Comments (4)
It looks like your BAM file is empty. Please provide error logs (.tar.gz
).
from atac-seq-pipeline.
I'm not sure if either of these are the BAM file you're referring to:
call-ataqc/shard-0/inputs/789850838/${SAMPLE}.trim.merged.bam is 1.5G
call-ataqc/shard-0/inputs/-623782124/${SAMPLE}.trim.merged.nodup.bam is 667M.
from atac-seq-pipeline.
This will be fixed in v1.1.4. But if you want to fix it yourself then modify function get_chr_m()
in line 203-221 of /users/nicolerg/anaconda2/envs/encode-atac-seq-pipeline/bin/encode_ataqc.py
like the following.
def get_chr_m(sorted_bam_file):
'''
Get fraction of reads that are mitochondrial (chr M).
'''
logging.info('Getting mitochondrial chromosome fraction...')
chrom_list = pysam.idxstats(sorted_bam_file, split_lines=True)
tot_reads = 0
chr_m_reads = 0
for chrom in chrom_list:
chrom_stats = chrom.split('\t')
if chrom_stats[0] == 'chrM':
chr_m_reads = int(chrom_stats[2])
tot_reads += int(chrom_stats[2])
if tot_reads==0:
fract_chr_m = 0
else:
fract_chr_m = float(chr_m_reads) / tot_reads
return chr_m_reads, fract_chr_m
from atac-seq-pipeline.
That function is not in encode_ataqc.py
, but I modified it in /users/nicolerg/anaconda2/envs/encode-atac-seq-pipeline/bin/run_ataqc.py
.
from atac-seq-pipeline.
Related Issues (20)
- Finished parsing without consuming all tokens HOT 1
- How are mitochondrial reads aligned? HOT 1
- How are DNAse-seq data processed with this pipeline?
- Reuse the same files in case of error.
- Help with running the pipeline HOT 1
- Unable to run the pipeline. invalid jar file error HOT 3
- 6 days stuck on task=atac.read_genome_tsv:-1, retry=0, status=Running
- More than 10 replicates HOT 3
- Encode-atac-seq-pipeline environment can't be found?
- [Question]: Do reads need to be deduped before FRiP calculation HOT 6
- Invalid MEMLIMIT unit value with LSF jobs on Linux
- two replicates and the combined have different signal
- --read-len selection
- Memory Saving: too many large files?
- The pipeline stalled at "chip.read_genome_tsv" for local backend HOT 2
- Differences in qc when validating installation HOT 3
- Failed on fastqs having identical filename but different path HOT 3
- Confirming that separate conditions/treatments should be analyzed by separate pipelines HOT 2
- Don't need to trim adapters
- Add --ntasks-per-node or --exclusive option for your multi-process jobs.
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from atac-seq-pipeline.