Entering edit mode
3.8 years ago
xxingxrong
•
0
I am trying to run MEGARes (AMR++2) test according to their instructions (https://github.com/meglab-metagenomics/amrplusplus_v2/blob/master/docs/installation.md) and getting the error below...
Error executing process > 'AlignReadsToHost (S3_test)'
Caused by:
Process `AlignReadsToHost (S3_test)` terminated with an error exit status (1)
Command executed:
bwa mem chr21.fasta.gz S3_test.1P.fastq.gz S3_test.2P.fastq.gz -t 100 > S3_test.host.sam
samtools view -bS S3_test.host.sam | samtools sort -@ 100 -o S3_test.host.sorted.bam
rm S3_test.host.sam
Command exit status:
1
Command output:
(empty)
Command error:
[M::worker2@68] performed mate-SW for 285 reads
[M::worker2@66] performed mate-SW for 284 reads
executor > local (7)
[9a/f0606a] process > RunQC (S1_test) [100%] 3 of 3 ✔
[- ] process > QCStats [ 0%] 0 of 1
[50/9e5016] process > BuildHostIndex (chr21.fasta) [100%] 1 of 1 ✔
[3d/8a725f] process > AlignReadsToHost (S2_test) [ 50%] 1 of 2, failed: 1
[- ] process > RemoveHostDNA -
[- ] process > HostRemovalStats -
[- ] process > NonHostReads -
[6b/c560e1] process > BuildAMRIndex (megares_modified_database_v2.00) [100%] 1 of 1 ✔
[- ] process > AlignToAMR -
[- ] process > RunResistome -
[- ] process > ResistomeResults -
[- ] process > SamDedupRunResistome -
[- ] process > SamDedupResistomeResults -
[- ] process > RunRarefaction -
WARN: Killing pending tasks (1)
Error executing process > 'AlignReadsToHost (S3_test)'
Caused by:
Process `AlignReadsToHost (S3_test)` terminated with an error exit status (1)
Command executed:
bwa mem chr21.fasta.gz S3_test.1P.fastq.gz S3_test.2P.fastq.gz -t 100 > S3_test.host.sam
samtools view -bS S3_test.host.sam | samtools sort -@ 100 -o S3_test.host.sorted.bam
rm S3_test.host.sam
Command exit status:
1
Command output:
(empty)
Command error:
[M::worker2@68] performed mate-SW for 285 reads
[M::worker2@66] performed mate-SW for 284 reads
[M::worker2@63] performed mate-SW for 276 reads
[M::worker2@69] performed mate-SW for 245 reads
[M::worker2@67] performed mate-SW for 217 reads
[M::worker2@70] performed mate-SW for 277 reads
[M::worker2@72] performed mate-SW for 141 reads
[M::worker2@73] performed mate-SW for 242 reads
[M::worker2@64] performed mate-SW for 294 reads
[M::worker2@78] performed mate-SW for 182 reads
[M::worker2@79] performed mate-SW for 239 reads
[M::worker2@76] performed mate-SW for 230 reads
[M::worker2@81] performed mate-SW for 198 reads
[M::worker2@75] performed mate-SW for 186 reads
[M::worker2@83] performed mate-SW for 169 reads
[M::worker2@80] performed mate-SW for 269 reads
[M::worker2@77] performed mate-SW for 390 reads
[M::worker2@82] performed mate-SW for 278 reads
[M::worker2@74] performed mate-SW for 191 reads
[M::worker2@84] performed mate-SW for 228 reads
[M::worker2@86] performed mate-SW for 190 reads
[M::worker2@71] performed mate-SW for 280 reads
[M::worker2@93] performed mate-SW for 301 reads
[M::worker2@85] performed mate-SW for 260 reads
[M::worker2@95] performed mate-SW for 211 reads
[M::worker2@90] performed mate-SW for 263 reads
[M::worker2@94] performed mate-SW for 270 reads
[M::worker2@87] performed mate-SW for 259 reads
[M::worker2@91] performed mate-SW for 229 reads
[M::worker2@99] performed mate-SW for 241 reads
[M::worker2@89] performed mate-SW for 305 reads
[M::worker2@92] performed mate-SW for 312 reads
[M::worker2@97] performed mate-SW for 256 reads
[M::worker2@96] performed mate-SW for 432 reads
[M::worker2@88] performed mate-SW for 255 reads
[M::worker2@98] performed mate-SW for 363 reads
[main] Version: 0.7.5a-r405
[main] CMD: bwa mem -t 100 chr21.fasta.gz S3_test.1P.fastq.gz S3_test.2P.fastq.gz
[main] Real time: 3.184 sec; CPU: 9.976 sec
Usage: samtools sort [options] <in.bam> <out.prefix>
Options: -n sort by read name
-f use <out.prefix> as full file name instead of prefix
-o final output to stdout
-l INT compression level, from 0 to 9 [-1]
-@ INT number of sorting and compression threads [1]
-m INT max memory per thread; suffix K/M/G recognized [768M]
[samopen] SAM header is present: 1 sequences.
Work dir:
/mnt/nfs_storage10/xiangrong/Software/amrplusplus_v2-
master/work/62/75c9c1c788924345431f517fe2bd30
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script
file named `.command.sh`
Where are the errors? How can I solve it?
Thanks in advances
