lucapinello / CRISPResso

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
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Alignment error, please check your input #55

Closed StevenVB12 closed 5 years ago

StevenVB12 commented 5 years ago

Dear Luca,

I am encountering the below error when running the command:

CRISPResso \ -r1 /work/rpapa/sbelleghem/mutant_miSeq/fastq_trimmed/TL12_R1_paired.fastq.gz \ -r2 /work/rpapa/sbelleghem/mutant_miSeq/fastq_trimmed/TL12_R2_paired.fastq.gz \ --amplicon_seq ATTGGATCTTAAAAGCTTGGGCTAAGCTCATGTCGACGGTCAGTAATTAGCATTCCGCATATAGTTTACAAAGCATTGCCGTTGTAAATTATTGGAAACTATAATCTTGTGCAAAAACTTGTTTTTTTATAAATATTATAAAATATATTCGTACAGGATTGAAATATAAAAAAAACATATCAGCTGCGAATAAAATTAATAGAGAATAAAAAAATATACTTATATCACAGCGACATATTTATTTTATTCTCTATTTTATTCACATTATATTTTTACTCCATGCCAAATTGATAATAGAATATGAACCTGTAACAACAGTCCTTAAAAATCCAAAACGATTATTAAGTGGTTTAATATTTTTACATAACAACATCAAATAATTTAAATTATATCTATTTCTAGGTAATACAGACAGGTGCTCAACAGGCGGTTGAAGAGTGTCAATACCAATTCCGAAACAGCCGCTGGAACTGCAGCACTGTCGAAAACAGCACTGATATATTTGGAGGAGTACTTAAATTTAGTAAGTAAAAGTTAAATTTTTGATTTAAATTTGTAAATCCTTTTTAATTGACAACCTAAATACTTATTTTTATTTGGATATATTATATAAAAATGTTGGATGAGTTTGGATTCCACTTACTACTTGGCTTCTTGAGCACTAACTTTAAAAATATATAAATTCTATTTGGAAAACGAAAGAAATAAGATTTCAAATGATCTATAACTAACAATTTTTATTATGATAAACCACAAACAACTATACAAAACGATTTACACGTAAAATTAACATATTCTCAACATATTACACAAATAATACTACCGTTAACTCAAAATTGGCATATACATATAAATAAATCTTGAATCATAAAATTCATTTCCGCTCGGATTTCAAGTCAAAGTAAGTTGTAAATTCTCAAATAATTATCGGTTGCATACATCGGCAACTCTTCAAAGGACGTGTTAAGTG \ --max_paired_end_reads_overlap 150 \ --name TL12 \ --output_folder /work/rpapa/sbelleghem/mutant_miSeq/CRISPResso_out

############### INFO @ Wed, 05 Jun 2019 13:10:08: Finished reads; N_TOT_READS: 29195 N_COMPUTED_ALN: 0 N_CACHED_ALN: 0 N_COMPUTED_NOTALN: 6874 N_CACHED_NOTALN: 22321

INFO @ Wed, 05 Jun 2019 13:10:08: Done!

INFO @ Wed, 05 Jun 2019 13:10:08: Quantifying indels/substitutions...

INFO @ Wed, 05 Jun 2019 13:10:08: Done!

CRITICAL @ Wed, 05 Jun 2019 13:10:08: Alignment error, please check your input.

ERROR: Error: No alignments were found #############

Would you have any advice on what to check to know what is going wrong? The amplicon should be fine as I can easily find alignable sequences in my fastq files.

Thank you for any help!

Steven