rm error: impossible to remove blast_contigs_1_fmtd

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rm error: impossible to remove blast_contigs_1_fmtd

Post by Massimiliano Volpe on Tue May 16, 2017 4:35 pm

Dear all,

I'm trying to setup my dnaPipeTE installation using the test dataset for the first analysis.

Trinity and RepeatMasker seems to work properly, however I still have a problem during the
estimation of repeat phase, after the third Blast run. It seems that some files were not created
so it is impossible to remove them. Since my test folder is named "prova1", I ran:

python3 ./dnaPipeTE.py -input test_dataset.fastq -output prova1/ -genome_size 10000000 -genome_coverage 0.1 -sample_number 1

Code:

#########################################
### Making contigs annotation from RM ###
#########################################
Done


Making blast sample...
sampling file found, skipping sampling...
total number of reads: 100125
maximum number of reads to sample:  12048
fastq :  test_dataset.fastq
sampling 1 samples of max 12048 reads to reach coverage...
999984 bases sampled in 12048 reads
s_test_dataset.fastq_blast done.
#######################################################
### Blast 1 : raw reads against all repeats contigs ###
#######################################################
Blast 1 files found, skipping Blast 1 ...
###################################################
### Blast 2 : raw reads against annoted repeats ###
###################################################
Blast 2 files found, skipping Blast 2 ...
#####################################################
### Blast 3 : raw reads against unannoted repeats ###
#####################################################
Blast 3 files found, skipping Blast 3 ...
#######################################################
### Estimation of Repeat content from blast outputs ###
#######################################################
parsing blastout and adding RM annotations for each read...
awk: riga com.:1: attenzione: sequenza di escape `\$' considerata come semplice `$'
rm: impossibile rimuovere "prova1/blast_contigs_1_fmtd": File o directory non esistente
Done, results in: blast_out/blastout_final_fmtd_annoted
#########################################
### OK, lets build some pretty graphs ###
#########################################
Drawing graphs...
null device
          1
null device
          1
null device
          1
null device
          1
Warning message:
Removed 3 rows containing missing values (geom_bar).
Warning message:
Removed 3 rows containing missing values (geom_bar).
Done
Removing Trinity runs files...
done
Finishin time: Tue May 16 17:08:43 2017
########################
#   see you soon !!!   #
########################

Problem have been found for prova1/blast_contigs_1_fmtd

Checking results I can see difference expecially in the landscape.pdf output.
In my test analysis LTR/Pao are absent (I'm not able to post an url containing the link to the image).

What is going wrong?

EDIT:
I have also noticed an error at the beginning for which it is impossible to open readsToComponents.out.sort file:
Code:

           Let's go !!!                                    
                                                            
Start time: Tue May 16 17:07:21 2017
total number of reads: 100125
maximum number of reads to sample:  12048
fastq :  test_dataset.fastq
sampling 1 samples of max 12048 reads to reach coverage...
999984 bases sampled in 12048 reads
s_test_dataset.fastq done.
###################################
### TRINITY to assemble repeats ###
###################################

***** TRINITY iteration 1 *****

Selecting reads for Trinity iteration number 1...
awk: fatale: non riesco ad aprire file `prova1//Trinity_run0/chrysalis/readsToComponents.out.sort' in lettura (File o directory non esistente)
Done

I'm sorry I do not post the complete log but the forum says I have not permissions to post links even if the log have not any link.


Thank you in advantage!

Massimiliano

Massimiliano Volpe

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Re: rm error: impossible to remove blast_contigs_1_fmtd

Post by Clément Goubert on Wed Jul 19, 2017 11:03 pm

Hi all!

See answer to this error here: https://github.com/clemgoub/dnaPipeTE/issues/7

Cheers,

Clément
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Clément Goubert
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