# Bash script error at paste command

I wrote script for pasting rsids on CADD output. Here is script.

#!/bin/bash
cd tmp
cut -f 1,2 CADD.tsv > fileA
paste fileA <(cut -f 2,125  CADD.tsv) > myNewFile
bedtools intersect -a  myNewFile -b New.vcf -wb |cut -f 1-4,7 > CADD.rsids.tsv

I have tested commands one by one and they work fine. But when I run script of these commands, it gives me this error.

$sh cadd.rsids.sh 4: cadd.rsids.sh: Syntax error: "(" unexpected Can anyone please tell me how to resolve this error? Here are few lines of CADD.tsv file. "##CADD GRCh38-v1.4 (c) University of Washington, Hudson-Alpha Institute for Biotechnology and Berlin Institute of Health 2013-2018. All rights reserved." #Chrom Pos Ref Alt Type Length AnnoType Consequence ConsScore ConsDetail GC CpG motifECount motifEName motifEHIPos motifEScoreChng oAA nAA GeneID FeatureID GeneName CCDS Intron Exon cDNApos relcDNApos CDSpos relCDSpos protPos relProtPos Domain Dst2Splice Dst2SplType minDistTSS minDistTSE SIFTcat SIFTval PolyPhenCat PolyPhenVal priPhCons mamPhCons verPhCons priPhyloP mamPhyloP verPhyloP bStatistic targetScan mirSVR-Score mirSVR-E mirSVR-Aln cHmm_E1 cHmm_E2 cHmm_E3 cHmm_E4 cHmm_E5 cHmm_E6 cHmm_E7 cHmm_E8 cHmm_E9 cHmm_E10 cHmm_E11 cHmm_E12 cHmm_E13 cHmm_E14 cHmm_E15 cHmm_E16 cHmm_E17 cHmm_E18 cHmm_E19 cHmm_E20 cHmm_E21 cHmm_E22 cHmm_E23 cHmm_E24 cHmm_E25 GerpRS GerpRSpval GerpN GerpS tOverlapMotifs motifDist EncodeH3K4me1-sum EncodeH3K4me1-max EncodeH3K4me2-sum EncodeH3K4me2-max EncodeH3K4me3-sum EncodeH3K4me3-max EncodeH3K9ac-sum EncodeH3K9ac-max EncodeH3K9me3-sum EncodeH3K9me3-max EncodeH3K27ac-sum EncodeH3K27ac-max EncodeH3K27me3-sum EncodeH3K27me3-max EncodeH3K36me3-sum EncodeH3K36me3-max EncodeH3K79me2-sum EncodeH3K79me2-max EncodeH4K20me1-sum EncodeH4K20me1-max EncodeH2AFZ-sum EncodeH2AFZ-max EncodeDNase-sum EncodeDNase-max EncodetotalRNA-sum EncodetotalRNA-max Grantham Dist2Mutation Freq100bp Rare100bp Sngl100bp Freq1000bp Rare1000bp Sngl1000bp Freq10000bp Rare10000bp Sngl10000bp EnsembleRegulatoryFeature dbscSNV-ada_score dbscSNV-rf_score RemapOverlapTF RemapOverlapCL RawScore PHRED 1 3362704 T A SNV 0 Transcript INTRONIC 2 intron 0.536423841 0.04 NA NA NA NA NA NA ENSG00000142611 ENST00000270722 PRDM16 CCDS41236.2 12:00:00 AM NA NA NA NA NA NA NA NA NA NA 118572 24215 NA NA NA NA 0 0 0 -0.405 -1.689 -1.593 964 NA NA NA NA 0 1 1 5 0 0 1 0 0 0 0 1 0 1 12 0 0 0 0 0 8 11 5 2 0 NA NA 2.46 -4.93 1 0.02 4.53362 1.5498 3.49082 1.00224 9.30658 3.84201 5.88121 2.95189 9.31556 5.27366 4.01294 1.08327 25.99 5.10373 4.47027 1.51567 1.55624 0.7046 4.95028 1.49632 8.57929 1.45764 1.19689 0.644106 0.01783 0.01476 NA 16 1 0 15 4 10 184 17 101 1741 NA NA NA 5 19 -0.173019 0.424 1 7785635 T C SNV 0 Intergenic DOWNSTREAM 1 downstream 0.483443709 0.053333333 NA NA NA NA NA NA ENSG00000049245 ENST00000054666 VAMP3 CCDS88.1 NA NA NA NA NA NA NA NA NA NA NA 112 2704 NA NA NA NA 0.009 0 0 0.418 -0.242 -0.522 726 NA NA NA NA 0 0 0 3 1 0 14 1 0 0 1 0 0 0 22 0 0 0 0 0 1 1 4 0 0 NA NA 5.52 -11 NA NA 20.4013 3.22673 13.621 2.38936 11.7271 2.25561 9.94895 2.15059 16.5529 2.79938 11.0724 2.29032 12.2962 2.07181 32.6588 8.63119 15.114 2.76883 7.39549 2.14311 14.1811 3.08082 0.603948 0.246907 0.55734 0.16905 NA 9 1 1 15 3 5 174 35 68 1667 NA NA NA 2 4 0.049024 1.923 1 7785635 T C SNV 0 Transcript INTRONIC 2 intron 0.483443709 0.053333333 NA NA NA NA NA NA ENSG00000049246 ENST00000613533 PER3 CCDS72695.1 12:00:00 AM NA NA NA NA NA NA NA NA NA NA 112 2704 NA NA NA NA 0.009 0 0 0.418 -0.242 -0.522 726 NA NA NA NA 0 0 0 3 1 0 14 1 0 0 1 0 0 0 22 0 0 0 0 0 1 1 4 0 0 NA NA 5.52 -11 NA NA 20.4013 3.22673 13.621 2.38936 11.7271 2.25561 9.94895 2.15059 16.5529 2.79938 11.0724 2.29032 12.2962 2.07181 32.6588 8.63119 15.114 2.76883 7.39549 2.14311 14.1811 3.08082 0.603948 0.246907 0.55734 0.16905 NA 9 1 1 15 3 5 174 35 68 1667 NA NA NA 2 4 0.049024 1.923 1 7803233 C T SNV 0 Transcript INTRONIC 2 intron 0.331125828 0.013333333 NA NA NA NA NA NA ENSG00000049246 ENST00000613533 PER3 CCDS72695.1 12:00:00 AM NA NA NA NA NA NA NA NA NA NA 182 726 NA NA NA NA 0.014 0 0 -0.553 -1.498 -0.938 673 NA NA NA NA 0 0 0 6 0 0 23 5 0 0 0 0 0 0 14 0 0 0 0 0 0 0 0 0 0 NA NA 7.49 -15 NA NA 4.36329 1.02663 4.55863 1.4118 4.72226 1.51608 6.80823 2.09997 7.44497 2.86816 5.71457 2.35876 3.06623 0.62198 18.3251 3.23263 2.1423 0.84413 8.63178 2.70111 6.29127 1.59229 0.198671 0.048037 0.0465 0.01705 NA 6 1 1 15 2 2 134 26 39 1314 NA NA NA NA NA -0.395046 0.067 1 7808665 T C SNV 0 Intergenic DOWNSTREAM 1 downstream 0.344370861 0 NA NA NA NA NA NA ENSG00000236266 ENST00000451646 Z98884.1 NA NA NA NA NA NA NA NA NA NA NA NA 5614 1683 NA NA NA NA 0.082 0 0 0.463 -0.365 -0.373 659 NA NA NA NA 0 0 0 5 3 1 24 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 0 0 0 NA NA 5.23 -10.5 NA NA 7.16527 1.57568 5.63104 1.29085 5.96112 1.41329 8.31159 2.11434 4.41828 1.14843 5.03919 1.48679 3.91787 1.13788 4.97324 1.34708 5.22225 1.10759 7.38244 1.40721 11.4505 2.73652 0.977252 0.19269 0.09436 0.03409 NA 43 1 0 10 3 2 110 30 49 1288 NA NA NA 7 26 0.11875 2.796 1 7808665 T C SNV 0 Transcript INTRONIC 2 intron 0.344370861 0 NA NA NA NA NA NA ENSG00000049246 ENST00000613533 PER3 CCDS72695.1 12:00:00 AM NA NA NA NA NA NA NA NA NA NA 5614 1683 NA NA NA NA 0.082 0 0 0.463 -0.365 -0.373 659 NA NA NA NA 0 0 0 5 3 1 24 0 0 0 0 0 0 0 15 0 0 0 0 0 0 0 0 0 0 NA NA 5.23 -10.5 NA NA 7.16527 1.57568 5.63104 1.29085 5.96112 1.41329 8.31159 2.11434 4.41828 1.14843 5.03919 1.48679 3.91787 1.13788 4.97324 1.34708 5.22225 1.10759 7.38244 1.40721 11.4505 2.73652 0.977252 0.19269 0.09436 0.03409 NA 43 1 0 10 3 2 110 30 49 1288 NA NA NA 7 26 0.11875 2.796 1 7827519 C G SNV 0 CodingTranscript NON_SYNONYMOUS 7 missense 0.529801325 0.066666667 NA NA NA NA P A ENSG00000049246 ENST00000613533 PER3 CCDS72695.1 NA 18/22 2854 0.45172523 2590 0.712909441 864 0.714049587 lcompl NA NA 177 17277 tolerated 0.05 benign 0.127 0.041 0 0 -0.553 -0.852 0.026 525 NA NA NA NA 1 0 0 3 0 2 8 9 1 1 1 0 0 1 2 6 1 2 9 0 0 0 0 1 0 NA NA 12.1 -24.2 NA NA 8.89687 3.01407 58.9843 24.0334 58.3619 18.9077 55.4967 17.2149 10.5523 3.06178 87.6613 48.8498 8.66388 2.84705 31.4762 9.05454 11.8069 3.99886 8.7429 2.26128 72.4647 18.4371 1.08886 0.638979 2.10021 1.18017 27 2 2 1 19 4 8 204 31 59 1420 Promoter NA NA 86 94 0.346155 6.007 1 7827519 C G SNV 0 Intergenic UPSTREAM 1 upstream 0.529801325 0.066666667 NA NA NA NA NA NA ENSG00000236266 ENST00000451646 Z98884.1 NA NA NA NA NA NA NA NA NA NA NA NA 177 17277 NA NA NA NA 0.041 0 0 -0.553 -0.852 0.026 525 NA NA NA NA 1 0 0 3 0 2 8 9 1 1 1 0 0 1 2 6 1 2 9 0 0 0 0 1 0 NA NA 12.1 -24.2 NA NA 8.89687 3.01407 58.9843 24.0334 58.3619 18.9077 55.4967 17.2149 10.5523 3.06178 87.6613 48.8498 8.66388 2.84705 31.4762 9.05454 11.8069 3.99886 8.7429 2.26128 72.4647 18.4371 1.08886 0.638979 2.10021 1.18017 NA 2 2 1 19 4 8 204 31 59 1420 Promoter NA NA 86 94 0.346155 6.007 1 7827519 C G SNV 0 RegulatoryFeature REGULATORY 4 regulatory 0.529801325 0.066666667 NA NA NA NA NA NA NA ENSR00000000832 NA NA NA NA NA NA NA NA NA NA NA NA NA 177 17277 NA NA NA NA 0.041 0 0 -0.553 -0.852 0.026 525 NA NA NA NA 1 0 0 3 0 2 8 9 1 1 1 0 0 1 2 6 1 2 9 0 0 0 0 1 0 NA NA 12.1 -24.2 NA NA 8.89687 3.01407 58.9843 24.0334 58.3619 18.9077 55.4967 17.2149 10.5523 3.06178 87.6613 48.8498 8.66388 2.84705 31.4762 9.05454 11.8069 3.99886 8.7429 2.26128 72.4647 18.4371 1.08886 0.638979 2.10021 1.18017 NA 2 2 1 19 4 8 204 31 59 1420 Promoter NA NA 86 94 0.346155 6.007 1 7828155 A G SNV 0 Intergenic UPSTREAM 1 upstream 0.364238411 0.066666667 NA NA NA NA NA NA ENSG00000236266 ENST00000451646 Z98884.1 NA NA NA NA NA NA NA NA NA NA NA NA 813 17022 NA NA NA NA 0.009 0 0 -0.389 -0.735 -0.731 522 NA NA NA NA 0 0 0 4 0 0 20 4 1 0 0 0 0 0 14 1 0 0 3 0 0 0 0 1 0 NA NA 4.56 4.56 1 0.12 10.0753 2.35506 38.5512 20.107 21.923 10.3608 21.217 11.8934 5.61317 1.38406 9.74608 6.16783 3.76905 1.10216 24.6436 5.18488 14.8421 7.93141 4.56698 1.13989 18.7058 4.31099 0.500167 0.211141 0.16854 0.06818 NA 20 2 0 14 4 4 159 34 57 1421 NA NA NA 11 14 0.225659 4.402 Here are lines of New.vcf #CHROM POS ID REF ALT QUAL FILTER INFO 1 3362704 rs11807862 T A 923.01 PASS "BaseCounts=31,0,0,30;BaseQRankSum=-0.108;DB;Dels=0;FS=3.561;GC=61.35;HaplotypeScore=1.7256;MQ=60;MQ0=0;MQRankSum=-0.368;QD=15.13;ReadPosRankSum=0.498;DP=282;AF=0.5;MLEAC=1;MLEAF=0.5;AN=14;AC=7" 1 7785635 rs228729 T C 2294.01 PASS "BaseCounts=0,44,0,0;DB;Dels=0;FS=0;GC=42.39;HaplotypeScore=0;MQ=60;MQ0=0;QD=28.13;BaseQRankSum=2.114;MQRankSum=-1.268;ReadPosRankSum=-0.548;DP=1430;AF=0.5;MLEAC=1;MLEAF=0.5;AN=70;AC=51" 1 7803233 rs228642 C T 2082.01 PASS "BaseCounts=0,19,0,19;BaseQRankSum=-0.963;DB;Dels=0;FS=2.884;GC=44.89;HaplotypeScore=0.9999;MQ=60;MQ0=0;MQRankSum=0.058;QD=14.92;ReadPosRankSum=0.409;DP=1468;AF=0.5;MLEAC=1;MLEAF=0.5;AN=62;AC=44" 1 7808665 rs228666 T C 1925.01 PASS "BaseCounts=0,36,0,26;BaseQRankSum=0.064;DB;Dels=0;FS=0.979;GC=30.42;HaplotypeScore=1.7333;MQ=60;MQ0=0;MQRankSum=-0.82;QD=18.03;ReadPosRankSum=-1.32;DP=939;AF=0.5;MLEAC=1;MLEAF=0.5;AN=42;AC=25" 1 7827519 rs228697 C G 786.01 PASS "BaseCounts=0,14,24,0;BaseQRankSum=0.016;DB;Dels=0;FS=4.925;GC=58.35;HaplotypeScore=0;MQ=60;MQ0=0;MQRankSum=-0.698;QD=18.63;ReadPosRankSum=0.99;DP=355;AF=0.5;MLEAC=1;MLEAF=0.5;AN=18;AC=9" 1 7828155 rs2859388 A G 2385.01 PASS "BaseCounts=0,0,56,0;DB;Dels=0;FS=0;GC=35.41;HaplotypeScore=0;MQ=60;MQ0=0;QD=24.91;BaseQRankSum=-0.231;MQRankSum=0.948;ReadPosRankSum=-0.128;DP=1136;AF=0.5;MLEAC=1;MLEAF=0.5;AN=46;AC=31" 1 7830057 rs2640909 T C 1421.01 PASS "BaseCounts=0,19,0,19;BaseQRankSum=1.051;DB;Dels=0;FS=5.041;GC=56.11;HaplotypeScore=0.734;MQ=60;MQ0=0;MQRankSum=0.496;QD=16.61;ReadPosRankSum=-0.526;DP=638;AF=0.5;MLEAC=1;MLEAF=0.5;AN=32;AC=19" 1 11107089 rs12139042 G A 1668.01 PASS "BaseCounts=43,0,0,0;DB;Dels=0;FS=0;GC=45.64;HaplotypeScore=0.734;MQ=60;MQ0=0;QD=29.7;BaseQRankSum=-1.652;MQRankSum=0.027;ReadPosRankSum=-1.192;DP=354;AF=0.5;MLEAC=1;MLEAF=0.5;AN=18;AC=10" 1 11787392 rs3737967 G A 719.01 PASS "BaseCounts=23,0,23,0;BaseQRankSum=-0.475;DB;Dels=0;FS=4.566;GC=61.85;HaplotypeScore=0.734;MQ=60;MQ0=0;MQRankSum=-0.84;QD=15.63;ReadPosRankSum=0.329;DP=378;AF=0.5;MLEAC=1;MLEAF=0.5;AN=20;AC=10" 1 11790870 rs2274976 C T 777.01 PASS "BaseCounts=0,18,0,24;BaseQRankSum=-0.042;DB;Dels=0;FS=4.677;GC=56.11;HaplotypeScore=0.6651;MQ=60;MQ0=0;MQRankSum=1.204;QD=15.05;ReadPosRankSum=0.836;DP=355;AF=0.5;MLEAC=1;MLEAF=0.5;AN=20;AC=10" 1 11792243 rs1476413 C T 1751.01 PASS "BaseCounts=1,18,0,21;BaseQRankSum=1.028;DB;Dels=0;FS=0;GC=56.11;HaplotypeScore=1.7287;MQ=60;MQ0=0;MQRankSum=-0.408;QD=16.65;ReadPosRankSum=-0.099;DP=954;AF=0.5;MLEAC=1;MLEAF=0.5;AN=50;AC=29" 1 11794400 rs4846051 G A 2616.01 PASS "BaseCounts=46,0,0,0;DB;Dels=0;FS=0;GC=59.35;HaplotypeScore=6.2573;MQ=60;MQ0=0;QD=31.75;DP=1654;AF=1;MLEAC=2;MLEAF=1;AN=78;AC=78" 1 11794419 rs1801131 T G 2028.01 PASS "BaseCounts=0,1,21,21;BaseQRankSum=-0.117;DB;Dels=0;FS=9.995;GC=59.35;HaplotypeScore=2.4328;MQ=60;MQ0=0;MQRankSum=1.03;QD=14.84;ReadPosRankSum=0.665;DP=1176;AF=0.5;MLEAC=1;MLEAF=0.5;AN=54;AC=33" • The error complains about the parenthesis "(" – benn Dec 4 '18 at 10:42 • If I remove "(" parathesis, this gives me error of 4: c.rsids.sh: cannot open cut: No such file Dec 4 '18 at 10:51 • Try to write a pipe with cut followed by paste command, see manual for paste command here. – benn Dec 4 '18 at 10:53 • I have used this command cut -f 2,125 CADD.tsv | paste fileA but it gives me only first two columns which are 1 and 2. Dec 4 '18 at 10:59 • My first guess is that the script isn't being run by bash. What operating system are you using? What exact command do you use to launch the script? Also, both of your files have headers which are not the same so should be skipped when pasteing. Dec 4 '18 at 12:12 ## 1 Answer Your problem is that you have written a script in bash but are then running it using sh. Bash, the Bourne-again shell, is not the same as the Bourne shell (sh). What is more, on Ubuntu, sh is actually not even the Bourne shell but another minimal shell called dash. The /bin/sh on Ubuntu is a symlink to dash:$ ls -l /bin/sh
lrwxrwxrwx 1 root root 4 Mar  1  2018 /bin/sh -> dash

Dash is a POSIX compliant shell which means it has the features defined by the POSIX specification for the sh shell. In your case, the problem is caused by the fact that the <() input redirection construct is supported by bash but not by dash. So, in order to run your script, you can do one of two things:

1. Make the script executable (chmod a+x cadd.rsids.sh), and then run it directly: