###############
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.
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