Unable to use CRAM inputs for msisensor-pro

[seetarajpara]

My code below:

msisensor-pro msi -d ${MSI_LIST} \
-t ${T_CRAM} \
-n ${N_CRAM} \
-g ${REF} \
-z 1 \
-e ${BED_FILE} \
-o ${RUN_DIR}${T_CRAM}${N_CRAM} -b 2

Message I'm getting (1 file out of the 100 in the batch):

[rajpara@discovery1 MSI]$ cat msisensor_100_11248368.out
==========================================
SLURM_JOB_ID = 11248368
SLURM_JOB_NODELIST = e11-26
TMPDIR = /tmp/SLURM_11248368
==========================================
msi -d /scratch1/rajpara/WES/MSI/microsatellites.list -t /scratch1/rajpara/WES/tumor_normal_CRAMs2/A37649_st_t_markdup.cram -n /scratch1/rajpara/WES/tumor_normal_CRAMs2/A37650_st_g_markdup.cram -g /scratch1/rajpara/resources/hs38DH.fa -z 1 -e /scratch1/rajpara/resources/hg38_IDT_targets_sorted_merged_extended_sorted_merged.bed -o /scratch1/rajpara/WES/MSI//scratch1/rajpara/WES/tumor_normal_CRAMs2/A37649_st_t_markdup.cram/scratch1/rajpara/WES/tumor_normal_CRAMs2/A37650_st_g_markdup.cram -b 2 Start at:  Sat Oct  1 16:36:00 2022

ERROR: unrecognized option -g
please provide valid format normal bam file ! 

I saw that CRAM files were acceptable as input. If there is an option I'm missing, please let me know. Thank you so much!

[seetarajpara]

I'm also seeing this issue after I tested this on the demo data files in this repo:

(seeta_test) [rajpara@discovery2 MSI_TEST]$ msisensor-pro msi -d ${MSI_LIST} \
> -t ${T_CRAM} \
> -n ${N_CRAM} \
> -g ${REF} \
> -z 1 \
> -o ${RUN_DIR}${T_CRAM}${N_CRAM} -b 2
msi -d /scratch1/rajpara/WES/MSI/MSI_TEST/reference.list -t /scratch1/rajpara/WES/MSI/MSI_TEST/test_tumor_sorted.cram -n /scratch1/rajpara/WES/MSI/MSI_TEST/test_normal_sorted.cram -g /scratch1/rajpara/WES/MSI/MSI_TEST/reference.fa -z 1 -o /scratch1/rajpara/WES/MSI/MSI_TEST//scratch1/rajpara/WES/MSI/MSI_TEST/test_tumor_sorted.cram/scratch1/rajpara/WES/MSI/MSI_TEST/test_normal_sorted.cram -b 2 Start at:  Sat Oct  1 17:14:40 2022

ERROR: unrecognized option -g
please provide valid format normal bam file ! 

[PengJia6]

@seetarajpara Please, which version of msisensor-pro did you use?