Question: Make error for abyss-PE with many libraries
gravatar for ck178807
21 months ago by
ck1788070 wrote:

I'm assembling using abyss-pe installed via apt-get on an ubuntu build (16) and I'm getting a make error. The command run is:

abyss-pe -n v=-v -C tset np=4 k=96 name=test lib='1A18s_S1_L001 2A18s_S2_L001 \
                         2B18s_S10_L001 3A18s_S3_L001 3B18s_S11_L001 4A18s_S4_L001 \
                         4B18s_S12_L001 5A18s_S5_L001 5B18s_S9_L001 6A18s_S6_L001 \
                         7A18s_S7_L001 8A18s_S8_L001' \
                         1A18s_S1_L001='1A18s_S1_L001_R1_001.fastq 1A18s_S1_L001_R2_001.fastq' \
                         2A18s_S2_L001='2A18s_S2_L001_R1_001.fastq 2A18s_S2_L001_R2_001.fastq' \
                         2B18s_S10_L001='2B18s_S10_L001_R1_001.fastq 2B18s_S10_L001_R2_001.fastq' \
                         3A18s_S3_L001='3A18s_S3_L001_R1_001.fastq 3A18s_S3_L001_R2_001.fastq' \
                         3B18s_S11_L001='3B18s_S11_L001_R1_001.fastq 3B18s_S11_L001_R2_001.fastq' \
                         4A18s_S4_L001='4A18s_S4_L001_R1_001.fastq 4A18s_S4_L001_R2_001.fastq' \
                         4B18s_S12_L001='4B18s_S12_L001_R1_001.fastq 4B18s_S12_L001_R2_001.fastq' \
                         5A18s_S5_L001='5A18s_S5_L001_R1_001.fastq 5A18s_S5_L001_R2_001.fastq' \
                         5B18s_S9_L001='5B18s_S9_L001_R1_001.fastq 5B18s_S9_L001_R2_001.fastq' \
                         6A18s_S6_L001='6A18s_S6_L001_R1_001.fastq 6A18s_S6_L001_R2_001.fastq' \
                         7A18s_S7_L001='7A18s_S7_L001_R1_001.fastq 7A18s_S7_L001_R2_001.fastq' \
                         8A18s_S8_L001='8A18s_S8_L001_R1_001.fastq 8A18s_S8_L001_R2_001.fastq'

I'm getting an error when a make is called on the second library in the list

make: * No rule to make target '2A18s_S2_L001'. Stop.

I've tested to see if there is an error caused by each library starting with a number but that didn't fix anything. Any help would be appreciated.

abyss assembly • 444 views
ADD COMMENTlink modified 21 months ago by benv710 • written 21 months ago by ck1788070

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

ADD REPLYlink written 21 months ago by RamRS27k
gravatar for benv
21 months ago by
benv710 wrote:

Hi @ck178807,

Your abyss-pe command looks good in principle. Your problem has something to do with the newlines and line continuations ("\" characters) in your command. I sometimes struggle with this myself. Please try collapsing your command line into a single line, confirm that it fixes the error, and then work from there.

ADD COMMENTlink modified 21 months ago • written 21 months ago by benv710

So, when I paste the exact command, it works. The newlines/line continuations were added by the formatting I presume. The command was generated by a script I wrote to identify all pairs in a directory and generate the assembly command. For now, I've created a workaround, but I can't find any hidden characters that would cause any errors especially given that a copy and paste of the command works... Could this be caused by any issue associated with the fact that it is inside a bash script?

ADD REPLYlink written 21 months ago by ck1788070


I added the line continuations for the command to look better, OP's original command was all in a single line.

ADD REPLYlink written 21 months ago by RamRS27k
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