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rajewsky-lab / mirdeep2

Discovering known and novel miRNAs from small RNA sequencing data
GNU General Public License v3.0
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Error sort: cannot create temporary file in '/tmp/': Read-only file system #95

Closed RRebo closed 2 years ago

RRebo commented 2 years ago

Hello,

I am running mapper.pl and miRDeep2.pl in my cluster, using 23 sRNAseq libraries and a miRNA.fa file of known miRNAs. When I ran the code below on only 14 libraries (no matter which ones), it all runs smoothly. However, when I try to run with all the 23 libraries, I get an error sort: cannot create temporary file in '/tmp/': Read-only file system. If you have a solution for this, it would be great!

I installed with conda, and again, it does work when running just 14 libraries... Below are my command lines and log files.

mapper.pl Reads/config_unleash-Unmapped_test_sitophilus.txt -d -e -h -i -j -l 18 -m -p sitophilus_v2 -s Input_miRDeep2/Unleash-Unmapped_test04_collapsed.fa -t Input_miRDeep2/Unleash-Unmapped_test04_vs_refdb.arf -v -o 8

miRDeep2.pl Input_miRDeep2/Unleash-Unmapped_test04_collapsed.fa sitophilus_v2.fasta Input_miRDeep2/Unleash-Unmapped_test04_vs_refdb.arf none miRNA.fa none -g -1 2>Unleash-Unmapped_test04_report.log

Error file

sort: cannot create temporary file in '/tmp/': Read-only file system
RNAfold: invalid option -- n

Report log:

#Starting miRDeep2
/home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2.pl Input_miRDeep2/Unleash-Unmapped_test04_collapsed.fa sitophilus_v2.fasta Input_miRDeep2/Unleash-Unmapped_test04_vs_refdb.arf none miRNA.fa none -g -1

miRDeep2 started at 21:56:29

mkdir mirdeep_runs/run_02_02_2022_t_21_56_29

sort: cannot create temporary file in '/tmp/': Read-only file system
#testing input files
started: 21:56:30
sanity_check_mature_ref.pl miRNA.fa

ended: 21:56:31
total:0h:0m:1s

sanity_check_reads_ready_file.pl Input_miRDeep2/Unleash-Unmapped_test04_collapsed.fa

started: 21:56:31

ended: 22:0:18
total:0h:3m:47s

started: 22:0:18
sanity_check_genome.pl sitophilus_v2.fasta

ended: 22:0:25
total:0h:0m:7s

started: 22:0:25
sanity_check_mapping_file.pl Input_miRDeep2/Unleash-Unmapped_test04_vs_refdb.arf

ended: 22:1:02
total:0h:0m:37s

Pre-quantitation is skipped caused by missing file with known precursor miRNAs

rna2dna.pl miRNA.fa > mirdeep_runs/run_02_02_2022_t_21_56_29/tmp/miRNA.fa

ended: 22:1:02
total:0h:0m:37s

#parsing genome mappings
parse_mappings.pl Input_miRDeep2/Unleash-Unmapped_test04_vs_refdb.arf -a 0 -b 18 -c 25 -i 5 > mirdeep_runs/run_02_02_2022_t_21_56_29/tmp/Unmapped_test04_vs_refdb.arf_parsed.arf

started: 22:1:02

ended: 22:5:22
total:0h:4m:20s

#excising precursors
started: 22:5:22
excise_precursors_iterative_final.pl sitophilus_v2.fasta mirdeep_runs/run_02_02_2022_t_21_56_29/tmp/Unmapped_test04_vs_refdb.arf_parsed.arf mirdeep_runs/run_02_02_2022_t_21_56_29/tmp/precursors.fa mirdeep_runs/run_02_02_2022_t_21_56_29/tmp/precursors.coords -1
1   958278

ended: 22:10:02
total:0h:4m:40s

#preparing signature
prepare_signature.pl Input_miRDeep2/Unleash-Unmapped_test04_collapsed.fa mirdeep_runs/run_02_02_2022_t_21_56_29/tmp/precursors.fa 1 -o mirdeep_runs/run_02_02_2022_t_21_56_29/tmp/signature.arf 2>>error_02_02_2022_t_21_56_29.log

started: 22:10:02

ended: 22:42:18
total:0h:32m:16s

#folding precursors
started: 22:42:18
RNAfold < mirdeep_runs/run_02_02_2022_t_21_56_29/tmp/precursors.fa --noPS > mirdeep_runs/run_02_02_2022_t_21_56_29/tmp/precursors.str

ended: 0:16:27
total:1h:34m:9s

#computing randfold p-values
select_for_randfold.pl mirdeep_runs/run_02_02_2022_t_21_56_29/tmp/signature.arf mirdeep_runs/run_02_02_2022_t_21_56_29/tmp/precursors.str > mirdeep_runs/run_02_02_2022_t_21_56_29/tmp/precursors_for_randfold.ids

started: 0:16:27
Use of uninitialized value $db_old in hash element at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 277.
Use of uninitialized value $lng in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 283.
Use of uninitialized value $db_old in hash element at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 306.
Use of uninitialized value $db_old in hash element at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 307.
Use of uninitialized value $db_old in hash element at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 308.
Use of uninitialized value $query in hash element at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 441.
Use of uninitialized value $query in hash element at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 442.
Use of uninitialized value $query in hash element at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 454.
Use of uninitialized value $end in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 699.
Use of uninitialized value $beg in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 699.
Use of uninitialized value in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 703.
Use of uninitialized value $beg in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 703.
Use of uninitialized value $beg in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 706.
Use of uninitialized value $beg in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 706.
Use of uninitialized value $end in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 706.
Use of uninitialized value $seq in substr at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 706.
Use of uninitialized value $strand in string eq at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 709.
Use of uninitialized value $end in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 727.
Use of uninitialized value $beg in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 727.
Use of uninitialized value in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 731.
Use of uninitialized value $beg in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 731.
Use of uninitialized value $beg in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 734.
Use of uninitialized value $beg in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 734.
Use of uninitialized value $end in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 734.
Use of uninitialized value $struct in substr at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 734.
Use of uninitialized value $strand in string eq at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 467.
Use of uninitialized value $end in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 699.
Use of uninitialized value $beg in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 699.
Use of uninitialized value in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 703.
Use of uninitialized value $beg in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 703.
Use of uninitialized value $beg in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 706.
Use of uninitialized value $beg in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 706.
Use of uninitialized value $end in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 706.
Use of uninitialized value $seq in substr at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 706.
Use of uninitialized value $strand in string eq at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/select_for_randfold.pl line 709.

ended: 0:16:46
total:0h:0m:19s

started: 0:16:46
fastaselect.pl mirdeep_runs/run_02_02_2022_t_21_56_29/tmp/precursors.fa mirdeep_runs/run_02_02_2022_t_21_56_29/tmp/precursors_for_randfold.ids > mirdeep_runs/run_02_02_2022_t_21_56_29/tmp/precursors_for_randfold.fa

ended: 0:16:47
total:0h:0m:1s

started: 0:16:47
randfold -s mirdeep_runs/run_02_02_2022_t_21_56_29/tmp/precursors_for_randfold.fa 99 > mirdeep_runs/run_02_02_2022_t_21_56_29/tmp/precursors_for_randfold.rand

ended: 0:16:47
total:0h:0m:0s

#running miRDeep core algorithm
started: 0:16:47
miRDeep2_core_algorithm.pl mirdeep_runs/run_02_02_2022_t_21_56_29/tmp/signature.arf mirdeep_runs/run_02_02_2022_t_21_56_29/tmp/precursors.str -s mirdeep_runs/run_02_02_2022_t_21_56_29/tmp/miRNA.fa -v -50 -l 1 -y mirdeep_runs/run_02_02_2022_t_21_56_29/tmp/precursors_for_randfold.rand > mirdeep_runs/run_02_02_2022_t_21_56_29/output.mrd
Use of uninitialized value $db_old in hash element at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 743.
Use of uninitialized value $lng in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 749.
Use of uninitialized value $db_old in hash element at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 844.
Use of uninitialized value $db_old in hash element at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 845.
Use of uninitialized value $db_old in hash element at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 846.
Use of uninitialized value $query in hash element at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1101.
Use of uninitialized value $query in hash element at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1102.
Use of uninitialized value $query in hash element at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1091.
Use of uninitialized value $end in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1144.
Use of uninitialized value $beg in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1144.
Use of uninitialized value in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1148.
Use of uninitialized value $beg in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1148.
Use of uninitialized value $beg in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1151.
Use of uninitialized value $beg in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1151.
Use of uninitialized value $end in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1151.
Use of uninitialized value $seq in substr at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1151.
Use of uninitialized value $strand in string eq at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1154.
Use of uninitialized value $end in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1170.
Use of uninitialized value $beg in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1170.
Use of uninitialized value in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1174.
Use of uninitialized value $beg in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1174.
Use of uninitialized value $beg in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1177.
Use of uninitialized value $beg in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1177.
Use of uninitialized value $end in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1177.
Use of uninitialized value $struct in substr at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1177.
Use of uninitialized value $strand in string eq at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1010.
Use of uninitialized value $end in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1144.
Use of uninitialized value $beg in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1144.
Use of uninitialized value in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1148.
Use of uninitialized value $beg in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1148.
Use of uninitialized value $beg in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1151.
Use of uninitialized value $beg in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1151.
Use of uninitialized value $end in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1151.
Use of uninitialized value $seq in substr at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1151.
Use of uninitialized value $strand in string eq at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1154.

ended: 0:17:06
total:0h:0m:19s

Error:
    File mirdeep_runs/run_02_02_2022_t_21_56_29/output.mrd is empty

Now running miRDeep2_core_algorithm.pl with option -t to see why all precursors were discarded
Use of uninitialized value $db_old in hash element at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 743.
Use of uninitialized value $lng in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 749.
Use of uninitialized value $db_old in hash element at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 844.
Use of uninitialized value $db_old in hash element at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 845.
Use of uninitialized value $db_old in hash element at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 846.
Use of uninitialized value $query in hash element at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1101.
Use of uninitialized value $query in hash element at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1102.
Use of uninitialized value $query in hash element at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1091.
Use of uninitialized value $end in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1144.
Use of uninitialized value $beg in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1144.
Use of uninitialized value in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1148.
Use of uninitialized value $beg in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1148.
Use of uninitialized value $beg in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1151.
Use of uninitialized value $beg in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1151.
Use of uninitialized value $end in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1151.
Use of uninitialized value $seq in substr at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1151.
Use of uninitialized value $strand in string eq at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1154.
Use of uninitialized value $end in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1170.
Use of uninitialized value $beg in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1170.
Use of uninitialized value in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1174.
Use of uninitialized value $beg in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1174.
Use of uninitialized value $beg in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1177.
Use of uninitialized value $beg in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1177.
Use of uninitialized value $end in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1177.
Use of uninitialized value $struct in substr at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1177.
Use of uninitialized value $strand in string eq at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1010.
Use of uninitialized value $end in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1144.
Use of uninitialized value $beg in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1144.
Use of uninitialized value in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1148.
Use of uninitialized value $beg in numeric le (<=) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1148.
Use of uninitialized value $beg in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1151.
Use of uninitialized value $beg in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1151.
Use of uninitialized value $end in subtraction (-) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1151.
Use of uninitialized value $seq in substr at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1151.
Use of uninitialized value $strand in string eq at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1154.
Use of uninitialized value in transliteration (tr///) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1332.
Use of uninitialized value $hash_comp{"pri_seq"} in lc at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1333.
Use of uninitialized value $hash_comp{"pri_id"} in concatenation (.) or string at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1340.
Use of uninitialized value $hash_comp{"pri_seq"} in repeat (x) at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1407.
Use of uninitialized value $hash_comp{"pri_seq"} in lc at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1470.
Use of uninitialized value $hash_comp{"pri_struct"} in concatenation (.) or string at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1472.
Use of uninitialized value $lines in split at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1473.
Use of uninitialized value $skeys[0] in hash element at /home/INSA-LYON/rrebollo/miniconda3/envs/mirdeep2/bin/miRDeep2_core_algorithm.pl line 1491.
The debug file is called error.output.mrd_02_02_2022_t_21_56_29

Exiting now
mschilli87 commented 2 years ago

Sounds like an issue on your end to me. If I had to guess, I'd say you are running out of space on /tmp when writing temporary output files for more than 14 samples at a time.

RRebo commented 2 years ago

Yes I do think is an issue on my side too but unfortunately I don't know how to go about it. I searched for it and didn't find anything so thought I would post this here. I should mention I am not a bioinfo, starting slowly! Thanks.

mschilli87 commented 2 years ago

I'd avice contacting your local system administrator. There is nothing we could do for you I am afraid.