Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Advice ERROR ----------

I am using the workflow for best practices for variant calling. I used the sam files obtained with bowtie
So far I index and create the .dict files using this commands:

java -jar CreateSequenceDictionary.jar R= file.fasta O= file.dict (picard-tools-194)
samtools faidx file.fasta ( samtools-0.1.19)

Then I ran this commands with gatk latest version

java -jar picard.jar AddOrReplaceReadGroups I=file.sam O=file_added_sorted.bam SO=coordinate RGID=id RGLB=library RGPL=platform RGPU=machine RGSM=sample

java -jar picard.jar MarkDuplicates I=file_added_sorted.bam O=file_dedupped.bam CREATE_INDEX=true VALIDATION_STRINGENCY=SILENT M=output.metrics

So far so good, until i tried to ran the following commands:
java -jar GenomeAnalysisTK.jar -T SplitNCigarReads -R ref.fasta -I file_dedupped.bam -o file_split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS

This error appeared and the program stop running and no output was generated :
[email protected]:~/Bandamae_vs_gom/bowtie$ java -jar /user/shinojosa/GenomeAnalysisTK.jar -T SplitNCigarReads -R Dsil.fasta -I JV4a_gom.bam -o JV4a_split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS
INFO 14:30:57,696 HelpFormatter - --------------------------------------------------------------------------------
INFO 14:30:57,698 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18
INFO 14:30:57,698 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 14:30:57,698 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 14:30:57,698 HelpFormatter - [Tue Feb 07 14:30:57 CET 2017] Executing on Linux 3.16.0-4-amd64 amd64
INFO 14:30:57,698 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_111-b14
INFO 14:30:57,702 HelpFormatter - Program Args: -T SplitNCigarReads -R Dsil.fasta -I JV4a_gom.bam -o JV4a_split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS
INFO 14:30:57,705 HelpFormatter - Executing as [email protected] on Linux 3.16.0-4-amd64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_111-b14.
INFO 14:30:57,705 HelpFormatter - Date/Time: 2017/02/07 14:30:57
INFO 14:30:57,706 HelpFormatter - --------------------------------------------------------------------------------
INFO 14:30:57,706 HelpFormatter - --------------------------------------------------------------------------------
INFO 14:30:57,813 GenomeAnalysisEngine - Strictness is SILENT
comp9727, comp9728, comp9729, comp973, comp9730, comp9731, comp9732, comp9733, comp9734, comp9735, comp9736, comp9737, comp9738, comp9739, comp974, comp9740, comp9741, comp9742, comp9743, comp9744, comp9745, comp9746, comp9747, comp9748, comp9749, comp975, comp9750, comp9751, comp9752, comp9753, comp9754, comp9755, comp9756, comp9757, comp9758, comp9759, comp976, comp9760, comp9761, comp9762, comp9763, comp9764, comp9765, comp9766, comp9767, comp9768, comp9769, comp977, comp9770, comp9771, comp9772, comp9773, comp9774, comp9775, comp9776, comp9777, comp9778, comp9779, comp978, comp9780, comp9781, comp9782, comp9783, comp9784, comp9785, comp9786, comp9787, comp9788, comp9789, comp979, comp9790, comp9791, comp9792, comp9793, comp9794, comp9795, comp9796, comp9797, comp9798, comp9799, comp98, comp980, comp9800, comp9801, comp9802, comp9803, comp9804, comp9805, comp9806, comp9807, comp9808, comp9809, comp981, comp9810, comp9811, comp9812, comp9813, comp9814, comp9815, comp9816, comp9817, comp9818, comp9819, comp982, comp9820, comp9821, comp9822, comp9823, comp9824, comp9825, comp9826, comp9827, comp9828, comp9829, comp983, comp9830, comp9831, comp9832, comp9833, comp9834, comp9835, comp9836, comp9837, comp9838, comp9839, comp984, comp9840, comp9841, comp9842, comp9843, comp9844, comp9845, comp9846, comp9847, comp9848, comp9849, comp985, comp9850, comp9851, comp9852, comp9853, comp9854, comp9855, comp9856, comp9857, comp9858, comp9859, comp986, comp9860, comp9861, comp9862, comp9863, comp9864, comp9865, comp9866, comp9867, comp9868, comp9869, comp987, comp9870, comp9871, comp9872, comp9873, comp9874, comp9875, comp9876, comp9877, comp9878, comp9879, comp988, comp9880, comp9881, comp9882, comp9883, comp9884, comp9885, comp9886, comp9887, comp9888, comp9889, comp989, comp9890, comp9891, comp9892, comp9893, comp9894, comp9895, comp9896, comp9897, comp9898, comp9899, comp99, comp990, comp9900, comp9901, comp9902, comp9903, comp9904, comp9905, comp9906, comp9907, comp9908, comp9909, comp991, comp9910, comp9911, comp9912, comp9913, comp9914, comp9915, comp9916, comp9917, comp9918, comp9919, comp992, comp9920, comp9921, comp9922, comp9923, comp9924, comp9925, comp9926, comp9927, comp9928, comp9929, comp993, comp9930, comp9931, comp9932, comp9933, comp9934, comp9935, comp9936, comp9937, comp9938, comp9939, comp994, comp9940, comp9941, comp9942, comp9943, comp9944, comp9945, comp9946, comp9947, comp9948, comp9949, comp995, comp9950, comp9951, comp9952, comp9953, comp9954, comp9955, comp9956, comp9957, comp9958, comp9959, comp996, comp9960, comp9961, comp9962, comp9963, comp9964, comp9965, comp9966, comp9967, comp9968, comp9969, comp997, comp9970, comp9971, comp9972, comp9973, comp9974, comp9975, comp9976, comp9977, comp9978, comp9979, comp998, comp9980, comp9981, comp9982, comp9983, comp9984, comp9985, comp9986, comp9987, comp9988, comp9989, comp999, comp9990, comp9991, comp9992, comp9993, comp9994, comp9995, comp9996, comp9997, comp9998, comp9999]

ERROR ------------------------------------------------------------------------------------------

I have tried using the orignal bam file not the dedupped and I have the same Error

Any advice? I am doing something wrong?

Best Answer


Sign In or Register to comment.