I have been trying to run MetaPhlAn2 (also with HUMAnN2) on usegalaxy.be (public server). For both tools, I keep getting error that bowtie2 cannot be run.
Command line:
#!/bin/bash
# The following block can be used by the job system
# to ensure this script is runnable before actually attempting
# to run it.
if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
exit 42
fi
[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/srv/galaxy/shared/etc/dependencies/miniconda3/envs/mulled-v1-c5867e29ea0fba532ec8dc4a557d8798445dccb6ecf21f67e09143751a79b65d')" ] || {
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. '/srv/galaxy/shared/etc/dependencies/miniconda3/bin/activate' '/srv/galaxy/shared/etc/dependencies/miniconda3/envs/mulled-v1-c5867e29ea0fba532ec8dc4a557d8798445dccb6ecf21f67e09143751a79b65d' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done
} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/srv/galaxy/shared/etc/dependencies/miniconda3/envs/mulled-v1-c5867e29ea0fba532ec8dc4a557d8798445dccb6ecf21f67e09143751a79b65d')" ] || {
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. '/srv/galaxy/shared/etc/dependencies/miniconda3/bin/activate' '/srv/galaxy/shared/etc/dependencies/miniconda3/envs/mulled-v1-c5867e29ea0fba532ec8dc4a557d8798445dccb6ecf21f67e09143751a79b65d' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done
} ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/srv/galaxy/shared/etc/dependencies/miniconda3/envs/mulled-v1-c5867e29ea0fba532ec8dc4a557d8798445dccb6ecf21f67e09143751a79b65d')" ] || {
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. '/srv/galaxy/shared/etc/dependencies/miniconda3/bin/activate' '/srv/galaxy/shared/etc/dependencies/miniconda3/envs/mulled-v1-c5867e29ea0fba532ec8dc4a557d8798445dccb6ecf21f67e09143751a79b65d' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done
} ; metaphlan2.py -v > /srv/galaxy/shared/database/tmp/jobs/000/573/573002/outputs/COMMAND_VERSION 2>&1;
metaphlan2.py '/srv/galaxy/shared/database/files/000/890/dataset_890605.dat' -o '/srv/galaxy/shared/database/tmp/jobs/000/573/573002/outputs/dataset_8d6cb09d-2afd-4df3-bb0f-a0244646c6b0.dat' --input_type fasta --bowtie2_exe `which bowtie2` --bowtie2db /srv/galaxy/shared/database/reference_data/dm_data/metaphlan2/data/v20//mpa_v20_m200 --mpa_pkl /srv/galaxy/shared/database/reference_data/dm_data/metaphlan2/data/v20//mpa_v20_m200'.pkl' --no_map -t 'rel_ab_w_read_stats' --tax_lev 'a' --min_cu_len '2000' --min_alignment_len '0' --stat_q '0.1' -s '/srv/galaxy/shared/database/tmp/jobs/000/573/573002/outputs/dataset_b46a6de2-2126-432e-8998-9b803a7f328f.dat' --biom '/srv/galaxy/shared/database/tmp/jobs/000/573/573002/outputs/dataset_ebc2d918-589f-48fc-94c1-d236259a93f8.dat'
Error for MetaPhlAn2:
/srv/galaxy/shared/etc/dependencies/miniconda3/envs/mulled-v1-c5867e29ea0fba532ec8dc4a557d8798445dccb6ecf21f67e09143751a79b65d/bin/bowtie2-align-s: /srv/galaxy/shared/etc/dependencies/miniconda3/envs/mulled-v1-c5867e29ea0fba532ec8dc4a557d8798445dccb6ecf21f67e09143751a79b65d/bin/../lib/libstdc++.so.6: version `CXXABI_1.3.13' not found (required by /lib64/libtbb.so.2)
(ERR): Description of arguments failed!
Exiting now ...
Error while running bowtie2.
I thought there was a problem with my data and flow, so I produced this error by following the flow and data on this tutorial.
I would highly appreciate your help.
Hussnain