Closed:Picard tools: error with CollectInsertSizeMetrics

Question

[anais1396]

Hi everyone !!

I try to make a quality control of my ATAC-seq datas with the Picard tool CollectInserSizeMetrics. As input, I provided a BAM files which is sorted and with removed duplicates (this file is the output of the Picard tool MarkDuplicates)

I ran the following command line (as we can see here : https://broadinstitute.github.io/picard/command-line-overview.html) :

java -jar /gpfs/work/amontois/Programmes/picard/build/libs/picard.jar CollectInsertSizeMetrics I=alignSRR75_marked_duplicates.bam O=alignSRR75_insert_size_metrics.txt H=alignSRR75_insert_size_histogram.pdf M=0.5

But no file.txt and no histogram were generated...

I had the following error message :

12:06:51.065 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gpfs/work/amontois/Programmes/picard/build/libs/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Sun Feb 18 12:06:51 CET 2018] CollectInsertSizeMetrics HISTOGRAM_FILE=alignSRR75_insert_size_histogram.pdf INPUT=alignSRR75_marked_duplicates.bam OUTPUT=alignSRR75_insert_size_metrics.txt    DEVIATIONS=10.0 MINIMUM_PCT=0.05 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INCLUDE_DUPLICATES=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Sun Feb 18 12:06:51 CET 2018] Executing as amontois@nic65 on Linux 3.10.0-693.11.6.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_152-b16; Deflater: Intel; Inflater: Intel; Picard version: 2.17.6-8-ga8222cd-SNAPSHOT
WARNING 2018-02-18 12:06:51     CollectInsertSizeMetrics        All data categories were discarded because they contained < 0.05 of the total aligned paired data.
WARNING 2018-02-18 12:06:51     CollectInsertSizeMetrics        Total mapped pairs in all categories: 0.0
[Sun Feb 18 12:06:51 CET 2018] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2075918336

I don't understand what is wrong... Can someone help me to fix that ??

Thank you in advance !

Anais