Empty output and summary directories after a successful run

[ndoshi2921]

Hi,

I ran the indexer using the following command:

docker run -u $(id -u ${USER}):$(id -g ${USER}) 
-v /home/rstudio/data/a2i/final_bams:/data/aln:ro 
-v /home/rstudio/data/a2i/res1:/data/output:rw  dockerized-a2i/a2i_editing_index:1.0 RNAEditingIndex 
-d /data/aln  
-f _L003_R1_001Aligned_chr_final.bam 
-l /data/Korro/a2i/res1/logs_dir 
 -o /home/rstudio/data/Korro/a2i/res1/cmpileups 
-os /home/rstudio/data/Korro/a2i/res1/output_dir_summary --genome mm10 --paired_end  --keep_cmpileup

It runs successfully, and below is a snippet of the stdout after the run finishes:

Number of records read = 1442913 Number of records written = 1442913 [mpileup] 1 samples in 1 input files [bam_sort_core] merging from 0 files and 10 in-memory blocks... Arguments in effect: Input file : /home/rstudio/data/Korro/a2i/res1/cmpileups/KBIVM001_6-52A_339_238_S75/KBIVM001_6-52A_339_238_S75_region_ucscMM10SINE_B1_B2.bed.gz_alignments.bam Output file : /home/rstudio/data/Korro/a2i/res1/cmpileups/KBIVM001_6-52A_339_238_S75/KBIVM001_6-52A_339_238_S75_region_ucscMM10SINE_B1_B2.bed.gz_alignments.bam.trimmed_5.bam

Bases to trim from each side : 5

Number of records read = 1089538 Number of records written = 1089538 [mpileup] 1 samples in 1 input files [bam_sort_core] merging from 0 files and 10 in-memory blocks... Arguments in effect: Input file : /home/rstudio/data/Korro/a2i/res1/cmpileups/KBIVM001_6-54A_315_262_S77/KBIVM001_6-54A_315_262_S77_region_ucscMM10SINE_B1_B2.bed.gz_alignments.bam Output file : /home/rstudio/data/Korro/a2i/res1/cmpileups/KBIVM001_6-54A_315_262_S77/KBIVM001_6-54A_315_262_S77_region_ucscMM10SINE_B1_B2.bed.gz_alignments.bam.trimmed_5.bam

Bases to trim from each side : 5

[bam_sort_core] merging from 0 files and 10 in-memory blocks... Arguments in effect: Input file : /home/rstudio/data/Korro/a2i/res1/cmpileups/KBIVM001_6-53A_327_250_S76/KBIVM001_6-53A_327_250_S76_region_ucscMM10SINE_B1_B2.bed.gz_alignments.bam Output file : /home/rstudio/data/Korro/a2i/res1/cmpileups/KBIVM001_6-53A_327_250_S76/KBIVM001_6-53A_327_250_S76_region_ucscMM10SINE_B1_B2.bed.gz_alignments.bam.trimmed_5.bam

Bases to trim from each side : 5

Number of records read = 1233579 Number of records written = 1233579 [mpileup] 1 samples in 1 input files

Number of records read = 1332271 Number of records written = 1332271 [mpileup] 1 samples in 1 input files [bam_sort_core] merging from 0 files and 10 in-memory blocks... Arguments in effect: Input file : /home/rstudio/data/Korro/a2i/res1/cmpileups/KBIVM001_6-55A_303_274_S78/KBIVM001_6-55A_303_274_S78_region_ucscMM10SINE_B1_B2.bed.gz_alignments.bam Output file : /home/rstudio/data/Korro/a2i/res1/cmpileups/KBIVM001_6-55A_303_274_S78/KBIVM001_6-55A_303_274_S78_region_ucscMM10SINE_B1_B2.bed.gz_alignments.bam.trimmed_5.bam

Bases to trim from each side : 5

Number of records read = 1253102 Number of records written = 1253102 [mpileup] 1 samples in 1 input files [2020-04-24 03:55:00,802] general_functions WARNING GGPSResources.general_functions.remove_files Failed To Remove 24-04-2020-03.cnf [2020-04-24 03:55:00,802] general_functions WARNING GGPSResources.general_functions.remove_files Failed To Remove 24-04-2020-03.cnf

System Info:

Ubuntu 18.04.4 LTS

However, the output and summary directories are both empty. Any advise or correction in the input command will be greatly appreciated.

Best, N

[shalomhillelroth]

Hi,

Can you kindly attach the whole log please? ( if you don't want it to be available here for security reasons you can send it to my e-mail)

best Shalom Hillel Roth