raise ValueError("No lines parsed -- was an empty file provided?") ValueError: No lines parsed -- was an empty file provided?

[ncgrjsmiao]

I test the example dataset within singularity, but met some probelm until ###GMAP MAPPING STARTED AT: 13:06:26 21-03 ### ###BUILD INDEX###

bellow is Error message: Traceback (most recent call last): File "/opt/LoReAn/code/lorean.py", line 552, in main() File "/opt/LoReAn/code/lorean.py", line 497, in main args.verbose, Fflag=True) File "/opt/LoReAn/code/mapping.py", line 398, in gmap wd, Fflag, type_out, verbose) File "/opt/LoReAn/code/mapping.py", line 130, in gmap_map filename = longest_cds(list_fasta[0][1], list_fasta[1][1], verbose, working_dir, filename) File "/opt/LoReAn/code/mapping.py", line 188, in longest_cds db = gffutils.create_db(gff_file, ':memory:', merge_strategy='create_unique', keep_order=True, transform=transform) File "/usr/local/lib/python3.5/dist-packages/gffutils/create.py", line 1288, in create_db c.create() File "/usr/local/lib/python3.5/dist-packages/gffutils/create.py", line 504, in create self._populate_from_lines(self.iterator) File "/usr/local/lib/python3.5/dist-packages/gffutils/create.py", line 625, in _populate_from_lines raise ValueError("No lines parsed -- was an empty file provided?") ValueError: No lines parsed -- was an empty file provided?

[lfaino]

Hi, did you install via docker or singularity?

Cheers Luigi

[cgjosephlee]

Had same problem here on Crispa example. I installed using docker.

$ lorean.py -a -rp repeats.scaffold3.bed -sr scaffold3.short_1.fastq,scaffold3.short_2.fastq  -lr scaffold3.long.fasta  -pr scaffold3.prot.fasta -sp crispa scaffold3.fasta -d -f -mg -t 60 --keep_tmp

 ### LOREAN IS CHECKING THAT GMAP IS CORRECTLY BUILD ###


###GMAP MAPPING  STARTED AT:    08:49:22 01-04  ###
        ###BUILD INDEX###
        ###MAP###

 ### GMAP IS CORRECTLY BUILD ###



###MASKING THE GENOME STARTED AT:       08:49:21 01-04  ###

###STAR MAPPING  STARTED AT:    08:50:05 01-04  ###
        ###BUILD INDEX###
        ###MAP###
        ###SAM to BAM###
        ###SORTING BAM###

###TRINITY STARTS AT:   08:52:36 01-04  ###

###GMAP MAPPING  STARTED AT:    09:02:09 01-04  ###
        ###BUILD INDEX###
        ###MAP###
Traceback (most recent call last):
  File "/opt/LoReAn/code/lorean.py", line 552, in <module>
    main()
  File "/opt/LoReAn/code/lorean.py", line 180, in main
    args.verbose, Fflag=True)
  File "/opt/LoReAn/code/mapping.py", line 398, in gmap
    wd, Fflag, type_out, verbose)
  File "/opt/LoReAn/code/mapping.py", line 130, in gmap_map
    filename = longest_cds(list_fasta[0][1], list_fasta[1][1], verbose, working_dir, filename)
  File "/opt/LoReAn/code/mapping.py", line 188, in longest_cds
    db = gffutils.create_db(gff_file, ':memory:', merge_strategy='create_unique', keep_order=True, transform=transform)
  File "/usr/local/lib/python3.5/dist-packages/gffutils/create.py", line 1288, in create_db
    c.create()
  File "/usr/local/lib/python3.5/dist-packages/gffutils/create.py", line 504, in create
    self._populate_from_lines(self.iterator)
  File "/usr/local/lib/python3.5/dist-packages/gffutils/create.py", line 625, in _populate_from_lines
    raise ValueError("No lines parsed -- was an empty file provided?")
ValueError: No lines parsed -- was an empty file provided?

It seems to stop when aligning transcripts using GMAP. I then tried appending -mm to use minimap.

$ lorean.py -a -rp repeats.scaffold3.bed -sr scaffold3.short_1.fastq,scaffold3.short_2.fastq  -lr scaffold3.long.fasta  -pr scaffold3.prot.fasta -sp crispa scaffold3.fasta -d -f -mg -t 60 --keep_tmp -mm

 ### LOREAN IS CHECKING THAT GMAP IS CORRECTLY BUILD ###


###GMAP MAPPING  STARTED AT:    09:15:54 01-04  ###
        ###BUILD INDEX###
GMAP database existed already: /mnt/nas1/hhl/phellinus/cDNA/lorean/LoReAn_Example/Crispa/LoReAn_annotation/run//gmap_output/chr8.testGMAP.fasta_GMAPindex --- skipping  ###MAP###
GMAP done already: /mnt/nas1/hhl/phellinus/cDNA/lorean/LoReAn_Example/Crispa/LoReAn_annotation/run//gmap_output/gmap.long_reads.test.sam --- skipping
 ### GMAP IS CORRECTLY BUILD ###



###MASKING THE GENOME STARTED AT:       09:15:53 01-04  ###

###STAR MAPPING  STARTED AT:    09:15:54 01-04  ###
        ###BUILD INDEX###
STAR index existed already: /mnt/nas1/hhl/phellinus/cDNA/lorean/LoReAn_Example/Crispa/LoReAn_annotation/run//STAR/scaffold3.fasta.masked.fasta.rename.fasta_STARindex/SAindex --- skipping      ###MAP###
STAR alignment file existed already: /mnt/nas1/hhl/phellinus/cDNA/lorean/LoReAn_Example/Crispa/LoReAn_annotation/run//STAR/STAR_shortreadsAligned.out.bam --- skipping
        ###SAM to BAM###
BAM file existed already: /mnt/nas1/hhl/phellinus/cDNA/lorean/LoReAn_Example/Crispa/LoReAn_annotation/run//STAR/short_reads_mapped.bam --- skipping
        ###SORTING BAM###

###TRINITY STARTS AT:   09:17:42 01-04  ###
Trinity-GG file existed already: /mnt/nas1/hhl/phellinus/cDNA/lorean/LoReAn_Example/Crispa/LoReAn_annotation/run//Trinity/trinity_out_dir/Trinity-GG.fasta --- skipping

###GMAP MAPPING  STARTED AT:    09:17:42 01-04  ###
        ###BUILD INDEX###
GMAP database existed already: /mnt/nas1/hhl/phellinus/cDNA/lorean/LoReAn_Example/Crispa/LoReAn_annotation/run//gmap_output/scaffold3.fasta.masked.fasta.rename.fasta_GMAPindex --- skipping    ###MAP###
Traceback (most recent call last):
  File "/opt/LoReAn/code/lorean.py", line 552, in <module>
    main()
  File "/opt/LoReAn/code/lorean.py", line 180, in main
    args.verbose, Fflag=True)
  File "/opt/LoReAn/code/mapping.py", line 398, in gmap
    wd, Fflag, type_out, verbose)
  File "/opt/LoReAn/code/mapping.py", line 130, in gmap_map
    filename = longest_cds(list_fasta[0][1], list_fasta[1][1], verbose, working_dir, filename)
  File "/opt/LoReAn/code/mapping.py", line 188, in longest_cds
    db = gffutils.create_db(gff_file, ':memory:', merge_strategy='create_unique', keep_order=True, transform=transform)
  File "/usr/local/lib/python3.5/dist-packages/gffutils/create.py", line 1288, in create_db
    c.create()
  File "/usr/local/lib/python3.5/dist-packages/gffutils/create.py", line 504, in create
    self._populate_from_lines(self.iterator)
  File "/usr/local/lib/python3.5/dist-packages/gffutils/create.py", line 625, in _populate_from_lines
    raise ValueError("No lines parsed -- was an empty file provided?")
ValueError: No lines parsed -- was an empty file provided?

It did not swap to minimap and encounter the same error?

[cgjosephlee]

$ tail gmap_output/gmap_map.log
Checking compiler options for SSE4.2: 6B8B4567 __builtin_clz=1 __builtin_ctz=0 _mm_popcnt_u32=17 __builtin_popcount=17
Finished checking compiler assumptions
Looking for index files in directory /mnt/nas1/hhl/test/cDNA/lorean/LoReAn_Example/Crispa/LoReAn_annotation/run//gmap_output//scaffold3.fasta.masked.fasta.rename.fasta_GMAPindex
  Pointers file is scaffold3.fasta.masked.fasta.rename.fasta_GMAPindex.ref153offsets64meta
  Offsets file is scaffold3.fasta.masked.fasta.rename.fasta_GMAPindex.ref153offsets64strm
  Positions file is scaffold3.fasta.masked.fasta.rename.fasta_GMAPindex.ref153positions
Offsets compression type: bitpack64
Allocating memory for ref offset pointers, kmer 15, interval 3...done (134,217,744 bytes)
Starting alignment
Processed 0 queries in 0.00 seconds (-nan queries/sec)

No queries were passed to GMAP and the file size of Trinity/trinity_out_dir/Trinity-GG.fasta is 0. Seems to fail at trinity stage?

[lfaino]

Working on it. I will write ASAP i will find the problem

[lfaino]

Dear @cgjosephlee and @ncgrjsmiao , i did build a new image with some change. It looks that i fix the problems. you can try by running:

docker run -it --rm -v $PWD:/data lfaino/lorean:noiIPRS createUser.py $USER $UID

please let me know if it works that i came move this as default image Cheers Luigi

[cgjosephlee]

Hi @lfaino , Thank you for the reply. Unfortunately it stopped at the same stage with same error message, and Trinity-GG.fasta is still zero-size. Any additional info I can provide?

Best Joseph

[lfaino]

We need to check if mysql started.

you can test this by running: docker run -it --rm -v $PWD:/data lfaino/lorean:noiIPRS bash once the image start, you can run:

mysql -u root -p and when ask the password you can type lorean

you should be in mysql. if you get an error, let me know Cheers Luigi

[cgjosephlee]

Gocha!

root@332f11a6b0ee:/data# mysql -u root -p
Enter password:
ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2)

[lfaino]

do you have installed mysql on your system?

[cgjosephlee]

Yes, but it seems that I cannot access it since I have no root privilege.

$ mysql --help
mysql  Ver 14.14 Distrib 5.7.25, for Linux (x86_64) using  EditLine wrapper
Copyright (c) 2000, 2019, Oracle and/or its affiliates. All rights reserved.

[lfaino]

Hi @cgjosephlee , can you test again. I removed mysql and now it works with my data.

please let me know.

Cheers Luigi

[zcrself]

Dear @cgjosephlee and @ncgrjsmiao , i did build a new image with some change. It looks that i fix the problems. you can try by running:

docker run -it --rm -v $PWD:/data lfaino/lorean:noiIPRS createUser.py $USER $UID

please let me know if it works that i came move this as default image Cheers Luigi

With this docker://lfaino/lorean:noiIPRS, running Singularity 3.1.0 Using LoReAn_Example, completely finished! But as for my test data, there are some errors as follows, Using docker://lfaino/lorean, there are no errors like below, but error is "ValueError: No lines parsed -- was an empty file provided?"

`cp: cannot stat '/db2/ncgr/maozhu/Partial_Test/LoReAn_annotation/run/PASA/annotation.pasa_assemblies.gff3': No such file or directory Traceback (most recent call last): File "/opt/LoReAn/code/prepareEvmInputs.py", line 105, in move_single_file subprocess.check_call(args) File "/usr/lib/python3.5/subprocess.py", line 581, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['cp', '/db2/ncgr/maozhu/Partial_Test/LoReAn_annotation/run/PASA/annotation.pasa_assemblies.gff3', '/db2/ncgr/maozhu/Partial_Test/LoReAn_annotation/run//evm_inputs/']' returned non-zero exit status 1

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/opt/LoReAn/code/lorean.py", line 551, in main() File "/opt/LoReAn/code/lorean.py", line 363, in main list_soft, pred_file, transcript_file, protein_file = inputEvm.group_EVM_inputs(evm_inputs_dir, evm_inputs) File "/opt/LoReAn/code/prepareEvmInputs.py", line 234, in group_EVM_inputs move_EVM_inputs(evm_dir, inputs) File "/opt/LoReAn/code/prepareEvmInputs.py", line 161, in move_EVM_inputs new_files = move_single_file(filename, key, evm_dir, new_files) File "/opt/LoReAn/code/prepareEvmInputs.py", line 110, in move_single_file raise NameError('') NameError`

[zcrself]

Exit at "MOVING IMPORTANT FILES"

###PASA STARTS AT: 08:09:28 06-04 ###

###AUGUSTUS, GENEMARK-ES AND AAT STARTED AT:08:47:55 06-04 ### ###RUNNING AUGUSTUS ### ###RUNNING AAT ### ###RUNNING GENEMARK ### ###CONVERTING AUGUSTUS TO GFF3### ###CONVERTING GENEMARK TO GFF3###

###EVM STARTED AT: 14:29:52 06-04 ### ###MOVING IMPORTANT FILES###

[lfaino]

Hi @cgjosephlee , in the past few days I made few changes and few (about 50) new images. I see that that the image that you are using is a bit old. Please, remove the LoReAn _annotation folder and the lorean image, dowload again the image and run again. let me know how it goes.

Cheers Luigi

[zcrself]

ls -l /db2/ncgr/maozhu/Partial_Test/LoReAn_annotation/run/PASA/:

drwxr-xr-x 8 ncgr ncgr 4096 Apr 6 16:47 ./ drwxr-xr-x 14 ncgr ncgr 4096 Apr 6 22:29 ../ -rw-r--r-- 1 ncgr ncgr 239 Apr 6 16:09 alignAssembly.config -rw-r--r-- 1 ncgr ncgr 6240457 Apr 6 16:25 alignment.validations.output -rw-r--r-- 1 ncgr ncgr 5098995 Apr 6 16:33 annotation.sqlite.assemblies.fasta -rw-r--r-- 1 ncgr ncgr 4749973 Apr 6 16:25 annotation.sqlite.failed_gmap_alignments.gff3 -rw-r--r-- 1 ncgr ncgr 9816379 Apr 6 16:25 annotation.sqlite.failed_gmap_alignments.gtf -rw-r--r-- 1 ncgr ncgr 6068647 Apr 6 16:26 annotation.sqlite.pasa_alignment_assembly_building.ascii_illustrations.out -rw-r--r-- 1 ncgr ncgr 399257 Apr 6 16:47 annotation.sqlite.pasa_assemblies.bed -rw-r--r-- 1 ncgr ncgr 903605 Apr 6 16:47 annotation.sqlite.pasa_assemblies_described.txt -rw-r--r-- 1 ncgr ncgr 1414860 Apr 6 16:47 annotation.sqlite.pasa_assemblies.gff3 -rw-r--r-- 1 ncgr ncgr 2111630 Apr 6 16:47 annotation.sqlite.pasa_assemblies.gtf -rw-r--r-- 1 ncgr ncgr 1277577 Apr 6 16:25 annotation.sqlite.valid_gmap_alignments.bed -rw-r--r-- 1 ncgr ncgr 3255262 Apr 6 16:25 annotation.sqlite.valid_gmap_alignments.gff3 -rw-r--r-- 1 ncgr ncgr 6730264 Apr 6 16:25 annotation.sqlite.valid_gmap_alignments.gtf -rw-r--r-- 1 ncgr ncgr 13780996 Apr 6 16:14 gmap.spliced_alignments.gff3 -rw-r--r-- 1 ncgr ncgr 0 Apr 6 16:14 gmap.spliced_alignments.gff3.completed drwxr-xr-x 2 ncgr ncgr 4096 Apr 6 16:47 __pasa_annotation.sqlite_SQLite_chkpts/ -rw-r--r-- 1 ncgr ncgr 6100 Apr 6 16:47 __pasa_annotation.sqlite_SQLite_chkpts.cmds_log -rw-r--r-- 1 ncgr ncgr 4906250 Apr 6 16:47 pasa.err.log -rw-r--r-- 1 ncgr ncgr 414 Apr 6 16:47 pasa.out.log drwxr-xr-x 2 ncgr ncgr 4096 Apr 6 16:26 pasa_run.log.dir/ -rw-r--r-- 1 ncgr ncgr 303 Apr 6 16:14 pipeliner.6340.cmds -rw-r--r-- 1 ncgr ncgr 3321 Apr 6 16:20 pipeliner.6548.cmds -rw-r--r-- 1 ncgr ncgr 3138 Apr 6 16:20 pipeliner.7036.cmds drwxr-xr-x 3 ncgr ncgr 4096 Apr 6 16:11 test_scaffold.fa.masked.fasta.rename.fasta.gmap/ -rw-r--r-- 1 ncgr ncgr 1988655 Apr 6 16:20 Trinity-GG.fasta.transdecoder.bed -rw-r--r-- 1 ncgr ncgr 12196018 Apr 6 16:21 Trinity-GG.fasta.transdecoder.cds drwxr-xr-x 3 ncgr ncgr 4096 Apr 6 16:20 Trinity-GG.fasta.transdecoder_dir/ drwxr-xr-x 2 ncgr ncgr 4096 Apr 6 16:21 Trinity-GG.fasta.transdecoder_dir.__checkpoints/ drwxr-xr-x 2 ncgr ncgr 4096 Apr 6 16:16 Trinity-GG.fasta.transdecoder_dir.__checkpoints_longorfs/ -rw-r--r-- 1 ncgr ncgr 8775031 Apr 6 16:20 Trinity-GG.fasta.transdecoder.gff3 -rw-r--r-- 1 ncgr ncgr 76611 Apr 6 16:21 Trinity-GG.fasta.transdecoder.gff3.fl_accs -rw-r--r-- 1 ncgr ncgr 5253718 Apr 6 16:20 Trinity-GG.fasta.transdecoder.pep

[lfaino]

is this the output after that you re-downloaded the image?

[zcrself]

is this the output after that you re-downloaded the image? I have download docker://lfaino/lorean some days ago, Because you update your docker image, then I download this lfaino/lorean:noiIPRS image firstly ( I do not delete lfaino/lorean because of different image)

[zcrself]

This is the output after I download this image docker://lfaino/lorean:noiIPRS firstly

Could you tell me that the differences between docker://lfaino/lorean and docker://lfaino/lorean:noiIPRS?

On Sun, Apr 7, 2019 at 3:47 AM Luigi Faino [email protected] wrote:

is this the output after that you re-downloaded the image?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/lfaino/LoReAn/issues/16#issuecomment-480532424, or mute the thread https://github.com/notifications/unsubscribe-auth/AOSBuEkiLhTILYIRmhq4iIrIP8setSIsks5vePm9gaJpZM4cLtZj .

[lfaino]

I saw an old error (on my side) in your images: the image is not anymore docker://lfaino/lorean:noiIPRS but docker://lfaino/lorean:noIPRS. if you notice, there is not anymore the i before IPRS. it was a mistake from my side. The latest image is called docker://lfaino/lorean:noIPRS. There are few differences between docker://lfaino/lorean and docker://lfaino/lorean:noIPRS:

1. docker://lfaino/lorean:noIPRS does not require mysql anymore. this was a pain before because LoReAn need to start a service in the image and it is a bit difficult on some host systems. now PASA uses sqlite and it is managed better by the image
2. I update GeneMark. now i have the latest version in docker://lfaino/lorean:noIPRS
3. gffread tool was updated and few change need to be made to use the new version in docker://lfaino/lorean:noIPRS

these are the main changes.

Sorry for the problem with the naming. Please dowload the new version using docker run -it --rm -v $PWD:/data lfaino/lorean:noIPRS createUser.py $USER $UID and test again

[zcrself]

Thank for your good job and quick reply. Now I re-download docker://lfaino/lorean:noIPRS, then re-run my job. Tomorrow I will tell you my result of running lorean:noIPRS!

Best regards!

On Sun, Apr 7, 2019 at 3:04 PM Luigi Faino [email protected] wrote:

I saw an old error (on my side) in your images: the image is not anymore docker://lfaino/lorean:noiIPRS but docker://lfaino/lorean:noIPRS. if you notice, there is not anymore the i before IPRS. it was a mistake from my side. The latest image is called docker://lfaino/lorean:noIPRS. There are few differences between docker://lfaino/lorean and docker://lfaino/lorean:noIPRS:

1. docker://lfaino/lorean:noIPRS does not require mysql anymore. this was a pain before because LoReAn need to start a service in the image and it is a bit difficult on some host systems. now PASA uses sqlite and it is managed better by the image
2. I update GeneMark. now i have the latest version in docker://lfaino/lorean:noIPRS
3. gffread tool was updated and few change need to be made to use the new version in docker://lfaino/lorean:noIPRS

these are the main changes.

Sorry for the problem with the naming. Please dowload the new version using docker run -it --rm -v $PWD:/data lfaino/lorean:noIPRS createUser.py $USER $UID and test again

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/lfaino/LoReAn/issues/16#issuecomment-480564987, or mute the thread https://github.com/notifications/unsubscribe-auth/AOSBuAphjSMpD5D2DZ_zA8xW2VwbQzs-ks5veZiRgaJpZM4cLtZj .

[zcrself]

Using the image docker://lfaino/lorean:noIPRS

Errors as follows:

###RUNNING iASSEMBLER 02:07:27 08-04 ### Traceback (most recent call last): File "/opt/LoReAn/code//lorean.py", line 563, in main() File "/opt/LoReAn/code//lorean.py", line 440, in main adapter_value, threads_use, args.adapter_match_score, ref_rename, UnboundLocalError: local variable 'adapter_value' referenced before assignment

How to fix it ? Thanks a lot!

On Sun, Apr 7, 2019 at 10:56 PM Smith Waterman [email protected] wrote:

Thank for your good job and quick reply. Now I re-download docker://lfaino/lorean:noIPRS, then re-run my job. Tomorrow I will tell you my result of running lorean:noIPRS!

Best regards!

On Sun, Apr 7, 2019 at 3:04 PM Luigi Faino [email protected] wrote:

I saw an old error (on my side) in your images: the image is not anymore docker://lfaino/lorean:noiIPRS but docker://lfaino/lorean:noIPRS. if you notice, there is not anymore the i before IPRS. it was a mistake from my side. The latest image is called docker://lfaino/lorean:noIPRS. There are few differences between docker://lfaino/lorean and docker://lfaino/lorean:noIPRS:

1. docker://lfaino/lorean:noIPRS does not require mysql anymore. this was a pain before because LoReAn need to start a service in the image and it is a bit difficult on some host systems. now PASA uses sqlite and it is managed better by the image
2. I update GeneMark. now i have the latest version in docker://lfaino/lorean:noIPRS
3. gffread tool was updated and few change need to be made to use the new version in docker://lfaino/lorean:noIPRS

these are the main changes.

Sorry for the problem with the naming. Please dowload the new version using docker run -it --rm -v $PWD:/data lfaino/lorean:noIPRS createUser.py $USER $UID and test again

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/lfaino/LoReAn/issues/16#issuecomment-480564987, or mute the thread https://github.com/notifications/unsubscribe-auth/AOSBuAphjSMpD5D2DZ_zA8xW2VwbQzs-ks5veZiRgaJpZM4cLtZj .

[zcrself]

My running command list is : " nohup lorean.py -a -rp repeats.fix.bed -sr clean_R_1.fastq,clean_R_2.fastq -lr Long.fasta -pr rice_bamboo_prot.fasta -sp bamboo test_scaffold.fa -d -f -mg -t 4 --keep_tmp 1>1.out 2>2.out &"

On Mon, Apr 8, 2019 at 2:36 PM Smith Waterman [email protected] wrote:

Using the image docker://lfaino/lorean:noIPRS

Errors as follows:

###RUNNING iASSEMBLER 02:07:27 08-04 ### Traceback (most recent call last): File "/opt/LoReAn/code//lorean.py", line 563, in main() File "/opt/LoReAn/code//lorean.py", line 440, in main adapter_value, threads_use, args.adapter_match_score, ref_rename, UnboundLocalError: local variable 'adapter_value' referenced before assignment

How to fix it ? Thanks a lot!

On Sun, Apr 7, 2019 at 10:56 PM Smith Waterman [email protected] wrote:

Thank for your good job and quick reply. Now I re-download docker://lfaino/lorean:noIPRS, then re-run my job. Tomorrow I will tell you my result of running lorean:noIPRS!

Best regards!

On Sun, Apr 7, 2019 at 3:04 PM Luigi Faino [email protected] wrote:

I saw an old error (on my side) in your images: the image is not anymore docker://lfaino/lorean:noiIPRS but docker://lfaino/lorean:noIPRS. if you notice, there is not anymore the i before IPRS. it was a mistake from my side. The latest image is called docker://lfaino/lorean:noIPRS. There are few differences between docker://lfaino/lorean and docker://lfaino/lorean:noIPRS:

1. docker://lfaino/lorean:noIPRS does not require mysql anymore. this was a pain before because LoReAn need to start a service in the image and it is a bit difficult on some host systems. now PASA uses sqlite and it is managed better by the image
2. I update GeneMark. now i have the latest version in docker://lfaino/lorean:noIPRS
3. gffread tool was updated and few change need to be made to use the new version in docker://lfaino/lorean:noIPRS

these are the main changes.

Sorry for the problem with the naming. Please dowload the new version using docker run -it --rm -v $PWD:/data lfaino/lorean:noIPRS createUser.py $USER $UID and test again

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/lfaino/LoReAn/issues/16#issuecomment-480564987, or mute the thread https://github.com/notifications/unsubscribe-auth/AOSBuAphjSMpD5D2DZ_zA8xW2VwbQzs-ks5veZiRgaJpZM4cLtZj .

[lfaino]

The easiest way is to provide a file with the adapter sequence. Are you using PacBio or Nanopore data?

[cgjosephlee]

Still no luck after re-download latest image. I doubt it was stuck at trinity stage. trinity.log

--------------------------------------------------------------------------------
------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
--------------------------------------------------------------------------------

Monday, April 8, 2019: 02:03:26 CMD: /opt/LoReAn/third_party/software/Trinity/trinity-plugins/BIN/ParaFly -c trinity_GG.cmds -CPU 20 -v -shuffle
Number of Commands: 581
^Msucceeded(1)   0.172117% completed.    ^Msucceeded(2)   0.344234% completed.    ^Msucceeded(3)   0.516351% completed.    ^Msucceeded(4)   0.688468% completed.    ^Msucceeded(5)   0.860585% completed.    ^Msucceeded(6)   1.0327% completed.    ^Msucceeded(7)   1.20482% completed.    ^Msucceeded(8)   1.37694% complete

All commands completed successfully. :-)

Monday, April 8, 2019: 02:07:38 CMD: find Dir_*  -name '*inity.fasta'  | /opt/LoReAn/third_party/software/Trinity/util/support_scripts/GG_partitioned_trinity_aggregator.pl TRINITY_GG > /data/LoReAn_Example/Crispa/LoReAn_annotation/run/Trinity/trinity_out_dir/Trinity-GG.fasta.tmp
find: 'Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/0/y.reads.out.Trinity.fasta': No such file or directory
find: 'Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/0/reads.out.Trinity.fasta': No such file or directory
ERROR, filename: Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/0/y.reads.out.Trinity.fasta is indicated to not exist.
find: 'Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/0/eads.out.Trinity.fasta': No such file or directory
ERROR, filename: Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/0/reads.out.Trinity.fasta is indicated to not exist.
find: 'Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/0/.reads.out.Trinity.fasta': No such file or directory
ERROR, filename: Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/0/eads.out.Trinity.fasta is indicated to not exist.
find: 'Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/0/ty.reads.out.Trinity.fasta': No such file or directory
ERROR, filename: Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/0/.reads.out.Trinity.fasta is indicated to not exist.
find: 'Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/1/ty.reads.out.Trinity.fasta': No such file or directory
ERROR, filename: Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/0/ty.reads.out.Trinity.fasta is indicated to not exist.
find: 'Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/2/ity.reads.out.Trinity.fasta': No such file or directory
ERROR, filename: Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/1/ty.reads.out.Trinity.fasta is indicated to not exist.
find: 'Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/2/nity.reads.out.Trinity.fasta': No such file or directory
ERROR, filename: Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/2/ity.reads.out.Trinity.fasta is indicated to not exist.
find: 'Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/2/ty.reads.out.Trinity.fasta': No such file or directory
ERROR, filename: Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/2/nity.reads.out.Trinity.fasta is indicated to not exist.
find: 'Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/3/nity.reads.out.Trinity.fasta': No such file or directory
ERROR, filename: Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/2/ty.reads.out.Trinity.fasta is indicated to not exist.
find: 'Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/4/nity.reads.out.Trinity.fasta': No such file or directory
ERROR, filename: Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/3/nity.reads.out.Trinity.fasta is indicated to not exist.
find: 'Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/5/nity.reads.out.Trinity.fasta': No such file or directory
ERROR, filename: Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/4/nity.reads.out.Trinity.fasta is indicated to not exist.
find: 'Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/6/nity.reads.out.Trinity.fasta': No such file or directory
ERROR, filename: Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/5/nity.reads.out.Trinity.fasta is indicated to not exist.
find: 'Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/7/nity.reads.out.Trinity.fasta': No such file or directory
ERROR, filename: Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/6/nity.reads.out.Trinity.fasta is indicated to not exist.
ERROR, filename: Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/7/nity.reads.out.Trinity.fasta is indicated to not exist.
Monday, April 8, 2019: 02:07:38 CMD: /opt/LoReAn/third_party/software/Trinity/util/support_scripts/get_Trinity_gene_to_trans_map.pl /data/LoReAn_Example/Crispa/LoReAn_annotation/run/Trinity/trinity_out_dir/Trinity-GG.fasta > /data/LoReAn_Example/Crispa/LoReAn_annotation/run/Trinity/trinity_out_dir/Trinity-GG.fasta.ge


Finished. See /data/LoReAn_Example/Crispa/LoReAn_annotation/run/Trinity/trinity_out_dir/Trinity-GG.fasta for reconstructed transcripts

[lfaino]

do you mind to share your test data? I will test and see if i can find the error and fix it

[cgjosephlee]

The test data is LoReAn_Example/Crispa downloaded at https://github.com/lfaino/LoReAn_Example.

[lfaino]

@cgjosephlee ok. do you have /data/LoReAn_Example/Crispa/LoReAn_annotation/run/Trinity/trinity_out_dir/Trinity-GG.fasta file? is it empty or full? can you tell me about the system that you are using (amount of Memory and CPU)?

[lfaino]

@zcrself; do you mind to share your test data? I will test and see if i can find the error and fix it

[lfaino]

@cgjosephlee: Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/4/nity.reads.out.Trinity.fasta; this is strange... the file is truncated (4/nity.reads.out.Trinity.fasta).... no idea why

[cgjosephlee]

My system is Ubuntu 16.04 with 64 cpus and 128gb ram. I specified 40 cpus for the test.

docker run -it --rm -v $PWD:/data lfaino/lorean:noIPRS createUser.py $USER $UID
lorean.py -a -rp repeats.scaffold3.bed -sr scaffold3.short_1.fastq,scaffold3.short_2.fastq  -lr scaffold3.long.fasta  -pr scaffold3.prot.fasta -sp crispa scaffold3.fasta -d -f -mg -t 40 --keep_tmp

I previously tried on our NAS system and had no luck. I then tried on a local file system and it running now. Trinity-GG.fasta is full this time. Probably a conflict between docker and file system or symbolic links?