GATB
Can't open object can't open my reads
Hi there, I built an input file of my reads. It said can't read my reads with the same error when I ran simka. The example tested successfully. Could someone show me where the problem is? Thanks very much!
Here is the error:
Creating input
Nb input datasets: 1
HDF5-DIAG: Error detected in HDF5 (1.10.5) thread 0:
#000:
/scratch/fwang/simka-v1.5.3-Source/thirdparty/gatb-core/gatb-core/thirdparty/hdf5/src/H5A.c
line 425 in H5Aopen(): unable to load attribute info from object header
for attribute: 'version'
major: Attribute
minor: Can't open object
#001:
/scratch/fwang/simka-v1.5.3-Source/thirdparty/gatb-core/gatb-core/thirdparty/hdf5/src/H5Aint.c
line 433 in H5A__open(): unable to load attribute info from object
header for attribute: 'version'
major: Attribute
minor: Can't open object
#002:
/scratch/fwang/simka-v1.5.3-Source/thirdparty/gatb-core/gatb-core/thirdparty/hdf5/src/H5Oattribute.c
line 515 in H5O__attr_open_by_name(): can't locate attribute: 'version'
major: Attribute
minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.10.5) thread 0:
#000:
/scratch/fwang/simka-v1.5.3-Source/thirdparty/gatb-core/gatb-core/thirdparty/hdf5/src/H5A.c
line 704 in H5Aget_space(): not an attribute
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.5) thread 0:
#000:
/scratch/fwang/simka-v1.5.3-Source/thirdparty/gatb-core/gatb-core/thirdparty/hdf5/src/H5S.c
line 1013 in H5Sget_simple_extent_dims(): not a dataspace
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.5) thread 0:
#000:
/scratch/fwang/simka-v1.5.3-Source/thirdparty/gatb-core/gatb-core/thirdparty/hdf5/src/H5A.c
line 662 in H5Aread(): not an attribute
major: Invalid arguments to routine
minor: Inappropriate type
ERROR: Can't open dataset: ID1
Here are the IDs of my reads as input:
ID1: 2018031910_paired_1.fasta ; 2018031910_paired_2.fasta
ID2: 201803193_paired_1.fasta ; 201803193_paired_2.fasta
ID3: 20180319_paired_1.fasta ; 20180319_paired_2.fasta
ID4: 20180403_paired_1.fasta ; 20180403_paired_2.fasta
ID5: 20180405_paired_1.fasta ; 20180405_paired_2.fasta
ID6: 20180410_paired_1.fasta ; 20180410_paired_2.fasta
ID7: 2018041210_paired_1.fasta ; 2018041210_paired_2.fasta
ID8: 201804123_paired_1.fasta ; 201804123_paired_2.fasta
ID9: 20180412_paired_1.fasta ; 20180412_paired_2.fasta
ID10: 2018041710_paired_1.fasta ; 2018041710_paired_2.fasta
ID11: 201804173_paired_1.fasta ; 201804173_paired_2.fasta
ID12: 20180417_paired_1.fasta ; 20180417_paired_2.fasta
ID13: 20180419_paired_1.fasta ; 20180419_paired_2.fasta
ID14: 20180424_paired_1.fasta ; 20180424_paired_2.fasta
ID15: 2018042610_paired_1.fasta ; 2018042610_paired_2.fasta
ID16: 201804263_paired_1.fasta ; 201804263_paired_2.fasta
ID17: 20180426_paired_1.fasta ; 20180426_paired_2.fasta
ID18: 20180502_paired_1.fasta ; 20180502_paired_2.fasta
ID19: 20180503_paired_1.fasta ; 20180503_paired_2.fasta
ID20: 2018050810_paired_1.fasta ; 2018050810_paired_2.fasta
ID21: 201805083_paired_1.fasta ; 201805083_paired_2.fasta
ID22: 20180508_paired_1.fasta ; 20180508_paired_2.fasta
ID23: 2018051110_paired_1.fasta ; 2018051110_paired_2.fasta
ID24: 201805113_paired_1.fasta ; 201805113_paired_2.fasta
ID25: 20180511_paired_1.fasta ; 20180511_paired_2.fasta
ID26: 20180515_paired_1.fasta ; 20180515_paired_2.fasta
ID27: 20180517_paired_1.fasta ; 20180517_paired_2.fasta
ID28: 2018052210_paired_1.fasta ; 2018052210_paired_2.fasta
ID29: 201805223_paired_1.fasta ; 201805223_paired_2.fasta
ID30: 20180522_paired_1.fasta ; 20180522_paired_2.fasta
ID31: 20180524_paired_1.fasta ; 20180524_paired_2.fasta
ID32: 2018052910_paired_1.fasta ; 2018052910_paired_2.fasta
ID33: 201805293_paired_1.fasta ; 201805293_paired_2.fasta
ID34: 20180529_paired_1.fasta ; 20180529_paired_2.fasta
Hi,
This error occurs when the program does not find the files at the indicated path. Here, your input file contains only file names (and not absolute paths for instance), in this case, your fasta files must be in the same directory as the input file. Is it the case ?
Hi,
This error occurs when the program does not find the files at the indicated path. Here, your input file contains only file names (and not absolute paths for instance), in this case, your fasta files must be in the same directory as the input file. Is it the case?
Thanks for your reply. It seems not this case. The fasta files and the input files are in the same directory. I ran again after adding absolute paths in input files just now. It showed the same error. Are there specific requirements for the contigs headers? My contigs' headers are like this: >000000000011. Is there a possibility that simka didn't recognize my fasta files?
Are there specific requirements for the contigs headers? My contigs' headers are like this: >000000000011. Is there a possibility that simka didn't recognize my fasta files?
No, headers can be anything you want. The error is typical of a "file not found". Are you 100% sure that your files are correctly spelled in the input file and also readable by your system or user ?
Are there specific requirements for the contigs headers? My contigs' headers are like this: >000000000011. Is there a possibility that simka didn't recognize my fasta files?
No, headers can be anything you want. The error is typical of a "file not found". Are you 100% sure that your files are correctly spelled in the input file and also readable by your system or user?
Hi. Thanks for your reply. I checked my data and ran many times using different input.txt files. Luckily, I found the issue finally. It's because of my text format. I use another way to generate the input.txt with the same information and it's working now. I tried using the example txt file and it's proved that my text format is really the reason. It seems that my first text format can't be read by the program. Thanks very much! All the best!
I encountered the same issue. The program seems to have trouble recognizing plain .txt files. A quick way around this is to convert plain .txt files to UNIX format.
dos2unix input_file.txt
I encountered the same issue. The program seems to have trouble recognizing plain .txt files. A quick way around this is to convert plain .txt files to UNIX format.
dos2unix input_file.txt
Thanks very much!