Failed to create symbolic link. Trinity
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19 months ago
mailard • 0

This error appears if my output file is at /mnt/...(drive). But if an output file is in home directory - trinity runs well And some strange situation, when I wrote *sudo" the program cannot find salmon, but without this one, it runs well. When i run trinity i have the next error:

failed to create symbolic link 'left.norm.fq': Operation not supported Error, cmd: ln -sf /mnt/lapd/Vika_data/Denovo/trinity3/insilico_read_normalization/L3_R1_pair.fastq.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq died with ret 256 at /home/katya/Soft/trinityrnaseq-v2.11.0/util/insilico_read_normalization.pl line 793. Error, cmd: /home/katya/Soft/trinityrnaseq-v2.11.0/util/insilico_read_normalization.pl --seqType fq --JM 200G  --max_cov 200 --min_cov 1 --CPU 50 --output /mnt/lapd/Vika_data/Denovo/trinity3/insilico_read_normalization --max_CV 10000  --left /mnt/lapd/Vika_data/Denovo/trim2/L3_R1_pair.fastq --right /mnt/lapd/Vika_data/Denovo/trim2/L3_R2_pair.fastq --pairs_together  --PARALLEL_STATS   died with ret 512 at /home/katya/Soft/trinityrnaseq-v2.11.0/Trinity line 2826. main::process_cmd("/home/katya/Soft/trinityrnaseq-v2.11.0/util/insilico_read_nor"...) called at /home/katya/Soft/trinityrnaseq-v2.11.0/Trinity line 3379
main::normalize("/mnt/lapd/Vika_data/Denovo/trinity3/insilico_read_normalization", 200, ARRAY(0x558a27931ee0), ARRAY(0x558a27931ec8)) called at /home/katya/Soft/trinityrnaseq-v2.11.0/Trinity line 3319
main::run_normalization(200, ARRAY(0x558a27931ee0), ARRAY(0x558a27931ec8)) called at /home/katya/Soft/trinityrnaseq-v2.11.0/Trinity line 1372
trinity RNA-Seq Assembly • 2.4k views
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I guess the account you are running this from does not have write permissions to the mounted directory (/mnt/lapd/Vika_data/Denovo/trinity3/insilico_read_normalization/).

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But when i use other programs, i don't have the same error

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Is the drive filesystem NTFS or exFAT?

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I am not sure, but read in google, I think its NTFS

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Hello,

I have the exact same issue when trinity-2.4.0 runs from vdjpuzzle- version 3.

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ln: failed to create symbolic link 'left.norm.fq': Operation not supported
Error, cmd: ln -sf /ad/tasakis/D150-Projects/vlachou/Panosome/VDJ_p1_Cell1/trinity_out_dir/insilico_read_normalization/out1a.fastq.normalized_K25_C50_pctSD10000.fq left.norm.fq died with ret 256 at /home/tasakis/anaconda2/envs/vdjpuzzle/opt/trinity-2.4.0/util/insilico_read_normalization.pl line 758.
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Have you found out what was they issue?

Thank you in advance, Evi

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Sorry, but I cannot help you with anything, as I have not found this answer. We just asked to add more memory to our server because the error lies in using a network drive.

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10 months ago

Trinity does not work with NTFS, FAT32 partitions.

The reason for the error you are seeing is very likely that the Windows filesystem (NTFS or FAT32) on the mounted partition (/mnt/lapd/) does not support symbolic links. The solution is simple: When running Trinity under Linux, do not attempt to run Trinity on the mounted external hard drive, USB stick, etc. on which you received the data directly. Instead make a copy (including backup, should do that anyway) of the data to a directory within a "proper" POSIX-compliant file-system, e.g. easiest to your home directory or group network volume or a scratch disk attached to your server or workstation that has a Ext4, ZFS, XFS, etc. file-system. If you do not have enough space, you need to purchase a hard drive that you will create a partition on and format as Ext4 using Linux tools and copy the data to it.

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