Matlock bam to juicer : java.io.IOException: No space left on device #11
Description
Hi,
I have been using Matlock from last one year. But now I am the following issue:
INFO: converting bam to juicer on /gpfs/gifs_project/platforms/pip/users/irfan/Irfan/alfalfa/BV/BV_Revio/hifiasm/working/hifi_hic_21k/hic_pro/pro_final/motif_trimming/bowtie_results/bwt2/sample/Bv_Hic_D7_D8_BV_HiC_.asm.hic.p_ctg.fa.bwt2pairs.bam
INFO: detected bam filetype
INFO: reading file "/gpfs/gifs_project/platforms/pip/users/irfan/Irfan/alfalfa/BV/BV_Revio/hifiasm/working/hifi_hic_21k/hic_pro/pro_final/motif_trimming/bowtie_results/bwt2/sample/Bv_Hic_D7_D8_BV_HiC_.asm.hic.p_ctg.fa.bwt2pairs.bam"
INFO: parsed 1000000 read pairs
INFO: parsed 2000000 read pairs
INFO: parsed 3000000 read pairs
INFO: parsed 4000000 read pairs
INFO: parsed 5000000 read pairs
INFO: parsed 6000000 read pairs
INFO: parsed 7000000 read pairs
INFO: parsed 8000000 read pairs
INFO: parsed 9000000 read pairs
INFO: parsed 10000000 read pairs
INFO: parsed 11000000 read pairs
INFO: parsed 12000000 read pairs
INFO: parsed 13000000 read pairs
INFO: parsed 14000000 read pairs
INFO: parsed 15000000 read pairs
INFO: parsed 16000000 read pairs
INFO: parsed 17000000 read pairs
INFO: parsed 18000000 read pairs
INFO: parsed 19000000 read pairs
INFO: parsed 20000000 read pairs
INFO: parsed 21000000 read pairs
INFO: parsed 22000000 read pairs
INFO: parsed 23000000 read pairs
INFO: parsed 24000000 read pairs
INFO: parsed 25000000 read pairs
INFO: parsed 26000000 read pairs
INFO: parsed 27000000 read pairs
INFO: parsed 28000000 read pairs
INFO: parsed 29000000 read pairs
INFO: parsed 30000000 read pairs
INFO: parsed 31000000 read pairs
INFO: parsed 32000000 read pairs
INFO: parsed 33000000 read pairs
INFO: parsed 34000000 read pairs
INFO: parsed 35000000 read pairs
INFO: parsed 36000000 read pairs
INFO: parsed 37000000 read pairs
INFO: parsed 38000000 read pairs
INFO: parsed 39000000 read pairs
INFO: parsed 40000000 read pairs
INFO: parsed 41000000 read pairs
INFO: parsed 42000000 read pairs
INFO: parsed 43000000 read pairs
INFO: parsed 44000000 read pairs
INFO: parsed 45000000 read pairs
INFO: parsed 46000000 read pairs
INFO: parsed 47000000 read pairs
INFO: parsed 48000000 read pairs
INFO: parsed 49000000 read pairs
INFO: parsed 50000000 read pairs
INFO: parsed 51000000 read pairs
INFO: parsed 52000000 read pairs
INFO: parsed 53000000 read pairs
INFO: parsed 54000000 read pairs
INFO: parsed 55000000 read pairs
INFO: parsed 56000000 read pairs
INFO: parsed 57000000 read pairs
INFO: parsed 58000000 read pairs
INFO: parsed 59000000 read pairs
INFO: parsed 60000000 read pairs
INFO: parsed 61000000 read pairs
INFO: parsed 62000000 read pairs
INFO: parsed 63000000 read pairs
INFO: parsed 64000000 read pairs
INFO: parsed 65000000 read pairs
INFO: parsed 66000000 read pairs
INFO: parsed 67000000 read pairs
INFO: parsed 68000000 read pairs
INFO: parsed 69000000 read pairs
INFO: parsed 70000000 read pairs
INFO: parsed 71000000 read pairs
INFO: parsed 72000000 read pairs
INFO: parsed 73000000 read pairs
INFO: parsed 74000000 read pairs
INFO: parsed 75000000 read pairs
INFO: parsed 76000000 read pairs
INFO: parsed 77000000 read pairs
INFO: parsed 78000000 read pairs
INFO: parsed 79000000 read pairs
INFO: parsed 80000000 read pairs
INFO: parsed 81000000 read pairs
INFO: parsed 82000000 read pairs
INFO: parsed 83000000 read pairs
INFO: parsed 84000000 read pairs
INFO: parsed 85000000 read pairs
INFO: parsed 86000000 read pairs
INFO: parsed 87000000 read pairs
INFO: parsed 88000000 read pairs
INFO: parsed 89000000 read pairs
INFO: parsed 90000000 read pairs
INFO: parsed 91000000 read pairs
INFO: parsed 92000000 read pairs
INFO: parsed 93000000 read pairs
INFO: parsed 94000000 read pairs
INFO: parsed 95000000 read pairs
INFO: parsed 96000000 read pairs
INFO: parsed 97000000 read pairs
INFO: parsed 98000000 read pairs
INFO: parsed 99000000 read pairs
INFO: parsed 100000000 read pairs
INFO: parsed 101000000 read pairs
INFO: parsed 102000000 read pairs
INFO: parsed 103000000 read pairs
INFO: parsed 104000000 read pairs
INFO: parsed 105000000 read pairs
INFO: parsed 106000000 read pairs
INFO: parsed 107000000 read pairs
INFO: parsed 108000000 read pairs
INFO: parsed 109000000 read pairs
INFO: parsed 110000000 read pairs
INFO: parsed 111000000 read pairs
INFO: parsed 112000000 read pairs
INFO: parsed 113000000 read pairs
INFO: parsed 114000000 read pairs
INFO: parsed 115000000 read pairs
INFO: parsed 116000000 read pairs
INFO: parsed 117000000 read pairs
INFO: parsed 118000000 read pairs
INFO: parsed 119000000 read pairs
INFO: parsed 120000000 read pairs
INFO: parsed 121000000 read pairs
INFO: parsed 122000000 read pairs
INFO: parsed 123000000 read pairs
INFO: parsed 124000000 read pairs
INFO: parsed 125000000 read pairs
INFO: parsed 126000000 read pairs
INFO: parsed 127000000 read pairs
INFO: parsed 128000000 read pairs
INFO: parsed 129000000 read pairs
INFO: parsed 130000000 read pairs
INFO: parsed 131000000 read pairs
INFO: parsed 132000000 read pairs
INFO: parsed 133000000 read pairs
INFO: parsed 134000000 read pairs
INFO: parsed 135000000 read pairs
INFO: parsed 136000000 read pairs
INFO: parsed 137000000 read pairs
INFO: parsed 138000000 read pairs
INFO: parsed 139000000 read pairs
INFO: parsed 140000000 read pairs
INFO: parsed 141000000 read pairs
INFO: parsed 142000000 read pairs
INFO: parsed 143000000 read pairs
INFO: parsed 144000000 read pairs
INFO: parsed 145000000 read pairs
INFO: parsed 146000000 read pairs
INFO: parsed 147000000 read pairs
INFO: parsed 148000000 read pairs
INFO: parsed 149000000 read pairs
INFO: parsed 150000000 read pairs
INFO: parsed 151000000 read pairs
INFO: parsed 152000000 read pairs
INFO: parsed 153000000 read pairs
INFO: parsed 154000000 read pairs
INFO: parsed 155000000 read pairs
INFO: parsed 156000000 read pairs
INFO: parsed 157000000 read pairs
INFO: parsed 158000000 read pairs
INFO: parsed 159000000 read pairs
INFO: parsed 160000000 read pairs
INFO: parsed 161000000 read pairs
INFO: parsed 162000000 read pairs
INFO: parsed 163000000 read pairs
INFO: parsed 164000000 read pairs
INFO: parsed 165000000 read pairs
:) -p flag was triggered. Running with GNU Parallel support parameter set to false.
...Remapping contact data from the original contig set to assembly
...Building track files
...Building the hic file
Not including fragment map
Start preprocess
Writing header
Writing body
.java.io.IOException: No space left on device
at java.base/java.io.FileOutputStream.writeBytes(Native Method)
at java.base/java.io.FileOutputStream.write(FileOutputStream.java:354)
at java.base/java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:81)
at java.base/java.io.BufferedOutputStream.flush(BufferedOutputStream.java:142)
at java.base/java.io.FilterOutputStream.close(FilterOutputStream.java:182)
at java.base/java.io.FilterOutputStream.close(FilterOutputStream.java:191)
at juicebox.tools.utils.original.Preprocessor$MatrixZoomDataPP.dumpBlocks(Preprocessor.java:1438)
at juicebox.tools.utils.original.Preprocessor$MatrixZoomDataPP.incrementCount(Preprocessor.java:1386)
at juicebox.tools.utils.original.Preprocessor$MatrixPP.incrementCount(Preprocessor.java:1207)
at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:442)
at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:283)
at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:108)
at juicebox.tools.HiCTools.main(HiCTools.java:86)
Suppressed: java.io.IOException: No space left on device
at java.base/java.io.FileOutputStream.writeBytes(Native Method)
at java.base/java.io.FileOutputStream.write(FileOutputStream.java:354)
at java.base/java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:81)
at java.base/java.io.BufferedOutputStream.flush(BufferedOutputStream.java:142)
at java.base/java.io.FilterOutputStream.flush(FilterOutputStream.java:153)
at java.base/java.io.FilterOutputStream.close(FilterOutputStream.java:182)
... 7 more
I have discussed with HPC department of my institute they said there is no disc space issue from there end and I should contact the software developer.
For your reference I am using the following script:
matlock bam2 juicer /hifi_hic_17k/hic_pro/pro_final/motif_trimming/bowtie_results/bwt2/sample/Bv_Hic_D7_D8_ragtag.scaffold.fa.bwt2pairs.bam out.links.txt
sort -k2,2 -k6,6 out.links.txt > out.sorted.links.txt
bash ~/bin/3d-dna/visualize/run-assembly-visualizer.sh -p false ragtag.scaffold.assembly out.sorted.links.txt
I am able to see all the required files are being produced but the job is being interrupted due to above mentioned java issue.
Any suggestions to solve this issue will be highly appreciated.
Thanks,