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plagnollab / DNASeq_pipeline

Pipeline in place at the UGI for DNA level analysis
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Error: Stale NFS file handle #10

Closed pontikos closed 9 years ago

pontikos commented 9 years ago 
[rmhanpo@pchuckle:~/IBDAJE/1410AHP-0004_ElenaSchiff_211samples]$ cat Project_1410AHP-0004_ElenaSchiff_211samples/align/err/align_133_*_2488063.err
+ echo Project_1410AHP-0004_ElenaSchiff_211samples/align/scripts/align_133.sh
+ bash Project_1410AHP-0004_ElenaSchiff_211samples/align/scripts/align_133.sh
samblaster: Version 0.1.20
samblaster: Inputting from stdin
samblaster: Outputting to stdout
samblaster: Opening Project_1410AHP-0004_ElenaSchiff_211samples/align/data//133_disc.sam for write.
# novoalign (V3.02.08 - Build Oct 16 2014 @ 13:03:59 - A short read aligner with qualities.
# (C) 2008,2009,2010,2011 NovoCraft Technologies Sdn Bhd.
# License file: /cluster/project8/vyp/vincent/Software/novocraft3/novoalign.lic
# Licensed to UCL
#  novoalign -c 6 -o SAM @RG    ID:Levine_133   SM:Levine_133   LB:Levine_133   PL:ILLUMINA --rOQ --hdrhd 3 -H -k -a -o Soft -t 320 -F STDFQ -f /goon2/project99/IBDAJE_raw/1410AHP-0004_ElenaSchiff_211samples/133_1.fastq.gz /goon2/project99/IBDAJE_raw/1410AHP-0004_ElenaSchiff_211samples/133_2.fastq.gz -d /scratch2/vyp-scratch2/reference_datasets/human_reference_sequence/human_g1k_v37.fasta.k15.s2.novoindex
# Starting at Mon Dec 29 06:20:46 2014
# Interpreting input files as Sanger FASTQ.
# Index Build Version: 2.7
# Hash length: 15
# Step size: 2
samblaster: Loaded 84 header sequence entries.
File /goon2/project99/IBDAJE_raw/1410AHP-0004_ElenaSchiff_211samples/133_1.fastq.gz : Sequence and Qualities have different lengths at line 23271034.
Hdr:@HISEQ-MFG:427:HB553ADXX:2:1116:5097:66162 1:N:0:ACTTGA
#       Paired Reads:  5817758
#       Proper Pairs:  5594808 (96.2%)
#     Read Sequences: 11635516
#   Unique Alignment: 11290362 (97.0%)
#       Multi Mapped:   117836 ( 1.0%)
#   No Mapping Found:   212561 ( 1.8%)
# QC Failures...
# Homopolymer Filter:       80 ( 0.0%)
#        Read Length:    14677 ( 0.1%)
#       Elapsed Time: 2193.824 (secs.)
#           CPU Time: 200.46 (min.)
# Fragment Length Distribution
#   From    To  Count
#   15  29  4
#   30  44  307
#   45  59  3780
#   60  74  21257
#   75  89  126887
#   90  104 548136
#   105 119 1174070
#   120 134 1469478
#   135 149 1074709
#   150 164 565178
#   165 179 253815
#   180 194 111894
#   195 209 57786
#   210 224 34482
#   225 239 22081
#   240 254 14701
#   255 269 9772
#   270 284 6556
#   285 299 4115
#   300 314 19
#   315 329 1
#   330 344 1
# Mean   131, Std Dev  27.5
# Done at Mon Dec 29 06:57:22 2014
samblaster: Output 73229 discordant read pairs to Project_1410AHP-0004_ElenaSchiff_211samples/align/data//133_disc.sam
samblaster: Marked 893282 of 5817758 (15.35%) read ids as duplicates using 96060k memory in 20.764S CPU seconds and 36M37S(2197S) wall time.
# novosort (V1.03.02) - Build Oct 16 2014 @ 13:03:59
# (C) 2012 NovoCraft Technologies Sdn Bhd.
# /cluster/project8/vyp/vincent/Software/novocraft3/novosort - -t /scratch2/vyp-scratch2/vincent/temp/novoalign/133 -c 6 -m 7G -i -o Project_1410AHP-0004_ElenaSchiff_211samples/align/data//133_disc_sorted.bam
# License file: /cluster/project8/vyp/vincent/Software/novocraft3/novoalign.lic
# Licensed to UCL
# Worker Threads: 6
#   Sort Buffers: 7
# Process Headers..
# File -
# Sort Phase..
# File -, 146458 alignment records
Error: Unable to create temporary file /scratch2/vyp-scratch2/vincent/temp/novoalign/133/sorttmpfPTYGw - Stale NFS file handle# novosort (V1.03.02) - Build Oct 16 2014 @ 13:03:59
# (C) 2012 NovoCraft Technologies Sdn Bhd.
# /cluster/project8/vyp/vincent/Software/novocraft3/novosort -t /scratch2/vyp-scratch2/vincent/temp/novoalign/133 -c 6 -m 7G -i -o Project_1410AHP-0004_ElenaSchiff_211samples/align/data//133_sorted_unique.bam Project_1410AHP-0004_ElenaSchiff_211samples/align/data//133.bam
# License file: /cluster/project8/vyp/vincent/Software/novocraft3/novoalign.lic
# Licensed to UCL
# Worker Threads: 6
#   Sort Buffers: 7
# Process Headers..
# File Project_1410AHP-0004_ElenaSchiff_211samples/align/data//133.bam
# Sort Phase..
Error: Unable to create temporary file /scratch2/vyp-scratch2/vincent/temp/novoalign/133/sorttmpOm3FlV - Stale NFS file handle
vplagnol commented 9 years ago

NFS issues are the ones we can't fix. Some issues with the server, mostly scratch2 access (usually...). I don't have a solution for these, it's the IO failing.

On Mon, Dec 29, 2014 at 11:16 AM, Nikolas Pontikos <notifications@github.com

wrote:

[rmhanpo@pchuckle:~/IBDAJE/1410AHP-0004_ElenaSchiff_211samples]$ cat Project_1410AHP-0004_ElenaSchiff_211samples/align/err/align133*_2488063.err

  • echo Project_1410AHP-0004_ElenaSchiff_211samples/align/scripts/align_133.sh
  • bash Project_1410AHP-0004_ElenaSchiff_211samples/align/scripts/align_133.sh samblaster: Version 0.1.20 samblaster: Inputting from stdin samblaster: Outputting to stdout samblaster: Opening Project_1410AHP-0004_ElenaSchiff_211samples/align/data//133_disc.sam for write.

    novoalign (V3.02.08 - Build Oct 16 2014 @ 13:03:59 - A short read aligner with qualities.

    (C) 2008,2009,2010,2011 NovoCraft Technologies Sdn Bhd.

    License file: /cluster/project8/vyp/vincent/Software/novocraft3/novoalign.lic

    Licensed to UCL

    novoalign -c 6 -o SAM @RG ID:Levine_133 SM:Levine_133 LB:Levine_133 PL:ILLUMINA --rOQ --hdrhd 3 -H -k -a -o Soft -t 320 -F STDFQ -f /goon2/project99/IBDAJE_raw/1410AHP-0004_ElenaSchiff_211samples/133_1.fastq.gz /goon2/project99/IBDAJE_raw/1410AHP-0004_ElenaSchiff_211samples/133_2.fastq.gz -d /scratch2/vyp-scratch2/reference_datasets/human_reference_sequence/human_g1k_v37.fasta.k15.s2.novoindex

    Starting at Mon Dec 29 06:20:46 2014

    Interpreting input files as Sanger FASTQ.

    Index Build Version: 2.7

    Hash length: 15

    Step size: 2

    samblaster: Loaded 84 header sequence entries. File /goon2/project99/IBDAJE_raw/1410AHP-0004_ElenaSchiff_211samples/133_1.fastq.gz : Sequence and Qualities have different lengths at line 23271034. Hdr:@HISEQ-MFG:427:HB553ADXX:2:1116:5097:66162 1:N:0:ACTTGA

    Paired Reads: 5817758

    Proper Pairs: 5594808 (96.2%)

    Read Sequences: 11635516

    Unique Alignment: 11290362 (97.0%)

    Multi Mapped: 117836 ( 1.0%)

    No Mapping Found: 212561 ( 1.8%)

    QC Failures...

    Homopolymer Filter: 80 ( 0.0%)

    Read Length: 14677 ( 0.1%)

    Elapsed Time: 2193.824 (secs.)

    CPU Time: 200.46 (min.)

    Fragment Length Distribution

    From To Count

    15 29 4

    30 44 307

    45 59 3780

    60 74 21257

    75 89 126887

    90 104 548136

    105 119 1174070

    120 134 1469478

    135 149 1074709

    150 164 565178

    165 179 253815

    180 194 111894

    195 209 57786

    210 224 34482

    225 239 22081

    240 254 14701

    255 269 9772

    270 284 6556

    285 299 4115

    300 314 19

    315 329 1

    330 344 1

    Mean 131, Std Dev 27.5

    Done at Mon Dec 29 06:57:22 2014

    samblaster: Output 73229 discordant read pairs to Project_1410AHP-0004_ElenaSchiff_211samples/align/data//133_disc.sam samblaster: Marked 893282 of 5817758 (15.35%) read ids as duplicates using 96060k memory in 20.764S CPU seconds and 36M37S(2197S) wall time.

    novosort (V1.03.02) - Build Oct 16 2014 @ 13:03:59

    (C) 2012 NovoCraft Technologies Sdn Bhd.

    /cluster/project8/vyp/vincent/Software/novocraft3/novosort - -t /scratch2/vyp-scratch2/vincent/temp/novoalign/133 -c 6 -m 7G -i -o Project_1410AHP-0004_ElenaSchiff_211samples/align/data//133_disc_sorted.bam

    License file: /cluster/project8/vyp/vincent/Software/novocraft3/novoalign.lic

    Licensed to UCL

    Worker Threads: 6

    Sort Buffers: 7

    Process Headers..

    File -

    Sort Phase..

    File -, 146458 alignment records

    Error: Unable to create temporary file /scratch2/vyp-scratch2/vincent/temp/novoalign/133/sorttmpfPTYGw - Stale NFS file handle# novosort (V1.03.02) - Build Oct 16 2014 @ 13:03:59

    (C) 2012 NovoCraft Technologies Sdn Bhd.

    /cluster/project8/vyp/vincent/Software/novocraft3/novosort -t /scratch2/vyp-scratch2/vincent/temp/novoalign/133 -c 6 -m 7G -i -o Project_1410AHP-0004_ElenaSchiff_211samples/align/data//133_sorted_unique.bam Project_1410AHP-0004_ElenaSchiff_211samples/align/data//133.bam

    License file: /cluster/project8/vyp/vincent/Software/novocraft3/novoalign.lic

    Licensed to UCL

    Worker Threads: 6

    Sort Buffers: 7

    Process Headers..

    File Project_1410AHP-0004_ElenaSchiff_211samples/align/data//133.bam

    Sort Phase..

    Error: Unable to create temporary file /scratch2/vyp-scratch2/vincent/temp/novoalign/133/sorttmpOm3FlV - Stale NFS file handle

— Reply to this email directly or view it on GitHub https://github.com/vplagnol/pipelines/issues/10.

Vincent Plagnol University College London Genetics Institute Darwin building, office 210 Gower Street, London, WC1E 6BT Cell: +44-(0)7946-546923 Office: +44-(0) 2031-084002 Website: http://www.ucl.ac.uk/ugi/research/vincentplagnol Lab blog: http://plagnol-lab.blogspot.co.uk/