Sun Feb 13 07:12:12 JST 2022: Start: amalgkit getfastq
Single-end fastq was generated even though layout = paired
This sample will be treated as single-end sequencing.
unpigz: skipping: /gfe_data/transcriptome_assembly/tmp/1_Mayetiola_destructor/getfastq/Mayetiola_destructor/SRR042791.fastp.fastq.gz empty
Traceback (most recent call last):
File "/opt/conda/envs/biotools/bin/amalgkit", line 378, in <module>
args.handler(args)
File "/opt/conda/envs/biotools/bin/amalgkit", line 33, in command_getfastq
getfastq_main(args)
File "/opt/conda/envs/biotools/lib/python3.9/site-packages/amalgkit/getfastq.py", line 861, in getfastq_main
metadata = calc_2nd_ranges(metadata)
File "/opt/conda/envs/biotools/lib/python3.9/site-packages/amalgkit/getfastq.py", line 489, in calc_2nd_ranges
sra_target_reads = ((sra_target_bp/spot_lengths)/rate_obtained).astype(int)+1
File "/opt/conda/envs/biotools/lib/python3.9/site-packages/pandas/core/generic.py", line 5815, in astype
new_data = self._mgr.astype(dtype=dtype, copy=copy, errors=errors)
File "/opt/conda/envs/biotools/lib/python3.9/site-packages/pandas/core/internals/managers.py", line 418, in astype
return self.apply("astype", dtype=dtype, copy=copy, errors=errors)
File "/opt/conda/envs/biotools/lib/python3.9/site-packages/pandas/core/internals/managers.py", line 327, in apply
applied = getattr(b, f)(**kwargs)
File "/opt/conda/envs/biotools/lib/python3.9/site-packages/pandas/core/internals/blocks.py", line 591, in astype
new_values = astype_array_safe(values, dtype, copy=copy, errors=errors)
File "/opt/conda/envs/biotools/lib/python3.9/site-packages/pandas/core/dtypes/cast.py", line 1309, in astype_array_safe
new_values = astype_array(values, dtype, copy=copy)
File "/opt/conda/envs/biotools/lib/python3.9/site-packages/pandas/core/dtypes/cast.py", line 1257, in astype_array
values = astype_nansafe(values, dtype, copy=copy)
File "/opt/conda/envs/biotools/lib/python3.9/site-packages/pandas/core/dtypes/cast.py", line 1168, in astype_nansafe
return astype_float_to_int_nansafe(arr, dtype, copy)
File "/opt/conda/envs/biotools/lib/python3.9/site-packages/pandas/core/dtypes/cast.py", line 1213, in astype_float_to_int_nansafe
raise IntCastingNaNError(
pandas.errors.IntCastingNaNError: Cannot convert non-finite values (NA or inf) to integer
With SRR042791