Failed to create symbolic link. Trinity

Question

[mailard]

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

[GenoMax]

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/).

[mailard]

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

[h.mon]

Is the drive filesystem NTFS or exFAT?

[mailard]

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

[p.vlachou-efstathiou]

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

[mailard]

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.

Answer 1

[Michael]

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.