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It tells me that "Hash value of best assembly by assembly score: 89", however, goes on to fail during the looking for expected coverage with this error message:
Use of uninitialized value in numeric ne (!=) at /home/tntech.edu/hpalk42/.conda/envs/Velvet/bin/VelvetOptimiser.pl line 283.
Use of uninitialized value in numeric gt (>) at /home/tntech.edu/hpalk42/.conda/envs/Velvet/bin/VelvetOptimiser.pl line 284.
Use of uninitialized value in numeric ne (!=) at /home/tntech.edu/hpalk42/.conda/envs/Velvet/bin/VelvetOptimiser.pl line 283.
Use of uninitialized value $maxScore in numeric gt (>) at /home/tntech.edu/hpalk42/.conda/envs/Velvet/bin/VelvetOptimiser.pl line 284.
Use of uninitialized value in numeric gt (>) at /home/tntech.edu/hpalk42/.conda/envs/Velvet/bin/VelvetOptimiser.pl line 284.
Use of uninitialized value in numeric ne (!=) at /home/tntech.edu/hpalk42/.conda/envs/Velvet/bin/VelvetOptimiser.pl line 283.
Use of uninitialized value $maxScore in numeric gt (>) at /home/tntech.edu/hpalk42/.conda/envs/Velvet/bin/VelvetOptimiser.pl line 284.
Use of uninitialized value in numeric gt (>) at /home/tntech.edu/hpalk42/.conda/envs/Velvet/bin/VelvetOptimiser.pl line 284.
Use of uninitialized value in numeric ne (!=) at /home/tntech.edu/hpalk42/.conda/envs/Velvet/bin/VelvetOptimiser.pl line 283.
Use of uninitialized value $maxScore in numeric gt (>) at /home/tntech.edu/hpalk42/.conda/envs/Velvet/bin/VelvetOptimiser.pl line 284.
Use of uninitialized value in numeric gt (>) at /home/tntech.edu/hpalk42/.conda/envs/Velvet/bin/VelvetOptimiser.pl line 284.
Jul 19 16:05:53 Hash value of best assembly by assembly score: 89
Jul 19 16:05:53 Optimisation routine chosen for best assembly: shortPaired
Jul 19 16:05:53 Looking for the expected coverage
Unable to open /home/tntech.edu/hpalk42/FastQC/interleaved/auto_data_89/stats.txt for exp_cov determination.
at /home/tntech.edu/hpalk42/.conda/envs/Velvet/bin/VelvetOptimiser.pl line 832.
It also says this EARLIER in the error file: Velveth failed! Response:
1
Jul 19 16:05:30 Velveth with hash value 149 finished.
Velveth failed! Response:
1
Jul 19 16:05:39 Velveth with hash value 89 finished.
Velveth failed! Response:
1
Jul 19 16:05:42 Velveth with hash value 109 finished.
Velveth failed! Response:
1
Jul 19 16:05:44 Velveth with hash value 129 finished.
Is there a way to fix this error? Thank you very much, I have attached the entire error file in case that would help. VelvetErrorFile.txt
!
The text was updated successfully, but these errors were encountered:
I am attempting to use VelvetOptimiser on my short read, paired genome sequences. Using this command:
VelvetOptimiser.pl -s 89 -e 149 -x 20 -f '-shortPaired -fastq interleaved.fastq' -t ${SLURM_CPUS_PER_TASK}
It tells me that "Hash value of best assembly by assembly score: 89", however, goes on to fail during the looking for expected coverage with this error message:
Use of uninitialized value in numeric ne (!=) at /home/tntech.edu/hpalk42/.conda/envs/Velvet/bin/VelvetOptimiser.pl line 283.
Use of uninitialized value in numeric gt (>) at /home/tntech.edu/hpalk42/.conda/envs/Velvet/bin/VelvetOptimiser.pl line 284.
Use of uninitialized value in numeric ne (!=) at /home/tntech.edu/hpalk42/.conda/envs/Velvet/bin/VelvetOptimiser.pl line 283.
Use of uninitialized value $maxScore in numeric gt (>) at /home/tntech.edu/hpalk42/.conda/envs/Velvet/bin/VelvetOptimiser.pl line 284.
Use of uninitialized value in numeric gt (>) at /home/tntech.edu/hpalk42/.conda/envs/Velvet/bin/VelvetOptimiser.pl line 284.
Use of uninitialized value in numeric ne (!=) at /home/tntech.edu/hpalk42/.conda/envs/Velvet/bin/VelvetOptimiser.pl line 283.
Use of uninitialized value $maxScore in numeric gt (>) at /home/tntech.edu/hpalk42/.conda/envs/Velvet/bin/VelvetOptimiser.pl line 284.
Use of uninitialized value in numeric gt (>) at /home/tntech.edu/hpalk42/.conda/envs/Velvet/bin/VelvetOptimiser.pl line 284.
Use of uninitialized value in numeric ne (!=) at /home/tntech.edu/hpalk42/.conda/envs/Velvet/bin/VelvetOptimiser.pl line 283.
Use of uninitialized value $maxScore in numeric gt (>) at /home/tntech.edu/hpalk42/.conda/envs/Velvet/bin/VelvetOptimiser.pl line 284.
Use of uninitialized value in numeric gt (>) at /home/tntech.edu/hpalk42/.conda/envs/Velvet/bin/VelvetOptimiser.pl line 284.
Jul 19 16:05:53 Hash value of best assembly by assembly score: 89
Jul 19 16:05:53 Optimisation routine chosen for best assembly: shortPaired
Jul 19 16:05:53 Looking for the expected coverage
Unable to open /home/tntech.edu/hpalk42/FastQC/interleaved/auto_data_89/stats.txt for exp_cov determination.
at /home/tntech.edu/hpalk42/.conda/envs/Velvet/bin/VelvetOptimiser.pl line 832.
It also says this EARLIER in the error file:
Velveth failed! Response:
1
Jul 19 16:05:30 Velveth with hash value 149 finished.
Velveth failed! Response:
1
Jul 19 16:05:39 Velveth with hash value 89 finished.
Velveth failed! Response:
1
Jul 19 16:05:42 Velveth with hash value 109 finished.
Velveth failed! Response:
1
Jul 19 16:05:44 Velveth with hash value 129 finished.
Is there a way to fix this error? Thank you very much, I have attached the entire error file in case that would help.
VelvetErrorFile.txt
!
The text was updated successfully, but these errors were encountered: