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Tormes: ERROR: could not find input file #25

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Stigimoloch opened this issue Jul 23, 2020 · 2 comments
Open

Tormes: ERROR: could not find input file #25

Stigimoloch opened this issue Jul 23, 2020 · 2 comments
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bug Something isn't working question Further information is requested

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@Stigimoloch
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Hi,
I have a problem with Tormes. When I work on fastq reads. When I start analysis all output files are moved by Tormes to rubbish and after in analysis I got a lot of information about "ERROR: could not find input file". In the end, I'm gotten empty folders without reports.
When I analyze the assembled genome in fasta format everything is ok.
I'm looking forward to your answer.

error-tormes.txt
chmod: changing permissions of 'metadata.R': Operation not permitted
Software: /opt/anaconda3/envs/tormes-1.1/bin/abricate found
Software: /opt/anaconda3/envs/tormes-1.1/bin/convert found
Software: /opt/anaconda3/envs/tormes-1.1/bin/fasttree found
Software: /opt/anaconda3/envs/tormes-1.1/bin/kraken found
Software: /opt/anaconda3/envs/tormes-1.1/bin/kraken-report found
Software: /opt/anaconda3/envs/tormes-1.1/bin/megahit found
Software: /opt/anaconda3/envs/tormes-1.1/bin/mlst found
Software: /opt/anaconda3/envs/tormes-1.1/bin/parallel found
Software: /opt/anaconda3/envs/tormes-1.1/bin/prinseq-lite.pl found
Software: /opt/anaconda3/envs/tormes-1.1/bin/prokka found
Software: /opt/anaconda3/envs/tormes-1.1/bin/quast found
Software: /opt/anaconda3/envs/tormes-1.1/bin/roary found
Software: /opt/anaconda3/envs/tormes-1.1/bin/roary2svg.pl found
Software: /opt/anaconda3/envs/tormes-1.1/bin/sickle found
Software: /opt/anaconda3/envs/tormes-1.1/bin/spades.py found
Software: /opt/anaconda3/envs/tormes-1.1/bin/trimmomatic found
Software: /opt/anaconda3/envs/tormes-1.1/bin/../share/mauve-*/Mauve.jar found
Binaries for MAUVE found
Software: /opt/anaconda3/envs/tormes-1.1/bin/../CGE-modules/fimtyper/fimtyper.pl found
Software: /opt/anaconda3/envs/tormes-1.1/bin/../CGE-modules/serotypefinder/serotypefinder.py found
Binaries for BLAST version 2.6 or later found
Software: /opt/anaconda3/envs/tormes-1.1/bin/../CGE-modules/pointfinder/PointFinder.py found
chmod: changing permissions of '/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/metadata.R': Operation not permitted

Thanks for using tormes version 1.1
Status can be seen in "/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/tormes.log"

cp: cannot stat 'a': No such file or directory

Some reads are not gzipped... Let's gzip for optimize speed!

gzip: /media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/Raw_reads/EC5_S11_L001_R2_001.fastq_R1.fastq.gz: Operation not permitted
gzip: /media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/Raw_reads/EC5_S11_L001_R2_001.fastq_R1.fastq.gz: Operation not permitted
TrimmomaticPE: Started with arguments:
-threads 20 -phred33 /media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/Raw_reads/EC5_S11_L001_R2_001.fastq_R1.fastq.gz /media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/Raw_reads/EC5_S11_L001_R2_001.fastq_R2.fastq.gz /media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/cleaned_reads/EC5_S11_L001_R2_001.fastq.noadapt.R1.fastq.gz /dev/null /media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/cleaned_reads/EC5_S11_L001_R2_001.fastq.noadapt.R2.fastq.gz /dev/null ILLUMINACLIP:/opt/anaconda3/envs/tormes-1.1/bin/../files/adapters.fasta:1:30:11
Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG'
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG'
Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'
Skipping duplicate Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'
Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT'
Using Long Clipping Sequence: 'AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG'
Using Long Clipping Sequence: 'AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG'
Using Long Clipping Sequence: 'TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC'
Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT'
Using Long Clipping Sequence: 'TTTTTTTTTTCAAGCAGAAGACGGCATACGA'
Skipping duplicate Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
Using Long Clipping Sequence: 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
Using Long Clipping Sequence: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC'
Using Long Clipping Sequence: 'CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA'
Using Long Clipping Sequence: 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT'
ILLUMINACLIP: Using 2 prefix pairs, 17 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Exception in thread "main" java.io.FileNotFoundException: /media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/Raw_reads/EC5_S11_L001_R2_001.fastq_R2.fastq.gz (No such file or directory)
at java.io.FileInputStream.open0(Native Method)
at java.io.FileInputStream.open(FileInputStream.java:195)
at java.io.FileInputStream.(FileInputStream.java:138)
at org.usadellab.trimmomatic.fastq.FastqParser.parse(FastqParser.java:135)
at org.usadellab.trimmomatic.TrimmomaticPE.process(TrimmomaticPE.java:268)
at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:555)
at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)
gzip: /media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/cleaned_reads/*gz.gz: No such file or directory

ERROR: could not find input file "/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/cleaned_reads/EC5_S11_L001_R2_001.fastq.noadapt.R1.fastq".

Try 'perl prinseq-lite.pl -h' for more information.
Exit program.
gzip: /media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/cleaned_reads/*fastq: No such file or directory
paste: /media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/temp1: No such file or directory
cut: /media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/kraken_summary.tmp: No such file or directory
cut: /media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/kraken_summary.tmp: No such file or directory
sed: preserving permissions for ‘/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/sedXvpZWW’: Operation not permitted
sed: preserving permissions for ‘/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/mlst/sedyrBS9Y’: Operation not permitted
sed: preserving permissions for ‘/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/mlst/sedIVgKa0’: Operation not permitted

WARNING: Pangenome analysis was skipped automatically due to low number of genomes to compare.

sed: can't read /media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/serotyping/serotyping.txt: No such file or directory
cp: cannot stat '/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/antibiotic_resistance_genes/*/tab': No such file or directory
cp: cannot stat '/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/virulence_genes/tab': No such file or directory
cp: cannot stat '/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/point_mutations//_PointFinder_results.txt': No such file or directory
ERROR: Can't open '/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/report_files/*resfinder_min90.tab' to summarize.
ERROR: Can't open '/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/report_files/*card_min90.tab' to summarize.
ERROR: Can't open '/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/report_files/*argannot_min90.tab' to summarize.
sed: preserving permissions for ‘/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/report_files/sedjvhr0Z’: Operation not permitted
sed: preserving permissions for ‘/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/report_files/sed42WdP3’: Operation not permitted
sed: preserving permissions for ‘/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/report_files/sedwfVdN1’: Operation not permitted
sed: preserving permissions for ‘/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/report_files/sedY9FRy5’: Operation not permitted
sed: preserving permissions for ‘/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/report_files/sedjqnLE4’: Operation not permitted
sed: preserving permissions for ‘/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/report_files/sedW4M2W4’: Operation not permitted
sed: preserving permissions for ‘/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/report_files/sedbU8CC8’: Operation not permitted
sed: preserving permissions for ‘/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/report_files/sed2iWrG7’: Operation not permitted
sed: preserving permissions for ‘/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/report_files/sedmpg1ia’: Operation not permitted
sed: preserving permissions for ‘/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/report_files/sed5Um638’: Operation not permitted
sed: preserving permissions for ‘/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/report_files/sed7RzBwd’: Operation not permitted
sed: preserving permissions for ‘/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/report_files/sedyXv1mb’: Operation not permitted
sed: preserving permissions for ‘/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/report_files/sedLw9Eaf’: Operation not permitted
sed: preserving permissions for ‘/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/report_files/sed8SaZee’: Operation not permitted
sed: preserving permissions for ‘/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/report_files/sedHtkWve’: Operation not permitted
cut: '/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/report_files/*resfinder_min90.tab': No such file or directory
cut: /media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/report_files/tmp2.txt: No such file or directory
paste: /media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/report_files/tmp2.txt: No such file or directory
sed: preserving permissions for ‘/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/report_files/sedx1IG4i’: Operation not permitted
cp: cannot stat '/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/fimH_typing/fimH_typing.txt': No such file or directory
cp: cannot stat '/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/serotyping/serotyping.txt': No such file or directory
cp: cannot stat '/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/plasmids/*tab': No such file or directory
chmod: changing permissions of '/media/bioinformatyka/Documents/roboczy_rafal/20200706_Tormes/EC5_out_test_fasq_8/render_report.sh': Operation not permitted
Warning message:
package ‘rmarkdown’ was built under R version 3.6.3

processing file: tormes_report.Rmd

|
| | 0%
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|.. | 3%
ordinary text without R code

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|.... | 5%
label: unnamed-chunk-1 (with options)
List of 3
$ echo : logi FALSE
$ message: logi FALSE
$ warning: logi FALSE

Registered S3 method overwritten by 'treeio':
method from
root.phylo ape
ggtree v2.0.4 For help: https://yulab-smu.github.io/treedata-book/

If you use ggtree in published research, please cite the most appropriate paper(s):

�[36m-�[39m Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution 2018, 35(12):3041-3043. doi: 10.1093/molbev/msy194
�[36m-�[39m Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

last_plot

The following object is masked from 'package:stats':

filter

The following object is masked from 'package:graphics':

layout

treeio v1.10.0 For help: https://yulab-smu.github.io/treedata-book/

If you use treeio in published research, please cite:

LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. Molecular Biology and Evolution 2019, accepted. doi: 10.1093/molbev/msz240

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ordinary text without R code

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|........ | 11%
label: unnamed-chunk-2 (with options)
List of 1
$ echo: logi FALSE

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|......... | 14%
ordinary text without R code

|
|........... | 16%
label: unnamed-chunk-3 (with options)
List of 1
$ echo: logi FALSE

Quitting from lines 75-78 (tormes_report.Rmd)
Error in read.table("sequencing_assembly_report.txt", header = T, sep = "\t", :
no lines available in input
Calls: ... withCallingHandlers -> withVisible -> eval -> eval -> read.table
In addition: Warning messages:
1: package 'ggplot2' was built under R version 3.6.3
2: package 'knitr' was built under R version 3.6.3
3: package 'plotly' was built under R version 3.6.3
4: package 'RColorBrewer' was built under R version 3.6.3
5: package 'reshape2' was built under R version 3.6.3

Execution halted
@biobrad
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biobrad commented Jul 23, 2020 via email

@nmquijada nmquijada added the bug Something isn't working label Jul 27, 2020
@nmquijada
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Dear @Stigimoloch
As @biobrad said, it seems that you have a problem with permissions. Do you have permissions from the directory where you run tormes and where you set the output directory?
Best,
Narciso

@nmquijada nmquijada added the question Further information is requested label Aug 10, 2020
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