Two pass mode stuck halfway and does not generate log.final.out

[HafsaKM]

Hi, I am trying to call variants from RNA-seq data for the first time. I am doing this using the Mutect2 variant calling tool available on GATK. I am trying to align the FASTQ files using the STAR two-pass mode.
These are the commands I've used so far:

/share/apps/genomics/STAR-2.7.9a/source/STAR --genomeDir /SAN/colcc/ITH2/Hafsa/gatkFiles/genome_data/STARIndex --readFilesCommand zcat \
--readFilesIn /SAN/colcc/ITH2_RN21225_1/alignment_out_20220202_merge_replicates/fastq/UH25_Tc_1.merged.fastq.gz /SAN/colcc/ITH2_RN21225_1/alignment_out_20220202_merge_replicates/fastq/UH25_Tc_2.merged.fastq.gz \
--outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 16000000000 --outSAMunmapped Within \
--twopassMode Basic --outFilterMultimapNmax 1 --quantMode TranscriptomeSAM \
--runThreadN 20 --outFileNamePrefix "rna_two_pass_mode_for_vc_UH25Tc_rerun"

/share/apps/genomics/STAR-2.7.9a/source/STAR --genomeDir /SAN/colcc/ITH2/Hafsa/gatkFiles/genome_data/STARIndex --readFilesCommand zcat \
--readFilesIn /SAN/colcc/ITH2_RN21225_1/alignment_out_20220202_merge_replicates/fastq/UH25_Th_1.merged.fastq.gz /SAN/colcc/ITH2_RN21225_1/alignment_out_20220202_merge_replicates/fastq/UH25_Th_2.merged.fastq.gz \
--outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 16000000000 --outSAMunmapped Within \
--twopassMode Basic --outFilterMultimapNmax 1 --quantMode TranscriptomeSAM \
--runThreadN 20 --outFileNamePrefix "rna_two_pass_mode_for_vc_UH25Th_rerun"

These are the output files that have been generated for this:

Before running these commands, I requested the following: qrsh -l tmem=40G, h_vmem=40G

Not sure why this is failing. Any advice is greatly appreciated! Thanks a lot!

[alexdobin]

Hi Hafsa,

what is the error message?
Please send me the *Log.out file.

Best,
Alex