Different minimap2 alignment results of different FunAnnotate version #444
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Thanks for reporting -- likely a bug in the master code. I added the |
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The BAM file is not empty, but I notice the file size of this file increase by 1byte compared to my previous run of v1.7.2 |
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okay, so |
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And if you wouldn't mind checking the header for both of them? |
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BAM from v1.8.0 has 36947 lines; from v1.7.2 has 37492 lines |
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Okay -- that means its not there, its in the processing of the bam to gff3 (alignments). Its likely then a python2/3 issue -- which version of python? |
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Python 2.7 |
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Hmm, okay. Well when I test it locally I'm not seeing a problem. You can test the bam2gff3 conversion in the utility menu, ie. I guess I didn't ask if the |
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bam2gff3 could generate non-empty gff3 results |
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So if the |
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Hi, I have the same issue. After checking the codes in I'm not sure if I fixed it correctly , but it works for me. |
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@lyl8086 thanks -- I think you are right, those look like leftover errors from using pybam which is now just samtools for compatibility. I appreciate the help. |
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Please reopen if after installing master branch and it is still a problem. |
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When I used FunAnnotate v1.7.2, I was able to align transcripts to genome with minimap2, log as
`[06/22/20 12:34:13]: Aligning transcript evidence to genome with minimap2
[06/22/20 12:34:13]: /home/qliang/0.soft/miniconda2/envs/funannotate/lib/python2.7/site-packages/funannotate/aux_scripts/sam2bam.sh minimap2 -ax splice -t 36 --cs -u b -G 3000 /home/qliang/results_minimap/predict_misc/genome.softmasked.fa results_minimap/predict_misc/transcripts.combined.fa 4 results_minimap/predict_misc/transcripts.minimap2.bam
[06/22/20 12:34:18]: [M::mm_idx_gen::0.4261.00] collected minimizers
[M::mm_idx_gen::0.4962.30] sorted minimizers
[M::main::0.4962.30] loaded/built the index for 21 target sequence(s)
[M::mm_mapopt_update::0.5402.19] mid_occ = 160
[M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 21
[M::mm_idx_stat::0.5722.12] distinct minimizers: 2337210 (92.46% are singletons); average occurrences: 1.407; average spacing: 2.929
[M::worker_pipeline::4.27019.98] mapped 30940 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax splice -t 36 --cs -u b -G 3000 /home/qliang/results_minimap/predict_misc/genome.softmasked.fa results_minimap/predict_misc/transcripts.combined.fa
[M::main] Real time: 4.290 sec; CPU: 85.338 sec; Peak RSS: 0.511 GB
[bam_sort_core] merging from 0 files and 4 in-memory blocks...
[06/22/20 12:34:25]: Found 20,273 alignments, wrote GFF3 and Augustus hints to file`
I updated FunAnnotate to v1.8.0 and repeated with same files/settings, but transcripts alignments were different with 0 alignments. Log as
[06/29/20 12:21:03]: Aligning transcript evidence to genome with minimap2 [06/29/20 12:21:03]: minimap2 -ax splice -t 36 --cs -u b -G 3000 /home/qliang/results_minimap/predict_misc/genome.softmasked.fa results_minimap/predict_misc/transcripts.combined.fa | samtools sort --reference /home/qliang/results_minimap/predict_misc/genome.softmasked.fa -@ 4 -o results_minimap/predict_misc/transcripts.minimap2.bam - [06/29/20 12:22:00]: Found 0 alignments, wrote GFF3 and Augustus hints to fileI ran the cmd in log
minimap2 -ax splice -t 36 --cs -u b -G 3000 /home/qliang/results_minimap/predict_misc/genome.softmasked.fa results_minimap/predict_misc/transcripts.combined.fa | samtools sort --reference /home/qliang/results_minimap/predict_misc/genome.softmasked.fa -@ 4 -o results_minimap/predict_misc/transcripts.minimap2.bam -The output was
[M::mm_idx_gen::0.414*1.00] collected minimizers [M::mm_idx_gen::0.480*2.30] sorted minimizers [M::main::0.480*2.30] loaded/built the index for 21 target sequence(s) [M::mm_mapopt_update::0.520*2.20] mid_occ = 160 [M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 21 [M::mm_idx_stat::0.548*2.14] distinct minimizers: 2337210 (92.46% are singletons); average occurrences: 1.407; average spacing: 2.929 [M::worker_pipeline::3.805*22.79] mapped 30940 sequences [M::main] Version: 2.17-r941 [M::main] CMD: minimap2 -ax splice -t 36 --cs -u b -G 3000 /home/qliang/results_minimap/predict_misc/genome.softmasked.fa results_minimap/predict_misc/transcripts.combined.fa [M::main] Real time: 3.828 sec; CPU: 86.715 sec; Peak RSS: 0.573 GB [bam_sort_core] merging from 0 files and 4 in-memory blocks...It seems like there is no explicit error of running minimap2, but it is weird that there is no alignment at all for transcripts2genome. Could you help troubleshooting this? Many thanks!
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