biobrad
commented
4 years ago Hey mate,
Looks like you are running it from root. Try running it again but use sudo before the tormes commands. If that doesn't work you should try installing everything under your username ie: /home/yourusername/ I have anaconda and everything installed there. Running stuff from root is a pain with permissions etc. Cheers Brad
On Thu, 23 Jul 2020, 5:52 pm Stigimoloch, notifications@github.com wrote:
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
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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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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
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nmquijada
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
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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':
The following object is masked from 'package:stats':
The following object is masked from 'package:graphics':
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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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