Error in write.table

[dridk]

Hi,

I m using the docker version of scramble.
I get the following error when I ran this command on my clusters file.

/bin/SCRAMble.R 
--out-name ${PWD}/test 
--cluster-file ${PWD}/MEN_CGH200860-I.sorted.clusters.txt 
--install-dir /app/cluster_analysis/bin/ 
--mei-refs /app/cluster_analysis/resources/MEI_consensus_seqs.fa 
--ref /app/validation/test.fa 
--eval-meis

Done analyzing MEIs
Writing VCF file to /data/share/genmol/sacha/projects/ALU/test.vcf...
Error in write.table(fixed, paste0(outFilePrefix, ".vcf"), row.names = F,  :
  unimplemented type 'list' in 'EncodeElement'
Execution halted

Seems the fixed dataframe contains list for the REF columns. Here is the output of print(fixed) and print(str(fixed) :

print(fixed)

   #CHROM       POS     ID  REF          ALT      QUAL FILTER
11  chr13  18212144 INS:ME NULL <INS:ME:ALU>  79.24415   PASS
10  chr13  38878403 INS:ME NULL <INS:ME:ALU>  60.81471   PASS
9   chr14  57041288 INS:ME NULL <INS:ME:ALU>  78.32513   PASS
8   chr15  40808120 INS:ME NULL <INS:ME:ALU>  73.71777   PASS
7   chr16  89224981 INS:ME NULL <INS:ME:ALU>  78.32513   PASS
3    chr2  97185492 INS:ME NULL  <INS:ME:L1>  57.59200   PASS
4    chr2 102706037 INS:ME NULL  <INS:ME:L1>  62.65276   PASS
6   chr22  23928275 INS:ME NULL <INS:ME:ALU> 103.66561   PASS
5   chr22  43928709 INS:ME NULL  <INS:ME:L1>  96.75457   PASS
2    chr4 185440770 INS:ME NULL <INS:ME:ALU>  86.15520   PASS
1    chr5  62561291 INS:ME NULL <INS:ME:ALU> 103.66561   PASS
                                                   INFO
11   MEINFO=chr13:18212144_ALU_Plus,18212144,18212145,+
10   MEINFO=chr13:38878403_ALU_Plus,38878403,38878404,+
9    MEINFO=chr14:57041288_ALU_Plus,57041288,57041289,+
8   MEINFO=chr15:40808120_ALU_Minus,40808120,40808121,-
7    MEINFO=chr16:89224981_ALU_Plus,89224981,89224982,+
3      MEINFO=chr2:97185492_L1_Plus,97185492,97185493,+
4   MEINFO=chr2:102706037_L1_Plus,102706037,102706038,+
6    MEINFO=chr22:23928275_ALU_Plus,23928275,23928276,+
5    MEINFO=chr22:43928709_L1_Minus,43928709,43928710,-
2  MEINFO=chr4:185440770_ALU_Plus,185440770,185440771,+
1     MEINFO=chr5:62561291_ALU_Plus,62561291,62561292,+

print(str(fixed))

'data.frame':   11 obs. of  8 variables:
 $ #CHROM: chr  "chr13" "chr13" "chr14" "chr15" ...
 $ POS   : int  18212144 38878403 57041288 40808120 89224981 97185492 102706037 23928275 43928709 185440770 ...
 $ ID    : chr  "INS:ME" "INS:ME" "INS:ME" "INS:ME" ...
 $ REF   :List of 11
  ..$ : NULL
  ..$ : NULL
  ..$ : NULL
  ..$ : NULL
  ..$ : NULL
  ..$ : NULL
  ..$ : NULL
  ..$ : NULL
  ..$ : NULL
  ..$ : NULL
  ..$ : NULL
 $ ALT   : chr  "<INS:ME:ALU>" "<INS:ME:ALU>" "<INS:ME:ALU>" "<INS:ME:ALU>" ...
 $ QUAL  : num  79.2 60.8 78.3 73.7 78.3 ...
 $ FILTER: chr  "PASS" "PASS" "PASS" "PASS" ...
 $ INFO  : chr  "MEINFO=chr13:18212144_ALU_Plus,18212144,18212145,+" "MEINFO=chr13:38878403_ALU_Plus,38878403,38878404,+" "MEINFO=chr14:57041288_ALU_Plus,57041288,57041289,+" "MEINFO=chr15:40808120_ALU_Minus,40808120,40808121,-" ...

First list of my cluster file

chr1:931134     right   6       gtgcccccccccccccccccccccgggccaccggttgggtggggagggg       tgggacgtgaacatctctttccgagaggcgtcctgcaggtaggagccgtgctgtgcgtgcataagagggggccgtgactcccc
chr1:939446     left    6       tgctccttgtgttggcccggtagcgcctctaccacctggg        cctccccagccacggtgaggacccaccctggcatgatctcccctcatcacctccccagccacatgtactcggccattcctgttgctga
chr1:955902     right   9       atgccccccaccccgcgtaacagcgggaatacatttgcaccaataaaaaaaacaaaatatgtagaaatccaaaaatgt  ctctgttgccatgtctctgtcctagccacaaggcctctggcttctcctgtgtgtggtcccgacccaccttccaccctacccccc
chr1:971019     right   10      ggggggggggggggggggggggggggggggggggggggggggg     gctggctttaccacctggagaagcagacggccctcctcggggggccgcggcgctgccactcggcacccccacaggtcagtgccgggg
chr1:1046488    right   10      cgccccccccccccggggccccccccaaacccccacaaccccaaccccccacccccc       ccagcactcacccgacatctgcctccgtgactgtgaccaccccagggctcctcctgagccaggcactgccggcccccccc
chr1:1046501    right   8       aggcgccccccaagaccccacccacccccacccccccaccccccacaaagcgaacgcggaccacaaaca   cccgacatctgcctccgtgactgtgaccaccccagggctcctcctgagccaggcactgccggcccccccccgcgcccaccccc
chr1:1048421    left    6       tgtggccgtttttgttagtgggtatgggttccccccgcctttggtggggggggcggccgccggggggggccatgtttg  ggggggggggctaagccaccatcaggctttgagttgggggcaggagcccggattaaggcggggtttcggccagatgcggtggc
chr1:1049076    left    5       gggggtattgtatttctggttttgggggttttttttgggcggggtgctgctcgggggggggggggggggcg ggggcgggggcagctcaggtgggcggggagggg
chr1:1050063    left    17      tgttttggggggggccccggggggggttggggccactttggccctccggggggggggggggggggctgggggggg     gggggggggggggggttgaacgtttgggcgggtacaggttccaggtagcattgcagttaggatgcggctcagtctagtctgggttttgag
chr1:1050070    left    6       cggggcggggccccgggggggggtggggcccctttcgcccccccggggggggggggggggctcgggggggggggggtt  ggggggggttgaacgtttgggcgggtacaggttccaggtagcattgcagttaggatgcggctcagtctagtctgggttttgag

[rebeccaito]

Thanks for this issue. We should return "N" instead of NULL when there is missing reference/alt information to keep the VCF formatted correctly.

I see that you're using the test.fa as input, but your data was aligned to a different reference. test.fa is not meant to be used on real data. Please use the original fasta reference that your sample was aligned to (for example, hg19.fa).