Hello,
I have received from my lab one HiSeq flowcell with 7 lanes single indexed and the 8th is dual indexed.
Something goes wrong during the computation.
Since I would like to put the use-base-mask argument, I prepared a truncated sample sheet for the first 7 lanes, and launched with my always working script with the argument --use-bases-mask Y101,I6N,Y101.
The program complains that it is not what it found in the conf files :
...and a little later...
And the last lines of my log:
...and it stops right here, with no other explanation.
For info :
Any idea that could help?
Cheers!
I have received from my lab one HiSeq flowcell with 7 lanes single indexed and the 8th is dual indexed.
Something goes wrong during the computation.
Since I would like to put the use-base-mask argument, I prepared a truncated sample sheet for the first 7 lanes, and launched with my always working script with the argument --use-bases-mask Y101,I6N,Y101.
The program complains that it is not what it found in the conf files :
Code:
$ grep -i warning run.err [2015-02-17 16:03:15] [configureBclToFastq.pl] WARNING: No sample sheet data for lane '8'. Skipping lane. [2015-02-17 16:03:15] [configureBclToFastq.pl] WARNING: use-base-mask length is 7 for read 2: expected length from config file is 8 [2015-02-17 16:03:15] [configureBclToFastq.pl] WARNING: Read 3: current cycle in mask is 109: first cycle in read is 110 [2015-02-17 16:03:15] [configureBclToFastq.pl] WARNING: use-base-mask length is 101 for read 3: expected length from config file is 8 [2015-02-17 16:03:15] [configureBclToFastq.pl] WARNING: Read 4: current cycle in mask is 210: first cycle in read is 118 [2015-02-17 16:03:15] [configureBclToFastq.pl] WARNING: use-base-mask length is 7 for read 2: expected length from config file is 8 [2015-02-17 16:03:15] [configureBclToFastq.pl] WARNING: Read 3: current cycle in mask is 109: first cycle in read is 110 [2015-02-17 16:03:15] [configureBclToFastq.pl] WARNING: use-base-mask length is 101 for read 3: expected length from config file is 8 [2015-02-17 16:03:15] [configureBclToFastq.pl] WARNING: Read 4: current cycle in mask is 210: first cycle in read is 118
Code:
$ grep -i error run.err [2015-02-17 16:07:56] [r103-n67] [Temp/L003_R3_demux_summary.xml] Error: 2015-Feb-17 16:07:53: No such file or directory: /tmp/bcl2fastq-1.8.4/src/c++/lib/alignment/BclReader.cpp(87): Throw in function unsigned int casava::alignment::BclReader::readClusterCount() make: *** [Temp/L003_R3_demux_summary.xml] Error 1 [2015-02-17 16:07:56] [r103-n67] [Temp/L006_R3_demux_summary.xml] Error: 2015-Feb-17 16:07:53: No such file or directory: /tmp/bcl2fastq-1.8.4/src/c++/lib/alignment/BclReader.cpp(87): Throw in function unsigned int casava::alignment::BclReader::readClusterCount() make: *** [Temp/L006_R3_demux_summary.xml] Error 1
Code:
tail run.err [2015-02-17 17:21:29] [r103-n67] [Temp/L004_R2_demux_summary.xml] /run/Data/Intensities/BaseCalls/L004/C105.1/s_4_2316.bcl.gz [2015-02-17 17:21:29] [r103-n67] [Temp/L004_R2_demux_summary.xml] /run/Data/Intensities/BaseCalls/L004/C106.1/s_4_2316.bcl.gz [2015-02-17 17:21:29] [r103-n67] [Temp/L004_R2_demux_summary.xml] /run/Data/Intensities/BaseCalls/L004/C107.1/s_4_2316.bcl.gz [2015-02-17 17:21:31] [r103-n67] [Temp/L004_R2_demux_summary.xml] mapClusterBarcodes: barcode/clusters: [2015-02-17 17:21:31] [r103-n67] [Temp/L004_R2_demux_summary.xml] /run/Demultiplexed_2015-02-17/Undetermined_indices/Sample_lane4:Undetermined:277429 [2015-02-17 17:21:31] [r103-n67] [Temp/L004_R2_demux_summary.xml] /run/Demultiplexed_2015-02-17/Project_run/Sample_15:ACTTGA:635531 [2015-02-17 17:21:31] [r103-n67] [Temp/L004_R2_demux_summary.xml] /run/Demultiplexed_2015-02-17/Project_run/Sample_87:ACAGTG:639074 [2015-02-17 17:21:31] [r103-n67] [Temp/L004_R2_demux_summary.xml] /run/Demultiplexed_2015-02-17/Project_run/Sample_55:GCCAAT:1036142 [2015-02-17 17:21:31] [r103-n67] [Temp/L004_R2_demux_summary.xml] /run/Demultiplexed_2015-02-17/Project_run/Sample_25:CAGATC:790545 [2015-02-17 17:21:31] [r103-n67] [Temp/L004_R2_demux_summary.xml] Processing BCL files for lane 4, tile 2316, read 2
For info :
Code:
$ grep Read run/RunInfo.xml <Reads> <Read Number="1" NumCycles="101" IsIndexedRead="N" /> <Read Number="2" NumCycles="8" IsIndexedRead="Y" /> <Read Number="3" NumCycles="8" IsIndexedRead="Y" /> <Read Number="4" NumCycles="101" IsIndexedRead="N" /> </Reads>
Any idea that could help?
Cheers!
Comment