Eu tenho o seguinte script .sh no qual estou tentando fazer todos os principais trabalhos em $ TMPDIR.
No entanto, quando chega à linha 86, retorna o seguinte erro:
/var/spool/uge/bnbhimem2/job_scripts/855849: line 86: /tmp/uge/855849.2.primary.q//tmp/uge/855849.2.primary.q/Alignments_2304_Header.sam: No such file or directory
/var/spool/uge/bnbhimem2/job_scripts/855849: line 86: /tmp/uge/855849.2.primary.q//tmp/uge/855849.2.primary.q/Alignments_2107_Header.sam: No such file or directory
/var/spool/uge/bnbhimem2/job_scripts/855849: line 86: /tmp/uge/855849.2.primary.q//tmp/uge/855849.2.primary.q/Alignments_1209_Header.sam: No such file or directory
/var/spool/uge/bnbhimem2/job_scripts/855849: line 86: /tmp/uge/855849.2.primary.q//tmp/uge/855849.2.primary.q/Alignments_1301_Header.sam: No such file or directory
/var/spool/uge/bnbhimem2/job_scripts/855849: line 86: /tmp/uge/855849.2.primary.q//tmp/uge/855849.2.primary.q/Alignments_2115_Header.sam: No such file or directory
/var/spool/uge/bnbhimem2/job_scripts/855849: line 86: /tmp/uge/855849.2.primary.q//tmp/uge/855849.2.primary.q/Alignments_2210_Header.sam: No such file or directory
/var/spool/uge/bnbhimem2/job_scripts/855849: line 86: /tmp/uge/855849.2.primary.q//tmp/uge/855849.2.primary.q/Alignments_2307_Header.sam: No such file or directory
/var/spool/uge/bnbhimem2/job_scripts/855849: line 86: /tmp/uge/855849.2.primary.q//tmp/uge/855849.2.primary.q/Alignments_2302_Header.sam: No such file or directory
/var/spool/uge/bnbhimem2/job_scripts/855849: line 86: /tmp/uge/855849.2.primary.q//tmp/uge/855849.2.primary.q/Alignments_2303_Header.sam: No such file or directory
/var/spool/uge/bnbhimem2/job_scripts/855849: line 86: /tmp/uge/855849.2.primary.q//tmp/uge/855849.2.primary.q/Alignments_1306_Header.sam: No such file or directory
/var/spool/uge/bnbhimem2/job_scripts/855849: line 86: /tmp/uge/855849.2.primary.q//tmp/uge/855849.2.primary.q/Alignments_1115_Header.sam: No such file or directory
/var/spool/uge/bnbhimem2/job_scripts/855849: line 86: /tmp/uge/855849.2.primary.q//tmp/uge/855849.2.primary.q/Alignments_1110_Header.sam: No such file or directory
/var/spool/uge/bnbhimem2/job_scripts/855849: line 86: /tmp/uge/855849.2.primary.q//tmp/uge/855849.2.primary.q/Alignments_1204_Header.sam: No such file or directory
/var/spool/uge/bnbhimem2/job_scripts/855849: line 86: /tmp/uge/855849.2.primary.q//tmp/uge/855849.2.primary.q/Alignments_2214_Header.sam: No such file or directory
/var/spool/uge/bnbhimem2/job_scripts/855849: line 86: /tmp/uge/855849.2.primary.q//tmp/uge/855849.2.primary.q/Alignments_2308_Header.sam: No such file or directory
Eu pensei que este arquivo deveria ser criado com a saída de cat, por que está reclamando que ele não existe?
Obrigado Carmen
1 #!/bin/sh
2
3 ##Usage: run_Split_by_Tile_AWK.sh [0-7]
4
5 # Run on the current working directory
6 #$ -cwd
7 # Give this job a name
8 #$ -N Split_by_Tile_AWK
9 # Join standard output and error to a single file
10 #$ -j y
11 # Name the file where to redirect standard output and error
12 ## -o AWK_Split_by_Tile
13 # Send an email when the job begins and when it ends running
14 #$ -m be
15 # Whom to send the email to
16 #$ -M [email protected]
17 # Local disk space and memory necessary
18 ## –l tmp_free=900G
19 #$ -l m_mem_free=400G
20 # Array job options
21 #$ -t 1-8
22
23 # Now let's keep track of some information just in case anything goes wrong.
24
25 echo "=========================================================="
26 echo "Starting on : $(date)"
27 echo "Running on node : $(hostname)"
28 echo "Current directory : $(pwd)"
29 echo "Current job ID : $JOB_ID"
30 echo "Current job name : $JOB_NAME"
31 echo "Task index number : $SGE_TASK_ID"
32 echo "=========================================================="
33
34 # Run some commands
35
36 export PATH=/opt/hpc/bin:$PATH
37 export PATH=$HOME/bin:$PATH
38
39 parent_tophat=/data/bsr/tforcier/tophat_results
40
41 folder_array=(tophat_WTyoungRep1take2_out tophat_WTyoungRep2_out tophat_WToldRep1_out tophat_WToldRep2take2_out tophat_Ago2youngRep1take2_out tophat_Ago2youngRep2_out tophat_Ago2oldRep1_out tophat_Ago 2oldRep2_out)
42
43 i=$(($SGE_TASK_ID - 1))
44
45 ##Build input
46
47 input=$parent_tophat/${folder_array[$i]}/accepted_hits.bam
48
49 ##Make output base name
50
51 y=${folder_array[$i]#tophat_}
52
53 outputBase=${y%_out}
54
55 ##outputBase ~=Ago2youngRep1take2 or ~=WTyoungRep2##
56
57 cp $input $TMPDIR/$outputBase.bam
58
59 temporal_input=$TMPDIR/$outputBase.bam
60
61 cp /data/bsr/csandova/mRNA_Seq/TileLists/Tile_Number_List.txt $TMPDIR/Tile_Number_List.txt
62
63 mkdir -v $outputBase\_Split
64
65 newDir=$outputBase\_Split
66
67 ##newDir ~=Ago2youngRep1take2_Split or ~=WTyoungRep2_Split##
68
69
70 #Process BAM files
71
72 samtools view $temporal_input | awk -F '[\t:]' -v opath="$TMPDIR" '
73
74 FNR == NR {
75 num[$1]
76 next
77 }
78
79 $5 in num {
80 f = opath"/Alignments_"$5".sam";
81 print > f
82 } ' $TMPDIR/Tile_Number_List.txt -
83
84 for x in $(find $TMPDIR -name '*.sam'); do
85
86 cat SAMHeader.txt $x >$TMPDIR/${x%.sam}_Header.sam;
87
88 rm $x;
89
90 done
91
92 for x in $(find $TMPDIR -name '*_Header.sam');
93
94 do samtools view -bS $x | samtools sort - $newDir/${x%.sam}.bam ;
95
96 done
A mensagem de erro
No such file or directory
significa que o diretório em que você está tentando criar o arquivo não existe.
O problema é que
for x in $(find $TMPDIR -name '*.sam'); do
já armazena o caminho completo na variável x , então você tem que usar
cat SAMHeader.txt $x > ${x%.sam}_Header.sam
em vez de
cat SAMHeader.txt $x > $TMPDIR/${x%.sam}_Header.sam