ERROR: Adapter sequence is empty

[ch8316f5eyu]

Thanks for this great tool!

I encountered a error: "ERROR: Adapter sequence is empty
mv: cannot stat 'XXX.cutadapt.deduped.barcoded.fasta': No such file or directory"

Then the process was stuck.

May be the adaptor file wrong?

My adaptor file is:
#SampleID #5'Adapter #3'Adapter #5'Barcode #3'Barcode
Primed_ESC_IP_1 CAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA
Primed_ESC_IP_2 CAAGCAGAAGACGGCATACGAGATATTGGCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA
Primed_ESC_IgG CAAGCAGAAGACGGCATACGAGATGATCTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA
em1_TSC_IP_1 CAAGCAGAAGACGGCATACGAGATAAGCTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA

Any ideas?

Thanks.

[williamtmillsiv]

Thanks for using SCRAP! It is possible that the adapter file is wrong but is difficult to tell without seeing the format of the actual file. Do you have a 5' and 3' adapter or just one adapter? Could you paste in one row of your adapter file as a code block like this:

SRR959751 GTTCAGAGTTCTACAGTCCGACGATC TGGAATTCTCGGGTGCCAAG

Could you also provide the code you used to run SCRAP?

-Billy

[ch8316f5eyu]

Thanks for your prompt reply!
The code I run is:
bash SCRAP/bin/SCRAP.sh -d /mnt/weiyu/nfs_share2/AGO_CLIP/h/Naive_EPSC_Primed/fq/ -a /mnt/weiyu/nfs_share2/AGO_CLIP/h/Naive_EPSC_Primed/SCRAP.txt -p yes -f yes -r SCRAP -m hsa -g hg38.
The first and second row of adapter file is:
#SampleID #5'Adapter #3'Adapter #5'Barcode #3'Barcode Primed_ESC_IP_1 CAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA

I am a little confused here, because my fastq is already multiplexed.

[williamtmillsiv]

Could you email me the adapter file (wmillsi1@jhmi.edu)? I just want to make sure it formatted correctly overall