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alekseyzimin / masurca

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Could not parse delta file, /dev/stdin #4

Open rwhetten opened 6 years ago

rwhetten commented 6 years ago

MaSuRCA 2.3.1 running on Ubuntu 14.04 LTS produces work1 directory and super1.err output file, then reports "Refining alignments". The next output is "ERROR: Could not parse delta file, /dev/stdin", followed by "error no: 402", then by "rm: cannot remove 't..matches.0.maximal_mr.fa' - this continues for a series of tmp files numbered up to about 850

alekseyzimin commented 6 years ago

Please upgrade to MaSuRCA 3.2.4

kavonrtep commented 6 years ago

I am getting the same error with MaSuRCA-3.2.6 End of the output is:

ERROR: Could not parse delta file, /dev/stdin error no: 402 ERROR: Could not parse delta file, /dev/stdin error no: 402 ERROR: Could not parse delta file, /dev/stdin error no: 402 Joining refine/join alignments failed [Wed Jun 13 17:43:14 CEST 2018] Assembly stopped or failed, see CA.mr.41.15.15.0.02.log

I cannot however find CA.mr.41.15.15.0.02.log

alekseyzimin commented 6 years ago

Hi, please make sure the MaSuRCA installed/compiled properly; it is likely that MUMmer4 component of MaSuRCA failed to compile. Please re-run install.sh and capture both stdout and stderr and grep for "error".

On Wed, Jun 13, 2018 at 2:14 PM kavonrtep notifications@github.com wrote:

I am getting the same error with MaSuRCA-3.2.6 End of the output is:

ERROR: Could not parse delta file, /dev/stdin error no: 402 ERROR: Could not parse delta file, /dev/stdin error no: 402 ERROR: Could not parse delta file, /dev/stdin error no: 402 Joining refine/join alignments failed [Wed Jun 13 17:43:14 CEST 2018] Assembly stopped or failed, see CA.mr.41.15.15.0.02.log

I cannot however find CA.mr.41.15.15.0.02.log

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answer19831020 commented 6 years ago

Hi, I got the same error with MaSuRCA-3.2.7 compute_psa 5276493 16438176270 ERROR: failed to merge alignments at position 449 Please file a bug report ERROR: Could not parse delta file, /dev/stdin error no: 402 ERROR: Could not parse delta file, /dev/stdin error no: 402 I had set 200G, 16 threads and I check mummer in my install directory, it could work. I also check the memory usage: cpu=3297:36:29, mem=764714802.42013 GB s, io=12785.54210 GB, vmem=186.862G, maxvmem=189.205G cpu=4314:06:04, mem=1429661245.58854 GB s, io=15113.91274 GB, vmem=2.934G, maxvmem=189.205G

I installed the MaSuRCA-3.2.7 meet three error, "samtools, Soapdenovo-126mer, Soadenovo-63mer" and I had copy compiled binary file to the bin directory.

collect2: error: ld returned 1 exit status make[1]: *** [samtools] Error 1

/usr/bin/ld: cannot find -lbam collect2: error: ld returned 1 exit status /usr/bin/ld: cannot find -lbam collect2: error: ld returned 1 exit status make[1]: [SOAPdenovo-127mer] Error 1 make[1]: Waiting for unfinished jobs.... make[1]: *** [SOAPdenovo-63mer] Error 1