ValueError: Length mismatch: Expected axis has 0 elements ... about syri HOT 7 CLOSED

Hi. This issue is probably happening because of the BAM file format description which limits the chromosome size.
I will add a new reader for SAM files in some days, which I think should resolve this issue. Till then, could you please try using mummer3? It is slower than mummer4, but is more memory efficient and would bypass this issue.

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Hi. SyRI now reads SAM files directly and should work with large genomes.

from syri.

Hi,
Thanks for looking into this.
Unfortunately, I tried to resubmit with the sam file and now i return to this issue:

2020-08-20 11:04:53,669 - Running SyRI - WARNING - :135 - Using pandas version: 0.18.0. Expected vesion: 0.23.4. This might result in unexpected errors.
2020-08-20 11:04:53,682 - Running SyRI - DEBUG - :136 - Python and Pandas version are ok
2020-08-20 11:04:55,347 - Reading Coords - DEBUG - :163 - S
2020-08-20 11:04:55,348 - Reading Coords - INFO - :163 - Reading input from SAM file
2020-08-20 11:05:18,105 - Reading BAM/SAM file - ERROR - :163 - Error in reading BAM/SAM file. truncated file

I successfully converted to bam format so it is not the case that this is truncated.
Can you reopen my original issue with submitting a BAM as input.
Thank you.

from syri.

Hi. The error message is unexpected for SAM files. Is this happening with all SAM files or just one specific SAM file? Would it be possible to share a sample SAM file for me to test?

from syri.

Hi! I am actually having the same problem as mentioned here. How was this issue finally resolved? Thanks!

from syri.

Hi. I assume that you are talking about the issue with truncated file..
I did not receive any message, so I thought that this issue is fixed. Anyway, I think this has something to do with your specific SAM files as it is not happening to other people.

Have you tried the example analysis did it work? Also, how did you create the input file? Is it SAM or BAM? Is the issue happening with only one specific file or always?

If possible, could you test if you can read the SAM/BAM file with pysam?

from syri.

Hi, sorry because my first message was very vague. Let me explain it a little more in detail. Firstly, I had no problem in reproducing the example analysis. It just worked as expected. Then, I tried to run the protocol on my own genomes. I have different genome assemblies that I want to compare to the current reference, but none of these is at the chromosome level and have varying numbers of scaffolds. I aligned each of my queries independently to the reference using minimap2, and then tried to call the SR using SyRI, with the following parameters:

./syri/bin/syri -c path/to/sam -r path/to/reference -q path/to/query -F S -k -f --no-chrmatch

SyRI started running, it reported that the reference and the query have different number of scaffolds and some were not aligned, and continued to run until it crashed. The error message as follows:

SAM reader - WARNING - A1_scaffold0151 do not align with any reference sequence and cannot be analysed. Remove all unplaced scaffolds and contigs from the assemblies.
Reading Coords - WARNING - Chromosomes IDs do not match.
Reading Coords - WARNING - --no-chrmatch is set. Not matching chromosomes automatically.
Reading Coords - WARNING - BDIQ01000126.1, BDIQ01000179.1, BDIQ01000057.1, BDIQ01000041.1, BDIQ01000183.1, BDIQ01000086.1, BDIQ01000074.1, BDIQ01000107.1, BDIQ01000051.1, BDIQ01000167.1, BDIQ01000205.1, BDIQ01000152.1, BDIQ01000040.1, BDIQ01000030.1, BDIQ01000163.1, BDIQ01000135.1, BDIQ01000080.1, BDIQ01000117.1, BDIQ01000116.1, BDIQ01000088.1, BDIQ01000136.1, BDIQ01000169.1, BDIQ01000038.1, BDIQ01000055.1, BDIQ01000171.1, BDIQ01000160.1, BDIQ01000028.1, BDIQ01000193.1, BDIQ01000067.1, BDIQ01000191.1, BDIQ01000132.1, BDIQ01000014.1, BDIQ01000130.1, BDIQ01000121.1, BDIQ01000144.1, BDIQ01000024.1, BDIQ01000134.1, BDIQ01000139.1, BDIQ01000185.1, BDIQ01000058.1, BDIQ01000129.1, BDIQ01000032.1, BDIQ01000123.1, BDIQ01000063.1, BDIQ01000166.1, BDIQ01000035.1, BDIQ01000190.1, BDIQ01000102.1, BDIQ01000095.1, BDIQ01000076.1, BDIQ01000100.1, BDIQ01000125.1, BDIQ01000112.1, BDIQ01000006.1, BDIQ01000174.1, BDIQ01000178.1, BDIQ01000085.1, BDIQ01000011.1, BDIQ01000090.1, BDIQ01000151.1, BDIQ01000066.1, BDIQ01000108.1, BDIQ01000013.1, BDIQ01000017.1, BDIQ01000061.1, BDIQ01000098.1, BDIQ01000031.1, BDIQ01000198.1, BDIQ01000075.1, BDIQ01000137.1, BDIQ01000048.1, BDIQ01000156.1, BDIQ01000147.1, BDIQ01000127.1, BDIQ01000054.1, BDIQ01000164.1, BDIQ01000060.1, BDIQ01000081.1, BDIQ01000170.1, BDIQ01000012.1, BDIQ01000010.1, BDIQ01000068.1, BDIQ01000165.1, BDIQ01000184.1, BDIQ01000016.1, BDIQ01000050.1, BDIQ01000131.1, BDIQ01000077.1, BDIQ01000020.1, BDIQ01000042.1, BDIQ01000140.1, BDIQ01000158.1, BDIQ01000097.1, BDIQ01000168.1, BDIQ01000180.1, BDIQ01000105.1, BDIQ01000138.1, BDIQ01000022.1, BDIQ01000089.1, BDIQ01000122.1, BDIQ01000197.1, BDIQ01000161.1, BDIQ01000096.1, BDIQ01000047.1, BDIQ01000146.1, BDIQ01000128.1, BDIQ01000201.1, BDIQ01000001.1, BDIQ01000007.1, BDIQ01000194.1, BDIQ01000154.1, BDIQ01000091.1, BDIQ01000188.1, BDIQ01000120.1, BDIQ01000149.1, BDIQ01000083.1, BDIQ01000109.1, BDIQ01000079.1, BDIQ01000043.1, BDIQ01000143.1, BDIQ01000059.1, BDIQ01000114.1, BDIQ01000070.1, BDIQ01000118.1, BDIQ01000056.1, BDIQ01000033.1, BDIQ01000115.1, BDIQ01000025.1, BDIQ01000052.1, BDIQ01000093.1, BDIQ01000141.1, BDIQ01000199.1, BDIQ01000133.1, BDIQ01000065.1, BDIQ01000071.1, BDIQ01000195.1, BDIQ01000053.1, BDIQ01000039.1, BDIQ01000177.1, BDIQ01000073.1, BDIQ01000162.1, BDIQ01000192.1, BDIQ01000082.1, BDIQ01000034.1, BDIQ01000159.1, BDIQ01000101.1, BDIQ01000106.1, BDIQ01000157.1, BDIQ01000046.1, BDIQ01000145.1, BDIQ01000124.1, BDIQ01000111.1, BDIQ01000148.1, BDIQ01000104.1, BDIQ01000153.1, BDIQ01000150.1, BDIQ01000155.1, BDIQ01000002.1, BDIQ01000187.1, BDIQ01000196.1, BDIQ01000062.1, BDIQ01000078.1, BDIQ01000173.1, BDIQ01000186.1, BDIQ01000110.1, BDIQ01000027.1, BDIQ01000182.1, BDIQ01000021.1, BDIQ01000044.1, BDIQ01000172.1, BDIQ01000023.1, BDIQ01000064.1, BDIQ01000092.1, A1_scaffold0145, A1_scaffold0028, A1_scaffold0004, A1_scaffold0065, A1_scaffold0097, A1_scaffold0096, A1_scaffold0012, A1_scaffold0025, A1_scaffold0136, A1_scaffold0040, A1_scaffold0102, A1_scaffold0044, A1_scaffold0049, A1_scaffold0130, A1_scaffold0123, A1_scaffold0019, A1_scaffold0138, A1_scaffold0017, A1_scaffold0135, A1_scaffold0053, A1_scaffold0127, A1_scaffold0092, A1_scaffold0034, A1_scaffold0041, A1_scaffold0036, A1_scaffold0003, A1_scaffold0133, A1_scaffold0117, A1_scaffold0108, A1_scaffold0061, A1_scaffold0057, A1_scaffold0113, A1_scaffold0119, A1_scaffold0099, A1_scaffold0089, A1_scaffold0093, A1_scaffold0079, A1_scaffold0144, A1_scaffold0018, A1_scaffold0005, A1_scaffold0002, A1_scaffold0048, A1_scaffold0128, A1_scaffold0142, A1_scaffold0084, A1_scaffold0087, A1_scaffold0116, A1_scaffold0141, A1_scaffold0082, A1_scaffold0022, A1_scaffold0043, A1_scaffold0148, A1_scaffold0132, A1_scaffold0143, A1_scaffold0029, A1_scaffold0023, A1_scaffold0088, A1_scaffold0106, A1_scaffold0075, A1_scaffold0045, A1_scaffold0147, A1_scaffold0068, A1_scaffold0067, A1_scaffold0105, A1_scaffold0059, A1_scaffold0125, A1_scaffold0046, A1_scaffold0121, A1_scaffold0140, A1_scaffold0115, A1_scaffold0101, A1_scaffold0078, A1_scaffold0033, A1_scaffold0024, A1_scaffold0085, A1_scaffold0052, A1_scaffold0009, A1_scaffold0026, A1_scaffold0006, A1_scaffold0081, A1_scaffold0071, A1_scaffold0076, A1_scaffold0015, A1_scaffold0124, A1_scaffold0030, A1_scaffold0062, A1_scaffold0011, A1_scaffold0060, A1_scaffold0031, A1_scaffold0055, A1_scaffold0047, A1_scaffold0080, A1_scaffold0131, A1_scaffold0070, A1_scaffold0035, A1_scaffold0074, A1_scaffold0064, A1_scaffold0146, A1_scaffold0014, A1_scaffold0066, A1_scaffold0137, A1_scaffold0069, A1_scaffold0016, A1_scaffold0104, A1_scaffold0122, A1_scaffold0110, A1_scaffold0008, A1_scaffold0126, A1_scaffold0086, A1_scaffold0032, A1_scaffold0027, A1_scaffold0129, A1_scaffold0073, A1_scaffold0109, A1_scaffold0098, A1_scaffold0063, A1_scaffold0090, A1_scaffold0149, A1_scaffold0037, A1_scaffold0042, A1_scaffold0058, A1_scaffold0077, A1_scaffold0020, A1_scaffold0118, A1_scaffold0054, A1_scaffold0111, A1_scaffold0095, A1_scaffold0094, A1_scaffold0001, A1_scaffold0100, A1_scaffold0091, A1_scaffold0007, A1_scaffold0072, A1_scaffold0021, A1_scaffold0050, A1_scaffold0120, A1_scaffold0039, A1_scaffold0083, A1_scaffold0038, A1_scaffold0150, A1_scaffold0010, A1_scaffold0051, A1_scaffold0107, A1_scaffold0134, A1_scaffold0013, A1_scaffold0103, A1_scaffold0114, A1_scaffold0056, A1_scaffold0112, A1_scaffold0139 present in only one genome. Removing corresponding alignments
Traceback (most recent call last):
File "/scratch/jcruzcor/04_SyRI_analysis/syri/syri/bin/syri", line 250, in
startSyri(args, coords[["aStart", "aEnd", "bStart", "bEnd", "aLen", "bLen", "iden", "aDir", "bDir", "aChr", "bChr"]])
File "syri/pyxFiles/synsearchFunctions.pyx", line 467, in syri.pyxFiles.synsearchFunctions.startSyri
File "syri/pyxFiles/synsearchFunctions.pyx", line 860, in syri.pyxFiles.synsearchFunctions.outSyn
File "/scratch/jcruzcor/trial_minimap/SYRI/lib/python3.5/site-packages/pandas/core/generic.py", line 4389, in setattr
return object.setattr(self, name, value)
File "pandas/_libs/properties.pyx", line 69, in pandas._libs.properties.AxisProperty.set
File "/scratch/jcruzcor/trial_minimap/SYRI/lib/python3.5/site-packages/pandas/core/generic.py", line 646, in _set_axis
self._data.set_axis(axis, labels)
File "/scratch/jcruzcor/trial_minimap/SYRI/lib/python3.5/site-packages/pandas/core/internals.py", line 3323, in set_axis
'values have {new} elements'.format(old=old_len, new=new_len))
ValueError: Length mismatch: Expected axis has 0 elements, new values have 7 elements

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