How to use swiss army knife with batch file?

Hello guys,

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I try to run the swiss army knife with batch files, but it gave me some error. Here is my commands and the error.

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Command

(WGS) xueming@RNA:~/CHIP$ dx generate_batch_inputs --path "${projectid}:/Bulk/Exome sequences/Exome OQFE CRAM files/10/" -iin="(.*)_23143_0_0.cram$"

Found 9332 valid batch IDs matching desired pattern.

Created batch file dx_batch.0000.tsv

Created batch file dx_batch.0001.tsv

Created batch file dx_batch.0002.tsv

Created batch file dx_batch.0003.tsv

Created batch file dx_batch.0004.tsv

Created batch file dx_batch.0005.tsv

Created batch file dx_batch.0006.tsv

Created batch file dx_batch.0007.tsv

Created batch file dx_batch.0008.tsv

Created batch file dx_batch.0009.tsv

Created batch file dx_batch.0010.tsv

Created batch file dx_batch.0011.tsv

Created batch file dx_batch.0012.tsv

Created batch file dx_batch.0013.tsv

Created batch file dx_batch.0014.tsv

Created batch file dx_batch.0015.tsv

Created batch file dx_batch.0016.tsv

Created batch file dx_batch.0017.tsv

Created batch file dx_batch.0018.tsv

(WGS) xueming@RNA:~/CHIP$ head -n 3 dx_batch.0000.tsv > dx_example.tsv

(WGS) xueming@RNA:~$ dx run swiss-army-knife  --batch-tsv dx_example.tsv -icmd='samtools view -T "/mnt/project/Bulk/Exome sequences/Exome OQFE CRAM files/helper_files/GRCh38_full_analysis_set_plus_decoy_hla.fa" -L "/mnt/project/CH_yao/gene.bed" -o "$in_prefix".bam "$in_name" ' -y  --brief --priority normal --instance-type mem1_ssd1_v2_x2 --destination "${projectid}:/CH_yao/" --detach --tag "map"

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Error

Traceback (most recent call last):

 File "/i/melanoma_WGS/anaconda3/envs/WGS/lib/python3.10/site-packages/dxpy/utils/batch_utils.py", line 112, in _type_convert

  return _type_convert_array(val, klass)

 File "/i/melanoma_WGS/anaconda3/envs/WGS/lib/python3.10/site-packages/dxpy/utils/batch_utils.py", line 98, in _type_convert_array

  raise Exception("Malformed array {}".format(val))

Exception: Malformed array ${projectid}:file-G2Y0800JykJz1gjX3J7FvKXX

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During handling of the above exception, another exception occurred:

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Traceback (most recent call last):

 File "/i/melanoma_WGS/anaconda3/envs/WGS/lib/python3.10/site-packages/dxpy/scripts/dx.py", line 6133, in main

  args.func(args)

 File "/i/melanoma_WGS/anaconda3/envs/WGS/lib/python3.10/site-packages/dxpy/scripts/dx.py", line 3522, in run

  run_body(args, handler, dest_proj, dest_path)

 File "/i/melanoma_WGS/anaconda3/envs/WGS/lib/python3.10/site-packages/dxpy/scripts/dx.py", line 3134, in run_body

  run_batch_all_steps(args, executable, dest_proj, dest_path, input_json, run_kwargs)

 File "/i/melanoma_WGS/anaconda3/envs/WGS/lib/python3.10/site-packages/dxpy/scripts/dx.py", line 2982, in run_batch_all_steps

  b_args = batch_launch_args(executable, input_json, args.batch_tsv)

 File "/i/melanoma_WGS/anaconda3/envs/WGS/lib/python3.10/site-packages/dxpy/utils/batch_utils.py", line 182, in batch_launch_args

  val_w_correct_type, ref_files = _type_convert(val.strip(), klass)

 File "/i/melanoma_WGS/anaconda3/envs/WGS/lib/python3.10/site-packages/dxpy/utils/batch_utils.py", line 117, in _type_convert

  raise Exception("value={} cannot be converted into class {}".format(val, klass))

Exception: value=${projectid}:file-G2Y0800JykJz1gjX3J7FvKXX cannot be converted into class array:file

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I replace the subject id with ?${projectid}?? for safety.

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I have test the command using one file name rather than batch file and it goes well. I think it maybe the problem of dx-tools, but I do not know how to solve it.

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So, can anyone give me some suggestions? Thanks!

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Sincerely,

Xueming? Yao