature (50367-51037) with ID=EPlORYSAT000373805
Error: discarding overlapping duplicate tRNA feature (51219-51291) with ID=EPlORYSAT000373783
Error: discarding overlapping duplicate tRNA feature (64229-64303) with ID=EPlORYSAT000373867
Error: discarding overlapping duplicate pseudogenic_transcript feature (65198-65398) with ID=gene-rpl33
Error: discarding overlapping duplicate tRNA feature (81050-81124) with ID=EPlORYSAT000373812
Error: discarding overlapping duplicate tRNA feature (83139-83212) with ID=EPlORYSAT000373789
Error: discarding overlapping duplicate tRNA feature (84711-84791) with ID=EPlORYSAT000373826
Error: discarding overlapping duplicate tRNA feature (90996-91067) with ID=EPlORYSAT000373842
Error: discarding overlapping duplicate rRNA feature (91299-92789) with ID=EPlORYSAT000373849
Error: discarding overlapping duplicate tRNA feature (93100-94118) with ID=EPlORYSAT000373862
Error: discarding overlapping duplicate tRNA feature (94183-95067) with ID=EPlORYSAT000373820
Error: discarding overlapping duplicate rRNA feature (95213-98096) with ID=EPlORYSAT000373852
Error: discarding overlapping duplicate rRNA feature (98192-98286) with ID=EPlORYSAT000373870
Error: discarding overlapping duplicate rRNA feature (98514-98634) with ID=EPlORYSAT000373829
Error: discarding overlapping duplicate tRNA feature (98891-98964) with ID=EPlORYSAT000373788
Error: discarding overlapping duplicate tRNA feature (105074-105153) with ID=EPlORYSAT000373847
Error: discarding overlapping duplicate tRNA feature (116154-116227) with ID=EPlORYSAT000373837
Error: discarding overlapping duplicate rRNA feature (116484-116604) with ID=EPlORYSAT000373834
Error: discarding overlapping duplicate rRNA feature (116832-116926) with ID=EPlORYSAT000373845
Error: discarding overlapping duplicate rRNA feature (117022-119905) with ID=EPlORYSAT000373811
Error: discarding overlapping duplicate tRNA feature (120051-120935) with ID=EPlORYSAT000373790
Error: discarding overlapping duplicate tRNA feature (121000-122018) with ID=EPlORYSAT000373872
Error: discarding overlapping duplicate rRNA feature (122329-123819) with ID=EPlORYSAT000373839
Error: discarding overlapping duplicate tRNA feature (124051-124122) with ID=EPlORYSAT000373798
Error: discarding overlapping duplicate tRNA feature (130327-130407) with ID=EPlORYSAT000373803
Error: discarding overlapping duplicate tRNA feature (131906-131979) with ID=EPlORYSAT000373786
Error: discarding overlapping duplicate tRNA feature (133991-134068) with ID=EPlORYSAT000373848
build ANNOVAR index
RUN CMD: gtfToGenePred -genePredExt Oryza_sativa.IRGSP-1.0.61.gtf unknown_refGene.txt
RUN CMD: retrieve_seq_from_fasta.pl --format refGene --seqfile Oryza_sativa.IRGSP-1.0.dna.toplevel.fa unknown_refGene.txt --out unknown_refGeneMrna.fa
NOTICE: Reading region file unknown_refGene.txt ... Done with 45973 regions from 14 chromosomes
NOTICE: Finished reading 63 sequences from Oryza_sativa.IRGSP-1.0.dna.toplevel.fa
NOTICE: Finished reading 63 sequences from Oryza_sativa.IRGSP-1.0.dna.toplevel.fa
NOTICE: Finished reading 63 sequences from Oryza_sativa.IRGSP-1.0.dna.toplevel.fa
NOTICE: Finished reading 63 sequences from Oryza_sativa.IRGSP-1.0.dna.toplevel.fa
NOTICE: Finished reading 63 sequences from Oryza_sativa.IRGSP-1.0.dna.toplevel.fa
NOTICE: Finished reading 63 sequences from Oryza_sativa.IRGSP-1.0.dna.toplevel.fa
NOTICE: Finished reading 63 sequences from Oryza_sativa.IRGSP-1.0.dna.toplevel.fa
NOTICE: Finished reading 63 sequences from Oryza_sativa.IRGSP-1.0.dna.toplevel.fa
NOTICE: Finished reading 63 sequences from Oryza_sativa.IRGSP-1.0.dna.toplevel.fa
NOTICE: Finished reading 63 sequences from Oryza_sativa.IRGSP-1.0.dna.toplevel.fa
NOTICE: Finished reading 63 sequences from Oryza_sativa.IRGSP-1.0.dna.toplevel.fa
NOTICE: Finished reading 63 sequences from Oryza_sativa.IRGSP-1.0.dna.toplevel.fa
NOTICE: Finished reading 63 sequences from Oryza_sativa.IRGSP-1.0.dna.toplevel.fa
NOTICE: Finished reading 63 sequences from Oryza_sativa.IRGSP-1.0.dna.toplevel.fa
NOTICE: Finished writting FASTA for 45973 genomic regions to unknown_refGeneMrna.fa