StevenWingett
commented
4 years ago The same problem also occurs when using a HiCUP config file. However, the problem seems to be with Bowtie2 (v2.4.1) and not HiCUP.
The problem occurs after passing the --no-unal parameter to Bowtie2. I have reported this problem on the Bowtie2 GitHub page: https://github.com/BenLangmead/bowtie2/issues/293
Ran HiCUP without a configuration file and got the following errors:
[wingetts@headstone hicup_patches]$ hicup --zip --digest /bi/scratch/Genomes/Human/GRCh38/Digest_Homo_sapiens_GRCh38_HindIII_None_14-43-31_10-02-2016.txt.gz --index /bi/scratch/Genomes/Human/GRCh38/Homo_sapiens.GRCh38 --longest 700 --shortest 50 --bowtie2 /bi/apps/bowtie2/2.4.1/bowtie2 test_dataset/*.fastq Starting HiCUP pipeline (v0.7.3) FASTQ quality format not specified, analysing file 'test_dataset/test_dataset1.fastq' to predict file format used FASTQ quality set to 'Sanger' Detecting R automatically Found R at '/bi/apps/R/3.6.1/bin/R' Reading genome digest file '/bi/scratch/Genomes/Human/GRCh38/Digest_Homo_sapiens_GRCh38_HindIII_None_14-43-31_10-02-2016.txt.gz' to determine Hi-C restriction enzyme Truncating with HiCUP Truncater v0.7.3 Truncating sequences at occurrence of sequences '[AAGCTAGCTT]' Truncating sequences Truncating test_dataset/test_dataset1.fastq Truncating test_dataset/test_dataset2.fastq Truncating complete Mapping with HiCUP Mapper v0.7.3 Using aligner 'bowtie2' Mapping test_dataset1.trunc.fastq.gz test_dataset1.trunc.fastq.gz Aligner error: Use of uninitialized value $bt2_args[7] in join or string at /bi/apps/bowtie2/2.4.1/bowtie2 line 423. Use of uninitialized value $bt2_args[8] in join or string at /bi/apps/bowtie2/2.4.1/bowtie2 line 423. Use of uninitialized value in exists at /bi/apps/bowtie2/2.4.1/bowtie2 line 81. Use of uninitialized value in exists at /bi/apps/bowtie2/2.4.1/bowtie2 line 81. Use of uninitialized value $bt2_args[7] in join or string at /bi/apps/bowtie2/2.4.1/bowtie2 line 459. Use of uninitialized value $bt2_args[8] in join or string at /bi/apps/bowtie2/2.4.1/bowtie2 line 459. Mapping test_dataset2.trunc.fastq.gz test_dataset2.trunc.fastq.gz Aligner error: Use of uninitialized value $bt2_args[7] in join or string at /bi/apps/bowtie2/2.4.1/bowtie2 line 423. Use of uninitialized value $bt2_args[8] in join or string at /bi/apps/bowtie2/2.4.1/bowtie2 line 423. Use of uninitialized value in exists at /bi/apps/bowtie2/2.4.1/bowtie2 line 81. Use of uninitialized value in exists at /bi/apps/bowtie2/2.4.1/bowtie2 line 81. Use of uninitialized value $bt2_args[7] in join or string at /bi/apps/bowtie2/2.4.1/bowtie2 line 459. Use of uninitialized value $bt2_args[8] in join or string at /bi/apps/bowtie2/2.4.1/bowtie2 line 459. Mapping complete Pairing files with HiCUP Mapper v0.7.3 Pairing test_dataset1.map.sam and test_dataset2.map.sam Pairing complete Filtering with HiCUP Filter v0.7.3 Processing digest file /bi/scratch/Genomes/Human/GRCh38/Digest_Homo_sapiens_GRCh38_HindIII_None_14-43-31_10-02-2016.txt.gz Sonication protocol followed - Restriction_Enzyme1:HindIII [A^AGCTT] Filtering test_dataset1_2.pair.bam Filtering complete Removing duplicates with HiCUP Deduplicator v0.7.3 De-duplicating test_dataset1_2.filt.bam De-duplication complete Creating HTML and text file HiCUP summary reports HiCUP processing complete.