Error when passing HiCUP parameters via command line

[StevenWingett]

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.

[StevenWingett]

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: BenLangmead/bowtie2#293