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r3fang / SnapTools

A module for working with snap files in Python
Apache License 2.0
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Error running snaptools snap-pre #15

Open Austin-s-h opened 5 years ago

Austin-s-h commented 5 years ago

Hi! I'm trying to generate a snapfile, but I am running into the following error. Could you provide guidance as to why this may be happening? Thanks! Here is my command 

snaptools snap-pre  \
    --input-file 4_subsampled.HH8.filtered.tagged.Aligned.out.renamed.sorted.bam \
    --output-snap 4_subsampled.HH8.filtered.tagged.Aligned.out.renamed.snap  \  
    --genome-name galGal5 \
    --genome-size chick_chrNameLength.chrom.size  \
    --barcode-file sciATACchick.barcodes.txt \
    --min-mapq 30  \
    --min-flen 0  \
    --max-flen 1500  \
    --keep-chrm True  \
    --keep-single True  \
    --keep-secondary False  \
    --overwrite True  \
    --max-num 1000000  \
    --qc-file True \
    --verbose True

My bamfile looks like this...

@HD VN:1.4
@SQ SN:chr10    LN:21119840
@SQ SN:chr11    LN:20200042
@SQ SN:chr12    LN:20387278
@SQ SN:chr13    LN:19166714
@SQ SN:chr14    LN:16219308
@SQ SN:chr15    LN:13062184
@SQ SN:chr16    LN:2844601
@SQ SN:chr17    LN:10762512
@SQ SN:chr18    LN:11373140
@SQ SN:chr19    LN:10323212
@SQ SN:chr1 LN:197608386
@SQ SN:chr20    LN:13897287
@SQ SN:chr21    LN:6844979
@SQ SN:chr22    LN:5459462
@SQ SN:chr23    LN:6149580
@SQ SN:chr24    LN:6491222
@SQ SN:chr25    LN:3980610
@SQ SN:chr26    LN:6055710
@SQ SN:chr27    LN:8080432
@SQ SN:chr28    LN:5116882
@SQ SN:chr2 LN:149682049
@SQ SN:chr30    LN:1818525
@SQ SN:chr31    LN:6153034
@SQ SN:chr32    LN:725831
@SQ SN:chr33    LN:7821666
@SQ SN:chr3 LN:110838418
@SQ SN:chr4 LN:91315245
@SQ SN:chr5 LN:59809098
@SQ SN:chr6 LN:36374701
@SQ SN:chr7 LN:36742308
@SQ SN:chr8 LN:30219446
@SQ SN:chr9 LN:24153086
@SQ SN:chrM LN:16775
@SQ SN:chrW LN:6813114
@SQ SN:chrZ LN:82529921
@PG ID:STAR PN:STAR VN:2.7.0f_0328  CL:STAR   --runThreadN 20   --genomeDir /workdir/rs958/programs/STAR/galgal6   --readFilesType SAM   SE      --readFilesIn /workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8aa.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ab.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ac.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ad.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ae.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8af.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ag.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ah.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ai.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8aj.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ak.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8al.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8am.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8an.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ao.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ap.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8aq.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ar.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8as.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8at.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8au.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8av.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8aw.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ax.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ay.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8az.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ba.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8bb.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8bc.filtered.tagged.bam      --readFilesCommand samtools   view   -@   2      --outFileNamePrefix /workdir/rs958/20190907_sciSeqTest/galgal6/HH8.filtered.tagged.   --outStd SAM   --outSAMtype SAM      --outSAMunmapped Within      --outSAMmultNmax 1   --outFilterMultimapNmax 50   --sjdbGTFfile /workdir/rs958/programs/STAR/galgal6/galGal6.refGene.gtf   --sjdbOverhang 49
@CO user command line: STAR --readFilesCommand samtools view -@ 2 --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outSAMunmapped Within --outSAMtype SAM --outStd SAM --genomeDir /workdir/rs958/programs/STAR/galgal6 --sjdbGTFfile /workdir/rs958/programs/STAR/galgal6/galGal6.refGene.gtf --runThreadN 20 --readFilesIn /workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8aa.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ab.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ac.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ad.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ae.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8af.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ag.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ah.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ai.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8aj.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ak.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8al.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8am.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8an.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ao.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ap.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8aq.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ar.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8as.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8at.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8au.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8av.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8aw.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ax.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ay.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8az.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ba.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8bb.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8bc.filtered.tagged.bam --outFileNamePrefix /workdir/rs958/20190907_sciSeqTest/galgal6/HH8.filtered.tagged. --sjdbOverhang 49 --readFilesType SAM SE
AACTTGATGCGTGCTAGTAGGAAGGACGAT-ATTTACAC:NB500947:861:H3HWFBGXC:1:11101:9731:9824    4   *   0   0   *   *   0   0   CCTGTACACCTGATTGCCAGAAGAGGGCATCAGATCCCTTTATAGATGGT  AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE  NH:i:0  HI:i:0  AS:i:18 nM:i:0  uT:A:1  BX:Z:AACTTGATGCGTGCTAGTAGGAAGGACGAT BC:Z:AACTTGATGCGTGCTAGTAGGAAGGACGAT
GAGAGCTCTAGCCACACTGTACATACCGCT-AGACTAAT:NB500947:861:H3HWFBGXC:1:11101:15942:9826   16  chr7    11274343    255 50M *   0   0   CTGTGGTAGCCCAGAGGTCTCCCCAGCAGATGTTCTCTCCTACTTTAGGT  EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA  NH:i:1  HI:i:1  AS:i:49 nM:i:0  BX:Z:GAGAGCTCTAGCCACACTGTACATACCGCT BC:Z:GAGAGCTCTAGCCACACTGTACATACCGCT
ATTCATCTTGTTCTGCCGTCGCACAGTGTA-TTGAAGCG:NB500947:861:H3HWFBGXC:1:11101:14639:9832   16  chr1    55776983    255 50M *   0   0   CCAATGGTGAGATGCTTGCTAGTGGTTGCAACCCTTGGCTGGGGTTCACC  EEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEAEEEEEEEEE6AAAAA  NH:i:1  HI:i:1  AS:i:49 nM:i:0  BX:Z:ATTCATCTTGTTCTGCCGTCGCACAGTGTA BC:Z:ATTCATCTTGTTCTGCCGTCGCACAGTGTA
TTACACAACATGCGGTTTGATACCACACAA-GTCTTTAT:NB500947:861:H3HWFBGXC:1:11101:25172:9840   16  chr1    88366497    255 50M *   0   0   CCTCATTTGTCAACGGGTACATGCTGACAGAATAGCCAAGCATTTTGTGG  EEEEEEEEEEEEEEAEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA  NH:i:1  HI:i:1  AS:i:49 nM:i:0  BX:Z:TTACACAACATGCGGTTTGATACCACACAA BC:Z:TTACACAACATGCGGTTTGATACCACACAA
TATCTACGCGTGCGTGGCGACACGCTAATG-GCAGCGAA:NB500947:861:H3HWFBGXC:1:11101:8819:9841    16  chr1    20360291    255 48M2S   *   0   0   GCTCTGAGCTAGGATCTGCAAAGACAGCTGGGCCTGCCTTTGTCCTGAAG  EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA  NH:i:1  HI:i:1  AS:i:47 nM:i:0  BX:Z:TATCTACGCGTGCGTGGCGACACGCTAATG BC:Z:TATCTACGCGTGCGTGGCGACACGCTAATG
AACTTGATGCCTGGTTACTTCAAGTCACCA-ACTAAAGG:NB500947:861:H3HWFBGXC:1:11101:6519:9847    16  chr11   8646791 255 50M *   0   0   CTAACGTCTTCATTAGTGCCATAATACCAGCTAAGAAAACTCTCCTGGCC  EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA  NH:i:1  HI:i:1  AS:i:49 nM:i:0  BX:Z:AACTTGATGCCTGGTTACTTCAAGTCACCA BC:Z:AACTTGATGCCTGGTTACTTCAAGTCACCA
TGGAGCAATTTCGTGACCGCAGAGCGTACG-TATATTCC:NB500947:861:H3HWFBGXC:1:11101:1364:9862    4   *   0   0   *   *   0   0   GTACACTTACTACAAAGAAGATTATCTGAAATACTCCCCACTGGCTCCTT  AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEAEEEEEEEEE  NH:i:0  HI:i:0  AS:i:19 nM:i:0  uT:A:1  BX:Z:TGGAGCAATTTCGTGACCGCAGAGCGTACG BC:Z:TGGAGCAATTTCGTGACCGCAGAGCGTACG
TATCTACGCGGTCTGAAGAGTGCGGAGAGA-TCCCTTGA:NB500947:861:H3HWFBGXC:1:11101:9472:9885    0   chr10   6810885 255 50M *   0   0   GGAGTGATCTGTCTGTTAGCCTGCAGGTACTTACTGGTCTCACAGCAAGA  AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEE  NH:i:1  HI:i:1  AS:i:49 nM:i:0  BX:Z:TATCTACGCGGTCTGAAGAGTGCGGAGAGA BC:Z:TATCTACGCGGTCTGAAGAGTGCGGAGAGA

And the error I'm getting


Traceback (most recent call last):
  File "/usr/local/bin/snaptools", line 6, in <module>
    exec(compile(open(__file__).read(), __file__, 'exec'))
  File "/opt/snaptools/bin/snaptools", line 38, in <module>
    parse_args()    
  File "/opt/snaptools/snaptools/parser.py", line 144, in parse_args
    verbose=args.verbose)
  File "/opt/snaptools/snaptools/snap_pre.py", line 364, in snap_pre
    if barcode not in barcode_dict: continue  
UnboundLocalError: local variable 'barcode' referenced before assignment
error: unable to read genome information
r3fang commented 5 years ago

what’s the version of snap tools?

-- Rongxin Fang Ph.D. Student, Ren Lab Ludwig Institute for Cancer Research University of California, San Diego

On Sep 8, 2019, at 2:27 PM, Austin-s-h notifications@github.com wrote:

Hi! I'm trying to generate a snapfile, but I am running into the following error. Could you provide guidance as to why this may be happening? Thanks!

My bamfile looks like this...

@HD VN:1.4 @SQ SN:chr10 LN:21119840 @SQ SN:chr11 LN:20200042 @SQ SN:chr12 LN:20387278 @SQ SN:chr13 LN:19166714 @SQ SN:chr14 LN:16219308 @SQ SN:chr15 LN:13062184 @SQ SN:chr16 LN:2844601 @SQ SN:chr17 LN:10762512 @SQ SN:chr18 LN:11373140 @SQ SN:chr19 LN:10323212 @SQ SN:chr1 LN:197608386 @SQ SN:chr20 LN:13897287 @SQ SN:chr21 LN:6844979 @SQ SN:chr22 LN:5459462 @SQ SN:chr23 LN:6149580 @SQ SN:chr24 LN:6491222 @SQ SN:chr25 LN:3980610 @SQ SN:chr26 LN:6055710 @SQ SN:chr27 LN:8080432 @SQ SN:chr28 LN:5116882 @SQ SN:chr2 LN:149682049 @SQ SN:chr30 LN:1818525 @SQ SN:chr31 LN:6153034 @SQ SN:chr32 LN:725831 @SQ SN:chr33 LN:7821666 @SQ SN:chr3 LN:110838418 @SQ SN:chr4 LN:91315245 @SQ SN:chr5 LN:59809098 @SQ SN:chr6 LN:36374701 @SQ SN:chr7 LN:36742308 @SQ SN:chr8 LN:30219446 @SQ SN:chr9 LN:24153086 @SQ SN:chrM LN:16775 @SQ SN:chrW LN:6813114 @SQ SN:chrZ LN:82529921 @PG ID:STAR PN:STAR VN:2.7.0f_0328 CL:STAR --runThreadN 20 --genomeDir /workdir/rs958/programs/STAR/galgal6 --readFilesType SAM SE --readFilesIn /workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8aa.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ab.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ac.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ad.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ae.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8af.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ag.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ah.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ai.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8aj.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ak.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8al.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8am.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8an.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ao.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ap.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8aq.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ar.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8as.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8at.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8au.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8av.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8aw.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ax.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ay.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8az.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ba.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8bb.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8bc.filtered.tagged.bam --readFilesCommand samtools view -@ 2 --outFileNamePrefix /workdir/rs958/20190907_sciSeqTest/galgal6/HH8.filtered.tagged. --outStd SAM --outSAMtype SAM --outSAMunmapped Within --outSAMmultNmax 1 --outFilterMultimapNmax 50 --sjdbGTFfile /workdir/rs958/programs/STAR/galgal6/galGal6.refGene.gtf --sjdbOverhang 49 @CO user command line: STAR --readFilesCommand samtools view -@ 2 --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outSAMunmapped Within --outSAMtype SAM --outStd SAM --genomeDir /workdir/rs958/programs/STAR/galgal6 --sjdbGTFfile /workdir/rs958/programs/STAR/galgal6/galGal6.refGene.gtf --runThreadN 20 --readFilesIn /workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8aa.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ab.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ac.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ad.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ae.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8af.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ag.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ah.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ai.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8aj.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ak.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8al.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8am.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8an.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ao.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ap.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8aq.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ar.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8as.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8at.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8au.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8av.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8aw.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ax.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ay.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8az.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8ba.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8bb.filtered.tagged.bam,/workdir/rs958/20190907_sciSeqTest/galgal6/zUMIs_output/.tmpMerge//HH8.HH8bc.filtered.tagged.bam --outFileNamePrefix /workdir/rs958/20190907_sciSeqTest/galgal6/HH8.filtered.tagged. --sjdbOverhang 49 --readFilesType SAM SE AACTTGATGCGTGCTAGTAGGAAGGACGAT-ATTTACAC:NB500947:861:H3HWFBGXC:1:11101:9731:9824 4 0 0 0 0 CCTGTACACCTGATTGCCAGAAGAGGGCATCAGATCCCTTTATAGATGGT AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE NH:i:0 HI:i:0 AS:i:18 nM:i:0 uT:A:1 BX:Z:AACTTGATGCGTGCTAGTAGGAAGGACGAT BC:Z:AACTTGATGCGTGCTAGTAGGAAGGACGAT GAGAGCTCTAGCCACACTGTACATACCGCT-AGACTAAT:NB500947:861:H3HWFBGXC:1:11101:15942:9826 16 chr7 11274343 255 50M 0 0 CTGTGGTAGCCCAGAGGTCTCCCCAGCAGATGTTCTCTCCTACTTTAGGT EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA NH:i:1 HI:i:1 AS:i:49 nM:i:0 BX:Z:GAGAGCTCTAGCCACACTGTACATACCGCT BC:Z:GAGAGCTCTAGCCACACTGTACATACCGCT ATTCATCTTGTTCTGCCGTCGCACAGTGTA-TTGAAGCG:NB500947:861:H3HWFBGXC:1:11101:14639:9832 16 chr1 55776983 255 50M 0 0 CCAATGGTGAGATGCTTGCTAGTGGTTGCAACCCTTGGCTGGGGTTCACC EEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEAEEEEEEEEE6AAAAA NH:i:1 HI:i:1 AS:i:49 nM:i:0 BX:Z:ATTCATCTTGTTCTGCCGTCGCACAGTGTA BC:Z:ATTCATCTTGTTCTGCCGTCGCACAGTGTA TTACACAACATGCGGTTTGATACCACACAA-GTCTTTAT:NB500947:861:H3HWFBGXC:1:11101:25172:9840 16 chr1 88366497 255 50M 0 0 CCTCATTTGTCAACGGGTACATGCTGACAGAATAGCCAAGCATTTTGTGG EEEEEEEEEEEEEEAEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA NH:i:1 HI:i:1 AS:i:49 nM:i:0 BX:Z:TTACACAACATGCGGTTTGATACCACACAA BC:Z:TTACACAACATGCGGTTTGATACCACACAA TATCTACGCGTGCGTGGCGACACGCTAATG-GCAGCGAA:NB500947:861:H3HWFBGXC:1:11101:8819:9841 16 chr1 20360291 255 48M2S 0 0 GCTCTGAGCTAGGATCTGCAAAGACAGCTGGGCCTGCCTTTGTCCTGAAG EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA NH:i:1 HI:i:1 AS:i:47 nM:i:0 BX:Z:TATCTACGCGTGCGTGGCGACACGCTAATG BC:Z:TATCTACGCGTGCGTGGCGACACGCTAATG AACTTGATGCCTGGTTACTTCAAGTCACCA-ACTAAAGG:NB500947:861:H3HWFBGXC:1:11101:6519:9847 16 chr11 8646791 255 50M 0 0 CTAACGTCTTCATTAGTGCCATAATACCAGCTAAGAAAACTCTCCTGGCC EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA NH:i:1 HI:i:1 AS:i:49 nM:i:0 BX:Z:AACTTGATGCCTGGTTACTTCAAGTCACCA BC:Z:AACTTGATGCCTGGTTACTTCAAGTCACCA TGGAGCAATTTCGTGACCGCAGAGCGTACG-TATATTCC:NB500947:861:H3HWFBGXC:1:11101:1364:9862 4 0 0 0 0 GTACACTTACTACAAAGAAGATTATCTGAAATACTCCCCACTGGCTCCTT AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEAEEEEEEEEE NH:i:0 HI:i:0 AS:i:19 nM:i:0 uT:A:1 BX:Z:TGGAGCAATTTCGTGACCGCAGAGCGTACG BC:Z:TGGAGCAATTTCGTGACCGCAGAGCGTACG TATCTACGCGGTCTGAAGAGTGCGGAGAGA-TCCCTTGA:NB500947:861:H3HWFBGXC:1:11101:9472:9885 0 chr10 6810885 255 50M 0 0 GGAGTGATCTGTCTGTTAGCCTGCAGGTACTTACTGGTCTCACAGCAAGA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEE NH:i:1 HI:i:1 AS:i:49 nM:i:0 BX:Z:TATCTACGCGGTCTGAAGAGTGCGGAGAGA BC:Z:TATCTACGCGGTCTGAAGAGTGCGGAGAGA And the error I'm getting

Traceback (most recent call last): File "/usr/local/bin/snaptools", line 6, in exec(compile(open(file).read(), file, 'exec')) File "/opt/snaptools/bin/snaptools", line 38, in parse_args()
File "/opt/snaptools/snaptools/parser.py", line 144, in parse_args verbose=args.verbose) File "/opt/snaptools/snaptools/snap_pre.py", line 364, in snap_pre if barcode not in barcode_dict: continue
UnboundLocalError: local variable 'barcode' referenced before assignment error: unable to read genome information — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/r3fang/SnapTools/issues/15?email_source=notifications&email_token=ABT6GG67SFP35AKB3PGTNMTQIVU37A5CNFSM4IUU46U2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HKBERTA, or mute the thread https://github.com/notifications/unsubscribe-auth/ABT6GG672WKRQKRLQN2AO7DQIVU37ANCNFSM4IUU46UQ.

Austin-s-h commented 5 years ago

I'm running version 1.4.8

JiaqiLiZju commented 3 years ago

I solved this problem by adding barcode = None at line 281 in snap_pre to init barcode variable hope it will be helpful