Exception in thread "main" htsjdk.samtools.util.SequenceUtil$SequenceListsDifferException: Sequence dictionaries are not the same size (84, 195)

1

Hi everyone,

I've just started studying bioinformatics and I am struggling a hard nut to crack. I have no idea to deal with it.

I downloaded their data from an article that included ATAC-seq datas. There are hundreds of BAM files for different sample ages. These files have removed mitochondria and duplicated sequences.

First I merged a sets of BAM files.

samtools merge scATAC_joint_noDup_noMT_MERGE.bam -b bamlist.txt
samtools index scATAC_joint_noDup_noMT_MERGE.bam

Then I collect metrics (Code and explanation from the author)

java -Xmx8g -jar picard.jar CollectMultipleMetrics I=scATAC_joint_noDup_noMT_MERGE.bam O=scATAC_joint_noDup_noMT_MERGE_metrics R=/directory_to/Genomes/panTro4/whole_genome.fa

I got

Error: Unable to access jarfile picard.jar

I found the solution on the Internet. Need to give picard.jar absolute path. And the reference genome needs to be changed to my path.
So I changed it to the following code.

java -Xmx8g -jar /home/CaiCB/miniconda3/envs/atac/share/picard-2.25.7-0/picard.jar CollectMultipleMetrics I=scATAC_joint_noDup_noMT_MERGE.bam O=scATAC_joint_noDup_noMT_MERGE_metrics R=/Data/CaiCB/Genomes/human_hg38/hg38.fa 

Then I got new error

[Tue Aug 03 08:11:02 EDT 2021] Executing as [email protected] on Linux 3. 10.0-1127.10.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_121-b15; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.25.7

Exception in thread "main" htsjdk.samtools.util.SequenceUtil$SequenceListsDifferException: Sequence dictionaries are not the same size (84, 195)
at htsjdk.samtools.util.SequenceUtil.assertSequenceListsEqual(SequenceUtil. java:259)
at htsjdk.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(Sequen ceUtil.java:342)
at htsjdk.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(Sequen ceUtil.java:328)
at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java: 117)
at picard.analysis.CollectMultipleMetrics.doWork(CollectMultipleMetrics.jav a:739)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:3 08)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103 )
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)

Just pick some of them.

Can someone help me with my problem? be deeply grateful.


ATAC-seq


PICARD

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