Unable to use CRAM inputs for msisensor-pro
seetarajpara opened this issue · 2 comments
seetarajpara commented
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 commented
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 commented
@seetarajpara
Please, which version of msisensor-pro did you use?