Log snippet with some extra verbosity:
```
+ grep GI: nc0225.gbk
+ sed 's/.*GI://'
+ head
grep: write error: Broken pipe
+ cat GIs.txt
+ false
+ echo '---vecscreen test---'
+ /usr/bin/vecscreen -f 3 -d UniVec_Core
1042742242
1042742243
1042742244
1042742245
1042742246
1042742247
1042742248
1042742249
1042742250
1042742251
---vecscreen test---
+ '[' -s vecscreen.output ']'
++ grep '>' nc0225.fna
++ tail -1
++ sed 's/>//'
++ sed 's/ .*//'
+ last_in='gi|1349059418|emb|LT795113.2|'
++ grep '>' vecscreen.output
++ tail -1
++ sed 's/>Vector //'
++ sed 's/ .*//'
---asndisc test---
+ last_out='gi|1349059418|emb|LT795113.2|'
+ '[' 'gi|1349059418|emb|LT795113.2|==gi|1349059418|emb|LT795113.2|' ']'
+ echo '---asndisc test---'
+ /usr/bin/asndisc -i nc0225.text -a t -o nc0225.disc
+ '[' -s nc0225.disc ']'
+ echo '---asnval test---'
+ /usr/bin/asnval -i nc0225.text -a t -o nc0225.val -Q 2
---asnval test---
---asnmacro test---
+ '[' -s nc0225.val ']'
+ echo '---asnmacro test---'
+ /usr/bin/asnmacro -i nc0225.text -m autofix.prt -o asnmacro.output
+ '[' -s asnmacro.output ']'
+ echo '---asntool test---'
+ /usr/bin/asntool -m asnpub.all -v medline.prt -e medline.val
+ '[' -s medline.val ']'
+ echo '---indexpub test---'
+ /usr/bin/indexpub -i medline.val
---asntool test---
---indexpub test---
+ '[' -s medline.idx ']'
+ echo '---getpub test---'
+ /usr/bin/getpub -i medline.val -o getpub.output
+ '[' -s getpub.output ']'
+ echo '---getmesh test---'
+ /usr/bin/getmesh -i getpub.output -o getmesh.output
+ '[' -s getmesh.output ']'
+ echo '---debruijn test---'
+ /usr/bin/debruijn -a ncbistdaa -n 4
---getpub test---
---getmesh test---
---debruijn test---
autopkgtest [15:13:40]: test run-unit-test: -----------------------]
autopkgtest [15:13:40]: test run-unit-test: - - - - - - - - - - results - - -
- - - - - - -
run-unit-test FAIL non-zero exit status 160
autopkgtest [15:13:41]: - - - - - - - - - - running shell - - - - - - - - - -
You can now log into the VM through the serial terminal.
Depending on which terminal program you have installed, you can use one of
ssh -o UserKnownHostsFile=/dev/null -o StrictHostKeyChecking=no -p 10022
ubuntu@localhost
minicom -D unix#/tmp/autopkgtest-qemu.py17ka3m/ttyS0
nc -U /tmp/autopkgtest-qemu.py17ka3m/ttyS0
socat - UNIX-CONNECT:/tmp/autopkgtest-qemu.py17ka3m/ttyS0
The tested source package is in /tmp/autopkgtest.E1tTVh/build.f5C/real-
tree
Press Enter to resume running tests.
```
However, running the command manually in the vm has no issue:
```
ubuntu@autopkgtest:/tmp/autopkgtest.FcvjKG/autopkgtest_tmp$ grep 'GI:'
nc0225.gbk | head | sed 's/.*GI://'
1042742242
1042742243
1042742244
1042742245
1042742246
1042742247
1042742248
1042742249
1042742250
1042742251
ubuntu@autopkgtest:/tmp/autopkgtest.FcvjKG/autopkgtest_tmp$ grep 'GI:'
nc0225.gbk | head | sed 's/.*GI://' > GIs.txt
ubuntu@autopkgtest:/tmp/autopkgtest.FcvjKG/autopkgtest_tmp$ l
GIs.txt asnpub.all idfetch_g1234.npset nc0225.fna
nc0225_cleaned.text
Sc_16.fsa autofix.prt indexed_GIs nc0225.gbk
spidey_genome.fasta
Sc_16.sbt debruijn.output master.idx nc0225.idx
spidey_mRNA.fasta
Sc_16.tbl dsRNA_viruses.ags medline.idx nc0225.nuc
trnascan-se_sample.output
UniVec_Core.nhr dsRNA_viruses.gene_info medline.prt nc0225.prt
vecscreen.output
UniVec_Core.nin dsRNA_viruses.xgs medline.val nc0225.text
UniVec_Core.nsq getmesh.output nc0225.disc nc0225.val
asnmacro.output getpub.output nc0225.faa nc0225.xml
```
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You received this bug notification because you are a member of Ubuntu
Bugs, which is subscribed to Ubuntu.
https://bugs.launchpad.net/bugs/2121042
Title:
ncbi-tools6/amd64 vs glibc 2.42-0ubuntu1
To manage notifications about this bug go to:
https://bugs.launchpad.net/ubuntu/+source/ncbi-tools6/+bug/2121042/+subscriptions
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