diff --git a/workflow/rules/baseline_pipeline.smk b/workflow/rules/baseline_pipeline.smk
index c43149d..9403239 100644
--- a/workflow/rules/baseline_pipeline.smk
+++ b/workflow/rules/baseline_pipeline.smk
@@ -38,7 +38,7 @@ rule basecall_pod5:
         pod5='../data/raw_pod5/PBK98658_853a956f_57f83f46_{batch}.pod5',
         model=get_model_requirement
     output:
-        '../data/basecalled_reads/{model}/PBK98658_853a956f_57f83f46_{batch}.fastq.gz'
+        temp('../data/basecalled_reads/{model}/PBK98658_853a956f_57f83f46_{batch}.fastq')
     threads:
         32
     resources:
@@ -52,12 +52,12 @@ rule basecall_pod5:
         model="hac|fast"
     shell:
         """
-        dorado basecaller --models-directory {config[dorado_model_dir]} --emit-fastq {params.benchmarking} {params.min_qscore} {params.dorado_model} {input.pod5} | gzip -c > {output}
+        dorado basecaller --models-directory {config[dorado_model_dir]} --emit-fastq {params.benchmarking} {params.min_qscore} {params.dorado_model} {input.pod5} > {output}
         """
 
 rule concatenate_basecalled_fastq:
     input:
-        expand('../data/basecalled_reads/{{model}}/PBK98658_853a956f_57f83f46_{batch}.fastq.gz',batch=range(1,config["pod5_dataset_size"]+1,config["pod5_stride"]))
+        expand('../data/basecalled_reads/{{model}}/PBK98658_853a956f_57f83f46_{batch}.fastq',batch=range(1,config["pod5_dataset_size"]+1,config["pod5_stride"]))
     output:
         '../data/basecalled_reads/{model}.fastq.gz'
     threads: 1
@@ -65,7 +65,7 @@ rule concatenate_basecalled_fastq:
         model="hac|fast"
     shell:
         """
-        zcat {input} > {output}
+        cat {input} | gzip -c > {output}
         """
 
 rule align_reads_to_reference: