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.