Mapsplice2

Question

[nkmalini97]

No fusions generated.

python2 Mapsplice2/mapsplice.py mapsplice_fasta_files/ -x index_files/index -1 read_1_trim.fastq -2 read_2_trim.fastq -o mapsplice_out 2>log.txt

The log file is given below:

[Mon Jul 19 18:30:27 2021] Beginning Mapsplice run (MapSplice v2.2.1)
[Mon Jul 19 18:30:27 2021] Bin directory: MapSplice2/bin/
[Mon Jul 19 18:30:27 2021] Preparing output location masplice_out/
[Mon Jul 19 18:30:27 2021] Checking files or directory: read_1_trim.fastq
[Mon Jul 19 18:30:27 2021] Checking files or directory: read_2_trim.fastq
[Mon Jul 19 18:30:27 2021] Checking files or directory: /mapsplice_fasta_files//
[Mon Jul 19 18:30:27 2021] Checking Bowtie index files
[Mon Jul 19 18:30:27 2021] Inspecting Bowtie index files
[Mon Jul 19 18:30:27 2021] Checking reference sequence length
[Mon Jul 19 18:30:27 2021] Checking consistency of Bowtie index and reference sequence
[Mon Jul 19 18:30:27 2021] Checking read format
-----[Read Format: FASTQ]
-----[Read Type: Pair End]
-----[Total # Reads: 73556084]
-----[Max Read Length: 126]
-----[Min Read Length: 15]
-----[Max Quality Score: 70]
-----[Min Quality Score: 35]
-----[Quality Score Scale: Phred+33]
[Mon Jul 19 18:31:08 2021] Running MapSplice multi-thread
[Mon Jul 19 21:57:31 2021] Generating junctions from sam file
[Mon Jul 19 21:57:50 2021] Filtering junction by min mis and min lpq
[Mon Jul 19 21:57:50 2021] Filtering junction by ROC argu noncanonical
[Mon Jul 19 21:57:51 2021] Generating synthetic junction sequences
[Mon Jul 19 21:57:56 2021] Checking Bowtie index files
[Mon Jul 19 21:57:56 2021] Building Bowtie index for junction synthetic sequence
[Mon Jul 19 21:58:27 2021] Running MapSplice multi-thread
[Tue Jul 20 03:10:08 2021] Converting unmapped reads to sam
[Tue Jul 20 03:10:13 2021] Converting unmapped reads to sam
[Tue Jul 20 03:10:17 2021] Running alignment handler
[Tue Jul 20 03:28:31 2021] Sorting file
[Tue Jul 20 03:28:35 2021] Setting unmapped paired end reads bit flag
[Tue Jul 20 03:28:59 2021] Formatting SAM file
[Tue Jul 20 03:31:59 2021] Collecting stats of read alignments and junctions
[Tue Jul 20 03:32:08 2021] Mapsplice finished running (time used: 9:01:41.682755)

Answer 1

[nkmalini97]

I did not add --fusion as the alignment option to the command and so the problem. The issue is sorted now.

[Ram]

Please do not delete your posts unless you've a really good reason. Someone running into the same error might benefit from your experience.

Instead, please accept your answer so the post is marked as resolved.