ABySS fungal de novo genome assembly, Fatal error: Matched on ERROR:

Hello,

I am new to fungal de novo assembly, new to ABySS, and its been many years since I’ve used Galaxy Main 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 (v0.19.5+galaxy1). That produced a total of six datasets, three pairs of forward and reverse reads which I input into ABySS (v2.2.3) 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. Could it be relate to the memory advisory? 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.