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Commit b7c628aa authored by Blaise Li's avatar Blaise Li
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Wrong percentage escape attempt.

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...@@ -27,7 +27,7 @@ def mapping_command(aligner): ...@@ -27,7 +27,7 @@ def mapping_command(aligner):
cmd="niceload --noswap -q hisat2 -p {snakemake.threads} --dta --seed 123 -t {snakemake.params.these_settings} --mm -x {snakemake.params.index} -U {snakemake.params.fastq} --no-unal -S /dev/null" cmd="niceload --noswap -q hisat2 -p {snakemake.threads} --dta --seed 123 -t {snakemake.params.these_settings} --mm -x {snakemake.params.index} -U {snakemake.params.fastq} --no-unal -S /dev/null"
echo ${{cmd}} 1> {snakemake.log.log} echo ${{cmd}} 1> {snakemake.log.log}
eval ${{cmd}} 1>> {snakemake.log.log} 2> {snakemake.log.err} eval ${{cmd}} 1>> {snakemake.log.log} 2> {snakemake.log.err}
rate=$(grep 'overall alignment rate' {snakemake.log.err} | tail -1 | tee -a {snakemake.log.log} | cut -d"%%" -f1) rate=$(grep 'overall alignment rate' {snakemake.log.err} | tail -1 | tee -a {snakemake.log.log} | cut -d"%" -f1)
echo -e "${{rate}}\\t{snakemake.params.these_settings}" >> {snakemake.params.rates_record} echo -e "${{rate}}\\t{snakemake.params.these_settings}" >> {snakemake.params.rates_record}
""" """
elif aligner == "bowtie2": elif aligner == "bowtie2":
...@@ -36,7 +36,7 @@ echo -e "${{rate}}\\t{snakemake.params.these_settings}" >> {snakemake.params.rat ...@@ -36,7 +36,7 @@ echo -e "${{rate}}\\t{snakemake.params.these_settings}" >> {snakemake.params.rat
cmd="niceload --noswap -q bowtie2 -p {snakemake.threads} --seed 123 -t {snakemake.params.these_settings} --mm -x {snakemake.params.index} -U {snakemake.params.fastq} --no-unal -S /dev/null" cmd="niceload --noswap -q bowtie2 -p {snakemake.threads} --seed 123 -t {snakemake.params.these_settings} --mm -x {snakemake.params.index} -U {snakemake.params.fastq} --no-unal -S /dev/null"
echo ${{cmd}} > {snakemake.log.log} echo ${{cmd}} > {snakemake.log.log}
eval ${{cmd}} 1>> {snakemake.log.log} 2> {snakemake.log.err} eval ${{cmd}} 1>> {snakemake.log.log} 2> {snakemake.log.err}
rate=$(grep 'overall alignment rate' {snakemake.log.err} | tail -1 | tee -a {snakemake.log.log} | cut -d"%%" -f1) rate=$(grep 'overall alignment rate' {snakemake.log.err} | tail -1 | tee -a {snakemake.log.log} | cut -d"%" -f1)
echo -e "${{rate}}\\t{snakemake.params.these_settings}" >> {snakemake.params.rates_record} echo -e "${{rate}}\\t{snakemake.params.these_settings}" >> {snakemake.params.rates_record}
""" """
# elif aligner == "crac": # elif aligner == "crac":
......
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