search

ENCODE-DCC / chip-seq-pipeline2

ENCODE ChIP-seq pipeline
MIT License
246 stars 123 forks source link

Failed to access *.gc.txt , for peak calling #118

Closed Baharehh closed 4 years ago

Baharehh commented 4 years ago

hi, I have the latest pipeline and the caper installed and the miniconda3 is also correctly installed. The pipeline runs fine until it reaches to peak calling and it stops with this error:

File "pandas/_libs/parsers.pyx", line 382, in pandas._libs.parsers.TextReader.cinit

File "pandas/_libs/parsers.pyx", line 689, in pandas._libs.parsers.TextReader._setup_parser_source

FileNotFoundError: [Errno 2] File b'hs_cpseq_cll_C1_bd_S9_R1_001.sorted.rmdup2.gc.txt' does not exist: b'hs_cpseq_cll_C1_bd_S9_R1_001.sorted.rmdup2.gc.txt'

I ran this:

"caper debug ~/afs-home/../metadata.json

and I got this:

ln: failed to access '/farmshare/user_data/baharehh/chip-seq-pipeline2/chip/52031527-edbb-4130-a1d7-3e61c6b5f39c/call-gc_bias/shard-0/attempt-2/execution/*.gc.txt': No such file or directory chip.call_peak_pr2 Failed. SHARD_IDX=0, RC=None, JOB_ID=None, RUN_START=2019-12-28T00:01:51.844Z, RUN_END=2019-12-28T00:01:52.709Z, STDOUT=/farmshare/user_data/baharehh/chip-seq-pipeline2/chip/52031527-edbb-4130-a1d7-3e61c6b5f39c/call-call_peak_pr2/shard-0/execution/stdout, STDERR=/farmshare/user_data/baharehh/chip-seq-pipeline2/chip/52031527-edbb-4130-a1d7-3e61c6b5f39c/call-call_peak_pr2/shard-0/execution/stderr

would be great if you give me some advice on how to keep the run going my best regards

April/B

Baharehh commented 4 years ago

The issue is solved by the code Jin provided:

Until it's fixed, disable GC bias in your input JSON.


{
    "chip.enable_gc_bias" : false
}