Hello!

I am experiencing an error with Flo that I was hoping you might be able to help me with. Rake aborts when blat begins, I believe. I searched for this issue and found it has happened for a few others, and noticed that one piece of advice was to update parallel. I did that through a conda environment and am now using GNU parallel 20201122, which I realize is still GNU parallel. Nonetheless, I am getting the following error:

mkdir run
cp /path/genomic.fa run/source.fa
cp /path/target.fa
faToTwoBit run/source.fa run/source.2bit
faToTwoBit run/target.fa run/target.2bit
twoBitInfo run/source.2bit stdout | sort -k2nr > run/source.sizes
twoBitInfo run/target.2bit stdout | sort -k2nr > run/target.sizes
faSplit sequence run/target.fa 20 run/chunk_
parallel --joblog run/joblog.faSplit -j 20 -a run/joblst.faSplit
29164 pieces of 29164 written
26770 pieces of 26770 written
23287 pieces of 23287 written
25387 pieces of 25387 written
25525 pieces of 25525 written
25448 pieces of 25448 written
25555 pieces of 25555 written
26474 pieces of 26474 written
25992 pieces of 25992 written
27046 pieces of 27046 written
26153 pieces of 26153 written
26728 pieces of 26728 written
26526 pieces of 26526 written
27621 pieces of 27621 written
26588 pieces of 26588 written
26266 pieces of 26266 written
26387 pieces of 26387 written
25897 pieces of 25897 written
27300 pieces of 27300 written
25692 pieces of 25692 written
parallel --joblog run/joblog.blat -j 20 -a run/joblst.blat
Loaded 2510587379 letters in 14543 sequences
Searched 116386128 bases in 23287 sequences
Loaded 2510587379 letters in 14543 sequences
Searched 127615767 bases in 25555 sequences
Loaded 2510587379 letters in 14543 sequences
Searched 127103007 bases in 25448 sequences
Loaded 2510587379 letters in 14543 sequences
Searched 132315417 bases in 26474 sequences
Loaded 2510587379 letters in 14543 sequences
Searched 132646279 bases in 26588 sequences
Loaded 2510587379 letters in 14543 sequences
Searched 129744868 bases in 25992 sequences
Loaded 2510587379 letters in 14543 sequences
Searched 134829202 bases in 27046 sequences
Loaded 2510587379 letters in 14543 sequences
Searched 130548735 bases in 26153 sequences
Loaded 2510587379 letters in 14543 sequences
Searched 126148018 bases in 25387 sequences
Loaded 2510587379 letters in 14543 sequences
Searched 133429151 bases in 26728 sequences
Loaded 2510587379 letters in 14543 sequences
Searched 145757029 bases in 29164 sequences
Loaded 2510587379 letters in 14543 sequences
Searched 137556497 bases in 27621 sequences
Loaded 2510587379 letters in 14543 sequences
Searched 131717084 bases in 26387 sequences
Loaded 2510587379 letters in 14543 sequences
Searched 130661225 bases in 26266 sequences
Loaded 2510587379 letters in 14543 sequences
Searched 128121430 bases in 25692 sequences
Loaded 2510587379 letters in 14543 sequences
Searched 126631904 bases in 25525 sequences
Loaded 2510587379 letters in 14543 sequences
Searched 132127474 bases in 26770 sequences
rake aborted!
Command failed with status (3): [parallel --joblog run/joblog.blat -j 20 -a...]
/home/user/bin/flo/Rakefile:161:in parallel' /home/user/bin/flo/Rakefile:107:in block in <top (required)>'
/home/user/bin/flo/Rakefile:37:in `block in <top (required)>'
Tasks: TOP => run/liftover.chn
(See full trace by running task with --trace)

My job log looks like this:
9 : 1606275293.957 28015.902 0 89 0 0 blat -noHead -fastMap -tileSize=12 -minIdentity=95 run/source.fa run/chunk_11.fa rujoblog.blat
Seq Host Starttime JobRuntime Send Receive Exitval Signal Command
18 : 1606275293.989 45.953 0 0 0 9 blat -noHead -fastMap -tileSize=12 -minIdentity=95 run/source.fa run/chunk_06.fa run/chunk_06.fa.psl
17 : 1606275293.975 46.491 0 0 0 9 blat -noHead -fastMap -tileSize=12 -minIdentity=95 run/source.fa run/chunk_10.fa run/chunk_10.fa.psl
16 : 1606275293.972 872.307 0 0 0 9 blat -noHead -fastMap -tileSize=12 -minIdentity=95 run/source.fa run/chunk_13.fa run/chunk_13.fa.psl
5 : 1606275293.949 19148.322 0 89 0 0 blat -noHead -fastMap -tileSize=12 -minIdentity=95 run/source.fa run/chunk_19.fa run/chunk_19.fa.psl
12 : 1606275293.963 20725.125 0 89 0 0 blat -noHead -fastMap -tileSize=12 -minIdentity=95 run/source.fa run/chunk_14.fa run/chunk_14.fa.psl
7 : 1606275293.953 22003.258 0 89 0 0 blat -noHead -fastMap -tileSize=12 -minIdentity=95 run/source.fa run/chunk_15.fa run/chunk_15.fa.psl
2 : 1606275293.943 23220.606 0 89 0 0 blat -noHead -fastMap -tileSize=12 -minIdentity=95 run/source.fa run/chunk_18.fa run/chunk_18.fa.psl
11 : 1606275293.961 23502.038 0 89 0 0 blat -noHead -fastMap -tileSize=12 -minIdentity=95 run/source.fa run/chunk_04.fa run/chunk_04.fa.psl
8 : 1606275293.955 23821.197 0 89 0 0 blat -noHead -fastMap -tileSize=12 -minIdentity=95 run/source.fa run/chunk_16.fa run/chunk_16.fa.psl
3 : 1606275293.945 24157.292 0 89 0 0 blat -noHead -fastMap -tileSize=12 -minIdentity=95 run/source.fa run/chunk_05.fa run/chunk_05.fa.psl
13 : 1606275293.966 24351.732 0 89 0 0 blat -noHead -fastMap -tileSize=12 -minIdentity=95 run/source.fa run/chunk_01.fa run/chunk_01.fa.psl
1 : 1606275293.941 24630.828 0 89 0 0 blat -noHead -fastMap -tileSize=12 -minIdentity=95 run/source.fa run/chunk_07.fa run/chunk_07.fa.psl
14 : 1606275293.968 24792.986 0 89 0 0 blat -noHead -fastMap -tileSize=12 -minIdentity=95 run/source.fa run/chunk_02.fa run/chunk_02.fa.psl
4 : 1606275293.947 25343.822 0 89 0 0 blat -noHead -fastMap -tileSize=12 -minIdentity=95 run/source.fa run/chunk_17.fa run/chunk_17.fa.psl
6 : 1606275293.951 25997.266 0 89 0 0 blat -noHead -fastMap -tileSize=12 -minIdentity=95 run/source.fa run/chunk_08.fa run/chunk_08.fa.psl
19 : 1606275293.993 26497.434 0 89 0 0 blat -noHead -fastMap -tileSize=12 -minIdentity=95 run/source.fa run/chunk_00.fa run/chunk_00.fa.psl
15 : 1606275293.970 26656.599 0 89 0 0 blat -noHead -fastMap -tileSize=12 -minIdentity=95 run/source.fa run/chunk_09.fa run/chunk_09.fa.psl
20 : 1606275294.002 27909.093 0 89 0 0 blat -noHead -fastMap -tileSize=12 -minIdentity=95 run/source.fa run/chunk_03.fa run/chunk_03.fa.psl
9 : 1606275293.957 28015.902 0 89 0 0 blat -noHead -fastMap -tileSize=12 -minIdentity=95 run/source.fa run/chunk_11.fa run/chunk_11.fa.psl
10 : 1606275293.959 28659.995 0 89 0 0 blat -noHead -fastMap -tileSize=12 -minIdentity=95 run/source.fa run/chunk_12.fa run/chunk_12.fa.psl

Do you have any thoughts as to what might be going on?

Thanks so much,
Zoe