The genome file annotation_chr.genome has no valid entries about craft

[annadalmolin]

Hi Kingatsu, thank you for using CRAFT. As you have experienced, and as reported in the CRAFT manual ( https://github.com/annadalmolin/CRAFT and https://hub.docker.com/repository/docker/annadalmolin/craft), "the gene annotation (in GTF format) and the genome sequence (in FASTA format) files must be downloaded by the user from Ensembl database", so any file from other databases has a compatible format. Try rather to convert the circRNA Gencode coordinates into Ensembl format. Moreover, I suggest you follow the manual instructions to avoid other drawbacks. Regards, Anna Il giorno ven 28 ott 2022 alle ore 10:27 Kingatsu ***@***.***> ha scritto:

…

Hello, The CRAFT software is a power tools for me. However, I got the following error messages when I want to use fasta file from GENCODE, which is used to find my circRNA. Error: The genome file annotation_chr.genome has no valid entries. Exiting. Error: The genome file annotation_chr.genome has no valid entries. Exiting. mv: cannot stat '/data/input/backsplice_gene_name.txt': No such file or directory I have changed the list_backsplice.txt and backsplice_gene_name.txt from 1 to chr1, to adapt my fasta file. But the error still here. I don't know whether I MUST use the genome file from Ensembl for CRAFT. Can you give me some helps? Thanks in advance. Regards, Kingatsu — Reply to this email directly, view it on GitHub <#2>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AWKFLFJCPLOFX6L3HG2QFW3WFOE75ANCNFSM6AAAAAARQ2VX3Y> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Kingatsu]

Hello Anna,
Thanks for the prompt reply.

Yes, I used the Ensembl genome file and it seems work!
But it took me more than 12h but just finished the MiRNA binding site prediction analysis for ~20 circRNAs.
I am not sure if it is normal.

Thanks again for the help!

Regards,
Kingatsu

[annadalmolin]

Hi Kingatsu, yes, it seems a bit long time. How many CPUs does your computer have? And do you enabled the overlapping with the AGO2 binding sites? Regards, Anna Il sab 29 ott 2022, 04:08 Kingatsu ***@***.***> ha scritto:

…

Hello Anna, Thanks for the prompt reply. Yes, I used the Ensembl genome file and it seems work! But it took me more than 12h but just finished the MiRNA binding site prediction analysis for ~20 circRNAs. I am not sure if it is normal. Thanks again for the help! Regards, Kingatsu — Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AWKFLFIOZCOGEQD7RL5PZPLWFSBJRANCNFSM6AAAAAARQ2VX3Y> . You are receiving this because you commented.Message ID: ***@***.***>

[Kingatsu]

Hi Anna,

Here is my computer data:

cat /proc/cpuinfo| grep "cpu cores"| uniq
cpu cores       : 10
cat /proc/cpuinfo| grep "processor"| wc -l
20

And my param.txt is:

MRO
hsa
80      -15
all     all
hg38
1       1       30      FALSE   both
l=160000
l=160000

I think it doesn't check the overlapping with AGO2 binding sites because I don't put the AGO2_binding_sites.bed into /input.
Also, I tested the data with same parameters except changed "MRO" to "RO" yesterday.
And I got the output this morning

...
Quitting from lines 94-165 (functional_predictions_single_circRNA.Rmd)
Error in read.table(file_beRBP, header = T, sep = "\t") :
  no lines available in input
Calls: <Anonymous> ... withCallingHandlers -> withVisible -> eval -> eval -> read.table
In addition: Warning messages:
1: In system("timedatectl", intern = TRUE) :
  running command 'timedatectl' had status 1
2: package(s) not installed when version(s) same as current; use `force = TRUE` to
  re-install: 'org.Hs.eg.db'

Execution halted
mv: cannot stat 'functional_predictions_single_circRNA.html': No such file or directory
...
Quitting from lines 90-153 (functional_predictions_all_circRNAs.Rmd)
Error in read.table(file_beRBP, header = T, sep = "\t") :
  no lines available in input
Calls: <Anonymous> ... withCallingHandlers -> withVisible -> eval -> eval -> read.table
In addition: Warning message:
package(s) not installed when version(s) same as current; use `force = TRUE` to
  re-install: 'grid'

Execution halted

It seems the RBP prediction failed, and here is the beRBP.log:

working on M001_0.6 Sat Oct 29 03:43:26 UTC 2022
analysis_RBP featureMat_start=Sat Oct 29 03:43:26 UTC 2022
1 rank...Sat Oct 29 03:43:29 UTC 2022
Warning: [blastn] Examining 5 or more matches is recommended
BLAST Database error: Error pre-fetching sequence data 
cp: cannot stat 'siteSegment_1.csrv': No such file or directory
2 rank...Sat Oct 29 03:43:58 UTC 2022
Warning: [blastn] Examining 5 or more matches is recommended
BLAST Database error: Error pre-fetching sequence data 
cut: siteSegment_2.csrv: No such file or directory
paste: csrvI.txt: No such file or directory
3 rank...Sat Oct 29 03:44:19 UTC 2022
Warning: [blastn] Examining 5 or more matches is recommended
BLAST Database error: Error pre-fetching sequence data 
cut: siteSegment_3.csrv: No such file or directory
4 rank...Sat Oct 29 03:44:47 UTC 2022
Warning: [blastn] Examining 5 or more matches is recommended
BLAST Database error: Error pre-fetching sequence data 
cut: siteSegment_4.csrv: No such file or directory
5 rank...Sat Oct 29 03:45:16 UTC 2022
Warning: [blastn] Examining 5 or more matches is recommended
BLAST Database error: Error pre-fetching sequence data 
cut: siteSegment_5.csrv: No such file or directory
6 rank...Sat Oct 29 03:45:44 UTC 2022
Warning: [blastn] Examining 5 or more matches is recommended
BLAST Database error: Error pre-fetching sequence data 
cut: siteSegment_6.csrv: No such file or directory
7 rank...Sat Oct 29 03:46:05 UTC 2022
Warning: [blastn] Examining 5 or more matches is recommended
BLAST Database error: Error pre-fetching sequence data 
cut: siteSegment_7.csrv: No such file or directory
8 rank...Sat Oct 29 03:46:28 UTC 2022
Warning: [blastn] Examining 5 or more matches is recommended
BLAST Database error: Error pre-fetching sequence data 
cut: siteSegment_8.csrv: No such file or directory
9 rank...Sat Oct 29 03:46:54 UTC 2022
Warning: [blastn] Examining 5 or more matches is recommended
BLAST Database error: Error pre-fetching sequence data 
cut: siteSegment_9.csrv: No such file or directory
10 rank...Sat Oct 29 03:47:14 UTC 2022
Warning: [blastn] Examining 5 or more matches is recommended
BLAST Database error: Error pre-fetching sequence data 
cut: siteSegment_10.csrv: No such file or directory
analysis_RBP featureMat_finished=Sat Oct 29 03:47:40 UTC 2022
M001_0.6 all
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
Error in file(file, "rt") : cannot open the connection
Calls: generalPred -> read.delim -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'analysis_RBP.ftMat.txt': No such file or directory
Execution halted

Is this the circRNA sequence does not predict RBP or sth wrong before RBP prediction?

Thanks in advance.

Regards.
Kingatsu

[annadalmolin]

Hi Kingatsu, sorry for not replying earlier. Could you please re-run CRAFT with only the "MO" search and tell me the execution time? Moreover, as you correctly stated, the RBP prediction failed. I'll ask you some questions just to check if the input files are ok: -did you placed the UCSC genome and indexes in the *input/* directory? And *hg38 *is the corresponding genome version? -the parameters in the *params.txt* file are tab-separated? Thank you. Regards, Anna Il dom 30 ott 2022, 03:53 Kingatsu ***@***.***> ha scritto:

…

Hi Anna, Here is my computer data: cat /proc/cpuinfo| grep "cpu cores"| uniq cpu cores : 10 cat /proc/cpuinfo| grep "processor"| wc -l 20 And my param.txt is: MRO hsa 80 -15 all all hg38 1 1 30 FALSE both l=160000 l=160000 I think it doesn't check the overlapping with AGO2 binding sites because I don't put the AGO2_binding_sites.bed into /input. Also, I tested the data with same parameters except changed "MRO" to "RO" yesterday. And I got the output this morning ... Quitting from lines 94-165 (functional_predictions_single_circRNA.Rmd) Error in read.table(file_beRBP, header = T, sep = "\t") : no lines available in input Calls: <Anonymous> ... withCallingHandlers -> withVisible -> eval -> eval -> read.table In addition: Warning messages: 1: In system("timedatectl", intern = TRUE) : running command 'timedatectl' had status 1 2: package(s) not installed when version(s) same as current; use `force = TRUE` to re-install: 'org.Hs.eg.db' Execution halted mv: cannot stat 'functional_predictions_single_circRNA.html': No such file or directory ... Quitting from lines 90-153 (functional_predictions_all_circRNAs.Rmd) Error in read.table(file_beRBP, header = T, sep = "\t") : no lines available in input Calls: <Anonymous> ... withCallingHandlers -> withVisible -> eval -> eval -> read.table In addition: Warning message: package(s) not installed when version(s) same as current; use `force = TRUE` to re-install: 'grid' Execution halted It seems the RBP prediction failed, and here is the beRBP.log: working on M001_0.6 Sat Oct 29 03:43:26 UTC 2022 analysis_RBP featureMat_start=Sat Oct 29 03:43:26 UTC 2022 1 rank...Sat Oct 29 03:43:29 UTC 2022 Warning: [blastn] Examining 5 or more matches is recommended BLAST Database error: Error pre-fetching sequence data cp: cannot stat 'siteSegment_1.csrv': No such file or directory 2 rank...Sat Oct 29 03:43:58 UTC 2022 Warning: [blastn] Examining 5 or more matches is recommended BLAST Database error: Error pre-fetching sequence data cut: siteSegment_2.csrv: No such file or directory paste: csrvI.txt: No such file or directory 3 rank...Sat Oct 29 03:44:19 UTC 2022 Warning: [blastn] Examining 5 or more matches is recommended BLAST Database error: Error pre-fetching sequence data cut: siteSegment_3.csrv: No such file or directory 4 rank...Sat Oct 29 03:44:47 UTC 2022 Warning: [blastn] Examining 5 or more matches is recommended BLAST Database error: Error pre-fetching sequence data cut: siteSegment_4.csrv: No such file or directory 5 rank...Sat Oct 29 03:45:16 UTC 2022 Warning: [blastn] Examining 5 or more matches is recommended BLAST Database error: Error pre-fetching sequence data cut: siteSegment_5.csrv: No such file or directory 6 rank...Sat Oct 29 03:45:44 UTC 2022 Warning: [blastn] Examining 5 or more matches is recommended BLAST Database error: Error pre-fetching sequence data cut: siteSegment_6.csrv: No such file or directory 7 rank...Sat Oct 29 03:46:05 UTC 2022 Warning: [blastn] Examining 5 or more matches is recommended BLAST Database error: Error pre-fetching sequence data cut: siteSegment_7.csrv: No such file or directory 8 rank...Sat Oct 29 03:46:28 UTC 2022 Warning: [blastn] Examining 5 or more matches is recommended BLAST Database error: Error pre-fetching sequence data cut: siteSegment_8.csrv: No such file or directory 9 rank...Sat Oct 29 03:46:54 UTC 2022 Warning: [blastn] Examining 5 or more matches is recommended BLAST Database error: Error pre-fetching sequence data cut: siteSegment_9.csrv: No such file or directory 10 rank...Sat Oct 29 03:47:14 UTC 2022 Warning: [blastn] Examining 5 or more matches is recommended BLAST Database error: Error pre-fetching sequence data cut: siteSegment_10.csrv: No such file or directory analysis_RBP featureMat_finished=Sat Oct 29 03:47:40 UTC 2022 M001_0.6 all randomForest 4.6-14 Type rfNews() to see new features/changes/bug fixes. Error in file(file, "rt") : cannot open the connection Calls: generalPred -> read.delim -> read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file 'analysis_RBP.ftMat.txt': No such file or directory Execution halted Is this the circRNA sequence does not predict RBP or sth wrong before RBP prediction? Thanks in advance. Regards. Kingatsu — Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AWKFLFNARYJSHPMRM3SY2ULWFXPK5ANCNFSM6AAAAAARQ2VX3Y> . You are receiving this because you commented.Message ID: ***@***.***>

[Kingatsu]

Hi Anna,

• did you placed the UCSC genome and indexes in the input/ directory?
  Yes, here is my input files list:

backsplice_gene_name.txt  hg38.02.idx  hg38.nhr  hg38.not  hg38.nto                     Homo_sapiens.GRCh38.dna.primary_assembly.fa
hg38.00.idx               hg38.fa      hg38.nin  hg38.nsq  hg38.shd                     Homo_sapiens.GRCh38.dna.primary_assembly.fa.fai
hg38.01.idx               hg38.ndb     hg38.njs  hg38.ntf  Homo_sapiens.GRCh38.104.gtf

• And *hg38 *is the corresponding genome version?
  Yes, I used circompara2 to find the circRNAs with GRCh38.p12.genome.fa [from GENCODE]

• the parameters in the params.txt file are tab-separated?
  Yes, I am sure that.

Now I am re-running CRAFT with "MO" parameter.
I will tell you the error details later if it occurs.

Regards,
Kingatsu

[Kingatsu]

Hi Anna,
Here is the error log:

Error (circ1) : No ORFs found for the specified parameters
Error (circ1) : No ORFs found for the specified parameters
Error (circ1) : No ORFs found for the specified parameters
Error (circ1) : No ORFs found for the specified parameters
Error: Invalid record in file result_30.bed. Record is
circ2     101     10
ERROR: Received illegal bin number 262143 from getBin call.
ERROR: Unable to add record to tree.
ORF prediction analysis completed.

The circ1 is a 'chr_start-end' form and circ2 is a 'chr:start-end' form, I am sorry for blurring them off here.
Then it came to the R pipeline, and so many warnings and errors occured.
Such as:

- Maybe a connection error: 
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/workflows/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/workflows/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/books/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.14/books/src/contrib/PACKAGES'
Warning: unable to access index for repository https://cloud.r-project.org/src/contrib:
  cannot open URL 'https://cloud.r-project.org/src/contrib/PACKAGES'
PS: but actually I can download the PACKAGES from this URL by 'wget'

- Error in function
Quitting from lines 650-700 (functional_predictions_single_circRNA.Rmd)
Error in function (type, msg, asError = TRUE)  :
  Failed to connect to multimir.org port 80: Connection refused
Calls: <Anonymous> ... submit_request -> <Anonymous> -> .postForm -> <Anonymous> -> fun
In addition: Warning messages:
1: In system("timedatectl", intern = TRUE) :
  running command 'timedatectl' had status 1
2: package(s) not installed when version(s) same as current; use `force = TRUE` to
  re-install: 'org.Hs.eg.db'
3: position_stack requires non-overlapping x intervals
4: ggrepel: 287 unlabeled data points (too many overlaps). Consider increasing max.overlaps
5: position_stack requires non-overlapping x intervals
6: ggrepel: 292 unlabeled data points (too many overlaps). Consider increasing max.overlaps
7: ggrepel: 287 unlabeled data points (too many overlaps). Consider increasing max.overlaps

That is the error I have seen. it seems some circ analysis failed before (like can't find the ORF) and started cascade of Error in R later.

Thanks in advance.

Regards,
Kingatsu

[annadalmolin]

Hi Kingatsu, did the miRNA analysis work correctly? Do you know the execution time? Did you check if the ORF prediction output the result files? Anyway, the circRNAs and the input files MUST have the format described in the manual, otherwise a cascade of errors occurs. Please revise them. Regards, Anna Il giorno gio 3 nov 2022 alle ore 08:34 Kingatsu ***@***.***> ha scritto:

…

Hi Anna, Here is the error log: Error (circ1) : No ORFs found for the specified parameters Error (circ1) : No ORFs found for the specified parameters Error (circ1) : No ORFs found for the specified parameters Error (circ1) : No ORFs found for the specified parameters Error: Invalid record in file result_30.bed. Record is circ2 101 10 ERROR: Received illegal bin number 262143 from getBin call. ERROR: Unable to add record to tree. ORF prediction analysis completed. The circ1 is a 'chr_start-end' form and circ2 is a 'chr:start-end' form, I am sorry for blurring them off here. Then it came to the R pipeline, and so many warnings and errors occured. Such as: - Maybe a connection error: Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib: cannot open URL ' https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib: cannot open URL ' https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES ' Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib: cannot open URL ' https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES ' Warning: unable to access index for repository https://bioconductor.org/packages/3.14/workflows/src/contrib: cannot open URL ' https://bioconductor.org/packages/3.14/workflows/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.14/books/src/contrib: cannot open URL ' https://bioconductor.org/packages/3.14/books/src/contrib/PACKAGES' Warning: unable to access index for repository https://cloud.r-project.org/src/contrib: cannot open URL 'https://cloud.r-project.org/src/contrib/PACKAGES' PS: but actually I can download the PACKAGES from this URL by 'wget' - Error in function Quitting from lines 650-700 (functional_predictions_single_circRNA.Rmd) Error in function (type, msg, asError = TRUE) : Failed to connect to multimir.org port 80: Connection refused Calls: ... submit_request -> -> .postForm -> -> fun In addition: Warning messages: 1: In system("timedatectl", intern = TRUE) : running command 'timedatectl' had status 1 2: package(s) not installed when version(s) same as current; use force = TRUE to re-install: 'org.Hs.eg.db' 3: position_stack requires non-overlapping x intervals 4: ggrepel: 287 unlabeled data points (too many overlaps). Consider increasing max.overlaps 5: position_stack requires non-overlapping x intervals 6: ggrepel: 292 unlabeled data points (too many overlaps). Consider increasing max.overlaps 7: ggrepel: 287 unlabeled data points (too many overlaps). Consider increasing max.overlaps That is the error I have seen. it seems some circ analysis failed before (like can't find the ORF) and started cascade of Error in R after. Thanks in advance. Regards, Kingatsu — Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AWKFLFOODZTLHALD5IEXPY3WGNTJBANCNFSM6AAAAAARQ2VX3Y> . You are receiving this because you commented.Message ID: ***@***.***>

[annadalmolin]

Hi Kingatsu, were you able to correctly run CRAFT? Regards, Anna Il giorno gio 10 nov 2022 alle ore 16:17 Anna Dal Molin < ***@***.***> ha scritto:

…

Hi Kingatsu, did the miRNA analysis work correctly? Do you know the execution time? Did you check if the ORF prediction output the result files? Anyway, the circRNAs and the input files MUST have the format described in the manual, otherwise a cascade of errors occurs. Please revise them. Regards, Anna Il giorno gio 3 nov 2022 alle ore 08:34 Kingatsu ***@***.***> ha scritto: > Hi Anna, > Here is the error log: > > Error (circ1) : No ORFs found for the specified parameters > Error (circ1) : No ORFs found for the specified parameters > Error (circ1) : No ORFs found for the specified parameters > Error (circ1) : No ORFs found for the specified parameters > Error: Invalid record in file result_30.bed. Record is > circ2 101 10 > ERROR: Received illegal bin number 262143 from getBin call. > ERROR: Unable to add record to tree. > ORF prediction analysis completed. > > The circ1 is a 'chr_start-end' form and circ2 is a 'chr:start-end' form, > I am sorry for blurring them off here. > Then it came to the R pipeline, and so many warnings and errors occured. > Such as: > > - > > Maybe a connection error: > Warning: unable to access index for repository > https://bioconductor.org/packages/3.14/bioc/src/contrib: > cannot open URL ' > https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES' > Warning: unable to access index for repository > https://bioconductor.org/packages/3.14/data/annotation/src/contrib: > cannot open URL ' > https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES > ' > Warning: unable to access index for repository > https://bioconductor.org/packages/3.14/data/experiment/src/contrib: > cannot open URL ' > https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES > ' > Warning: unable to access index for repository > https://bioconductor.org/packages/3.14/workflows/src/contrib: > cannot open URL ' > https://bioconductor.org/packages/3.14/workflows/src/contrib/PACKAGES' > Warning: unable to access index for repository > https://bioconductor.org/packages/3.14/books/src/contrib: > cannot open URL ' > https://bioconductor.org/packages/3.14/books/src/contrib/PACKAGES' > Warning: unable to access index for repository > https://cloud.r-project.org/src/contrib: > cannot open URL 'https://cloud.r-project.org/src/contrib/PACKAGES' > PS: but actually I can download the PACKAGES from this URL by 'wget' > - > > Error in function > Quitting from lines 650-700 > (functional_predictions_single_circRNA.Rmd) > Error in function (type, msg, asError = TRUE) : > Failed to connect to multimir.org port 80: Connection refused > Calls: ... submit_request -> -> .postForm -> -> fun > In addition: Warning messages: > 1: In system("timedatectl", intern = TRUE) : > running command 'timedatectl' had status 1 > 2: package(s) not installed when version(s) same as current; use force > = TRUE to > re-install: 'org.Hs.eg.db' > 3: position_stack requires non-overlapping x intervals > 4: ggrepel: 287 unlabeled data points (too many overlaps). Consider > increasing max.overlaps > 5: position_stack requires non-overlapping x intervals > 6: ggrepel: 292 unlabeled data points (too many overlaps). Consider > increasing max.overlaps > 7: ggrepel: 287 unlabeled data points (too many overlaps). Consider > increasing max.overlaps > > That is the error I have seen. it seems some circ analysis failed before (like can't find the ORF) and started cascade of Error in R after. > > Thanks in advance. > > Regards, > Kingatsu > > — > Reply to this email directly, view it on GitHub > <#2 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AWKFLFOODZTLHALD5IEXPY3WGNTJBANCNFSM6AAAAAARQ2VX3Y> > . > You are receiving this because you commented.Message ID: > ***@***.***> >

[Kingatsu]

Hi Anna,
Sorry for the late reply.

Well, I cann't run the CRAFT with RBP detection yet. So maybe the problems are in the circRNA sequences, I guess.
I am running the circRNA detection tools again and try to find some other circRNAs, then run the CRAFT again.
I will tell you if it works!

Regards,
Kingatsu