Hello,

I am new to fungal de novo assembly, new to ABySS, and its been many years since I've used Galaxy but I'm starting a new chapter in my thesis and de novo assembly of fungal genomes will be at the core. I started by downloading three paired-end fastq files from NCBI SRA and ran them through fastp. That produced a total of six datasets, three pairs of forward and reverse reads which I input into ABySS as paired reads, read file 1 and read file 2. I've included the heads of two of the six output forward and reverse reads files from fastp, followed by the execution report for the unitigs file from the failed ABySS run. I cannot understand the cause of the error. Many thanks in advance!

/Rolando

---forward----

@SRR364077.1 HWUSI-EAS1767:5:1:2336:1173 length=81
AAATTAGGTTTATTCAGAAGAAATTCTTTTTCTAGAATTATAGGAAGATTTTTAAAACATCANTCTCATNNNNNNATGNNT
+SRR364077.1 HWUSI-EAS1767:5:1:2336:1173 length=81
FEC@@DDDDDHGBHHHHHGFHHHHHFFEHHHHHHHFGF@DDGE>E3DGDDBEBGGEBG7A?B#=A################
@SRR364077.2 HWUSI-EAS1767:5:1:2374:1176 length=81
TAGGTTTATCTGATTTAGAAGTCAAATATGATTTACCAGATAATTGGGTACAAGGATTTTTAACAGGTGANNGTNTATTTT
+SRR364077.2 HWUSI-EAS1767:5:1:2374:1176 length=81
GGGBFGGGGGHHDHHBG4GGG@GDEGEGEEHGHBHHHHHGHEHHGEDGEGGGGD3B,FEA@GGGG8?=BD##B=#8A;>91

----reverse---

@SRR364077.1 HWUSI-EAS1767:5:1:2336:1173 length=81
AANNAATTACNTACTCAAAATNNNNNNNGAATGAGATAATGANNNNNNNNNNNNATTAGGTACAANNNNNNNNNNGGGGNA
+SRR364077.1 HWUSI-EAS1767:5:1:2336:1173 length=81
AB##@A=;@@#BFFEDGGGG?#######8BB;=B;GD@G:?B#######################################
@SRR364077.2 HWUSI-EAS1767:5:1:2374:1176 length=81
TGNNAACCTTTATTTTTTAATNNNNNNNCTTTTTTCCAATCTNNNNNNNNNNNNTGTTTTCTAGTTNNNNNNNNATATTTA
+SRR364077.2 HWUSI-EAS1767:5:1:2374:1176 length=81
BB##<@B@BB@HIDIIID4BB#######;BDED?=D8DBGBD############=BABB<@+?FB################

---execution---

`/galaxy-repl/main/files/039/301/dataset_39301360.dat': discarded 14971 reads shorter than 41 bases
`/galaxy-repl/main/files/039/301/dataset_39301360.dat': discarded 1083 reads containing non-ACGT characters
`/galaxy-repl/main/files/039/301/dataset_39301361.dat': discarded 14282 reads shorter than 41 bases
`/galaxy-repl/main/files/039/301/dataset_39301361.dat': discarded 454 reads containing non-ACGT characters
[roundup49:21277] PMIX ERROR: NO-PERMISSIONS in file dstore_base.c at line 234
The minimum coverage of single-end contigs is 6.16667.
The minimum coverage of merged contigs is 7.0303.
Consider increasing the coverage threshold parameter, c, to 7.0303.
Building the suffix array...
Building the Burrows-Wheeler transform...
Building the character occurrence table...
Mateless          0
Unaligned     68025  0.185%
Singleton   1027198  2.79%
FR         27474503  74.8%
RF              289  0.000786%
FF             1739  0.00473%
Different   8180757  22.3%
Total      36752511
Running with max stack size of 65536 KB: SimpleGraph -s200 -n10 -d6 -j6 -k41 -o abyss-4.path1 abyss-4.dot abyss-3.dist
Reading `abyss-3.fa'...
Writing `abyss-3.fa.fai'...
Reading `abyss-4.fa'...
Writing `abyss-4.fa.fai'...
n   n:200   L50 min N75 N50 N25 E-size  max sum name
43031   3873    350 200 12876   30678   62793   45576   246232  41.98e6 abyss-4.path2
Running with max stack size of 65536 KB: PathConsensus --dot -k41 -a2 -p0.9 -o abyss-5.path -s abyss-5.fa -g abyss-5.dot - abyss-4.dot abyss-4.path3
Ambiguous paths: 1075
Merged:          149
No paths:        0
Too many paths:  569
Too complex:     33
Dissimilar:      324
The minimum coverage of single-end contigs is 6.16667.
The minimum coverage of merged contigs is 7.
Consider increasing the coverage threshold parameter, c, to 7.
Building the suffix array...
Building the Burrows-Wheeler transform...
Building the character occurrence table...
Mateless          0
Unaligned     68014  0.185%
Singleton   1026507  2.79%
FR         28867563  78.5%
RF             9292  0.0253%
FF            31313  0.0852%
Different   6749822  18.4%
Total      36752511
warning: Removed 22730 invalid edges.
n   n:1000  L50 min N75 N50 N25 E-size  max sum name
42197   2580    286 1005    15673   37631   73336   57502   454854  41.27e6 n=10 s=1000
42309   2692    282 1001    15673   37715   75588   58355   454854  41.25e6 n=10 s=2000
42437   2820    282 1001    15007   37715   76230   58467   454854  41.28e6 n=10 s=5000
42519   2902    290 1001    14457   36810   73336   56815   454854  41.42e6 n=10 s=10000

Best scaffold N50 is 37715 at n=10 s=2000.

n   n:1000  L50 min N75 N50 N25 E-size  max sum name
42309   2692    282 1001    15673   37715   75588   58355   454854  41.25e6 n=10 s=2000
Running with max stack size of 65536 KB: PathConsensus --dot -k41 -a2 -p0.9 -s abyss-7.fa -g abyss-7.dot -o abyss-7.path abyss-6.fa abyss-6.dot abyss-6.path
Ambiguous paths: 223
Merged:          14
No paths:        184
Too many paths:  19
Too complex:     0
Dissimilar:      6
The minimum coverage of single-end contigs is 6.16667.
The minimum coverage of merged contigs is 16.6419.
Consider increasing the coverage threshold parameter, c, to 16.6419.