Cannot read non-existent file: when executing MarkDuplicates in a script
I am running GATK4 MarkDuplicates and when it is run directly in the command line
gatk MarkDuplicates --INPUT ./minimap2_sort.sam --METRICS_FILE ./dupMetrics.txt --CREATE_INDEX true --OUTPUT ./sorted_rmdupMINIMAP.bam
This works fine. However, if I create a script with exactly the same code I got this error
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
htsjdk.samtools.SAMException: Cannot read non-existent file: file:///mainfs/home/mdb1c20/my_onw_NGS_pipeline/scripts_my_first_NGS/comparing_tools/results/assample_results/minipap/to_variants/./minimap_sort.sam
^^^ ^
Can you see the 3 ///
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alexcouzens •
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ManuelDB
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Are you running
MarkDuplicatesin the directory that hasminimap2_sort.sam?In other words, I think this file doesn't exist,
/mainfs/home/mdb1c20/my_onw_NGS_pipeline/scripts_my_first_NGS/comparing_tools/results/assample_results/minipap/to_variants/minimap_sort.sam, butminimap_sort.samexists somewhere. To avoid this issue, you could try providing the absolute path tominimap_sort.sam(e.g.--INPUT /mainfs/home/...intermediate_path.../minimap2_sort.sam)This exist
This doesn't
With the absolute path, the 3 /// are added as well
Why is GATK adding
///?What does "when I create a script" mean? Just a file that you try to submit as
bash script.shwith the command in it?It looks like this is Java's Path class doing this -
Sorry it is not a solution to the
file:///issue since from everything reported, it looks like MarkDuplicates isn't finding a file that exists. If it's a one-off analysis I would try to just add the absolute path.