[Debian-med-packaging] Bug#865130: reapr FTBFS on big endian: Error sampling from files '00.Sample/fragCov.gz', '00.assembly.fa.gc.gz'

[Adrian Bunk]

Source: reapr
Version: 1.0.18+dfsg-3
Severity: important

https://buildd.debian.org/status/package.php?p=reapr&suite=sid

...
[REAPR smaltmap] Running: samtools sort out.bam.tmp.6275.smaltmap.raw.bam -O bam -o out.bam.tmp.6275.smaltmap.raw.bam.sort.bam
[REAPR smaltmap] Running: samtools rmdup out.bam.tmp.6275.smaltmap.raw.bam.sort.bam out.bam.tmp.6275.smaltmap.rmdup.bam
[bam_rmdup_core] processing reference foo...
[bam_rmdup_core] 1 / 10000 = 0.0001 in library '	'
[REAPR smaltmap] Running: echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > out.bam.tmp.6275.smaltmap.header
[REAPR smaltmap] Running: samtools view -H out.bam.tmp.6275.smaltmap.rmdup.bam >> out.bam.tmp.6275.smaltmap.header
[REAPR smaltmap] Running: samtools reheader out.bam.tmp.6275.smaltmap.header out.bam.tmp.6275.smaltmap.rmdup.bam > out.bam
[REAPR smaltmap] Running: samtools index out.bam
[REAPR smaltmap] Running: rm out.bam.tmp.6275.smaltmap.*
Running reapr version 1.0.18 pipeline:
reapr foo1.fasta out.bam result
[REAPR pipeline] Running facheck
[REAPR pipeline] Running preprocess
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
Aborted
[REAPR preprocess] sampling region foo:1169-3476.  Already sampled 0 bases
[REAPR preprocess] No coverage in foo:1169-3476. Skipping
[REAPR preprocess] sampling region foo:3492-5726.  Already sampled 0 bases
[REAPR preprocess] No coverage in foo:3492-5726. Skipping
[REAPR preprocess] sampling region foo:5756-12551.  Already sampled 0 bases
[REAPR preprocess] No coverage in foo:5756-12551. Skipping
[REAPR preprocess] sampling region foo:12591-998105.  Already sampled 0 bases
[REAPR preprocess] No coverage in foo:12591-998105. Skipping
[REAPR preprocess] Error sampling from files '00.Sample/fragCov.gz', '00.assembly.fa.gc.gz'
Most likely causes are:
1. A character in the assembly sequence names that
   broke tabix, such as :,| or -. You can check for this by running
   reapr facheck
2. A mismatch of names in the input BAM and assembly fasta files.
   A common cause is trailing whitespace in the fasta file, or
   everything after the first whitesace character in a name being
   removed by the mapper, so the name is different in the BAM file.
3. There is not enough fragment coverage because the assembly is
   too fragmented. You may want to compare your mean contig length with
   the insert size of the reads. Also have a look at this plot of the
   insert size distribution:
   00.Sample/insert.in.pdf
debian/rules:33: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 1