Make error for abyss-PE with many libraries

Question

[ck178807]

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.

[Ram]

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

Answer 1

[benv]

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.

[ck178807]

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?

[Ram]

Hi,

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