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-   -   Problem with CEL-Seq-pipeline (http://seqanswers.com/forums/showthread.php?t=73659)

MaxwellShih 01-17-2017 11:27 AM

Problem with CEL-Seq-pipeline
 
Hello,
I wonder anyone is using the CEL-Seq pipeline. I am new to CEL-Seq as well as to bioinformatics. I got stuck at the very first step. Can anyone help?

Many thanks!

Below is the error message:

2017-01-17 14:04:09,541 - pijp - INFO - ===== Started pijpleiding with config file : ./config_file.txt =====
2017-01-17 14:04:09,557 - pijp - INFO - ===== pipeline at /sonas-hs/dubnau/hpc_norepl/data/mshih/CEL-Seq/CEL-Seq-pipeline-master/pijpleiding.py =====
2017-01-17 14:04:09,557 - pijp - INFO - ========== writing log to file at /sonas-hs/dubnau/hpc_norepl/data/mshih/CEL-Seq/CEL-Seq_t1/pijp.log ==========
2017-01-17 14:04:09,558 - pijp - INFO - Section : bc_demultiplex
2017-01-17 14:04:09,558 - pijp - INFO - parameters : {"strand_field": "2", "sample_sheet": "/sonas-hs/dubnau/hpc_norepl/data/mshih/CEL-Seq/sample_sheet", "bc_index_file": "/sonas-hs/dubnau/hpc_norepl/data/mshih/CEL-Seq/bc_index_file", "umi_length": "0", "bc_length": "8", "min_bc_quality": "10", "output_dir": "/sonas-hs/dubnau/hpc_norepl/data/mshih/CEL-Seq/CEL-Seq_t1", "lane_field": "1", "index_field": "0", "input_files": ["/sonas-hs/dubnau/hpc_norepl/data/mshih/CEL-Seq/T1/RPI1_L001_R1_001.fastq", "/sonas-hs/dubnau/hpc_norepl/data/mshih/CEL-Seq/T1/RPI1_L001_R2_001.fastq", "/sonas-hs/dubnau/hpc_norepl/data/mshih/CEL-Seq/T1/RPI1_L002_R1_001.fastq", "/sonas-hs/dubnau/hpc_norepl/data/mshih/CEL-Seq/T1/RPI1_L002_R2_001.fastq", "/sonas-hs/dubnau/hpc_norepl/data/mshih/CEL-Seq/T1/RPI3_L001_R1_001.fastq", "/sonas-hs/dubnau/hpc_norepl/data/mshih/CEL-Seq/T1/RPI3_L001_R2_001.fastq", "/sonas-hs/dubnau/hpc_norepl/data/mshih/CEL-Seq/T1/RPI3_L002_R1_001.fastq", "/sonas-hs/dubnau/hpc_norepl/data/mshih/CEL-Seq/T1/RPI3_L002_R2_001.fastq", "/sonas-hs/dubnau/hpc_norepl/data/mshih/CEL-Seq/T1/RPI7_L001_R1_001.fastq", "/sonas-hs/dubnau/hpc_norepl/data/mshih/CEL-Seq/T1/RPI7_L001_R2_001.fastq", "/sonas-hs/dubnau/hpc_norepl/data/mshih/CEL-Seq/T1/RPI7_L002_R1_001.fastq", "/sonas-hs/dubnau/hpc_norepl/data/mshih/CEL-Seq/T1/RPI7_L002_R2_001.fastq"], "stats_file": "stats.tab", "fname_delimiter": "_", "cut_length": "35"}
Traceback (most recent call last):
File "/sonas-hs/dubnau/hpc_norepl/data/mshih/CEL-Seq/CEL-Seq-pipeline-master/pijpleiding.py", line 129, in <module>
main(args.config_file)
File "/sonas-hs/dubnau/hpc_norepl/data/mshih/CEL-Seq/CEL-Seq-pipeline-master/pijpleiding.py", line 93, in main
segment(**parameters)
File "/sonas-hs/dubnau/hpc_norepl/data/mshih/CEL-Seq/CEL-Seq-pipeline-master/bc_demultiplex.py", line 37, in main
fastq_dict = create_fastq_dict(input_files, fname_delimiter, int(lane_field), int(index_field), int(strand_field))
File "/sonas-hs/dubnau/hpc_norepl/data/mshih/CEL-Seq/CEL-Seq-pipeline-master/bc_demultiplex.py", line 115, in create_fastq_dict
assert ("R1" in fastq_dict[fastq_file].strand), "File name does not contain R1 in field %d. Aborting (%r not R1)" %(strand_field, fastq_dict[fastq_file].strand)
AssertionError: File name does not contain R1 in field 2. Aborting ('R2' not R1)


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