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upendrak / lincRNA_pipeline

Optimizing the pipeline for lincRNA starting from TopHat output to final lincRNA detection
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Error messages, etc. #2

Open mfcovington opened 9 years ago

mfcovington commented 9 years ago

I ran the pipeline on my laptop like this:

time sh lincRNA_pipeline.sh -c sample.data/cuffcompare_out_annot_no_annot.combined.gtf -g sample.data/Brapa_sequence_v1.2.fa -r sample.data/Brassica_rapa_v1.2.cds -b sample.data/TE_RNA_transcripts.fa

Here's the output:

--2015-03-16 16:34:26--  https://github.com/TransDecoder/TransDecoder/archive/2.0.1.tar.gz
Resolving github.com... 192.30.252.130
Connecting to github.com|192.30.252.130|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://codeload.github.com/TransDecoder/TransDecoder/tar.gz/2.0.1 [following]
--2015-03-16 16:34:26--  https://codeload.github.com/TransDecoder/TransDecoder/tar.gz/2.0.1
Resolving codeload.github.com... 192.30.252.145
Connecting to codeload.github.com|192.30.252.145|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 9925281 (9.5M) [application/x-gzip]
Saving to: 'STDOUT'

 0% [                                                                                                                                            ] 0           --.-K/s              x TransDecoder-2.0.1/
x TransDecoder-2.0.1/LICENSE.txt
x TransDecoder-2.0.1/Makefile
x TransDecoder-2.0.1/PerlLib/
x TransDecoder-2.0.1/PerlLib/Fasta_reader.pm
x TransDecoder-2.0.1/PerlLib/GFF3_utils.pm
x TransDecoder-2.0.1/PerlLib/Gene_obj.pm
x TransDecoder-2.0.1/PerlLib/Gene_obj_indexer.pm
x TransDecoder-2.0.1/PerlLib/Longest_orf.pm
x TransDecoder-2.0.1/PerlLib/Nuc_translator.pm
x TransDecoder-2.0.1/PerlLib/TiedHash.pm
x TransDecoder-2.0.1/README
x TransDecoder-2.0.1/README.md
x TransDecoder-2.0.1/Release.Notes
 0% [                                                                                                                                            ] 47,513       223KB/s             
x TransDecoder-2.0.1/TransDecoder.Predict
x TransDecoder-2.0.1/notes
x TransDecoder-2.0.1/sample_data/
x TransDecoder-2.0.1/sample_data/blastp.results.outfmt6.gz
x TransDecoder-2.0.1/sample_data/cleanme.pl
x TransDecoder-2.0.1/sample_data/pfam.domtblout.gz
x TransDecoder-2.0.1/sample_data/runMe.sh
 1% [>                                                                                                                                           ] 139,079      324KB/s             
92% [=================================================================================================================================>          ] 9,219,351    212KB/s  eta 4s     
x TransDecoder-2.0.1/sample_data/transcripts.gtf.gz
x TransDecoder-2.0.1/transdecoder_plugins/
x TransDecoder-2.0.1/transdecoder_plugins/Makefile
99% [==========================================================================================================================================> ] 9,909,633    176KB/s  eta 1s     
x TransDecoder-2.0.1/util/
x TransDecoder-2.0.1/util/bin/
x TransDecoder-2.0.1/util/bin/.hidden
100%[===========================================================================================================================================>] 9,925,281    179KB/s   in 52s    

2015-03-16 16:35:18 (188 KB/s) - written to stdout [9925281/9925281]

x TransDecoder-2.0.1/util/compute_base_probs.pl
x TransDecoder-2.0.1/util/cufflinks_gtf_genome_to_cdna_fasta.pl
x TransDecoder-2.0.1/util/cufflinks_gtf_to_alignment_gff3.pl
x TransDecoder-2.0.1/util/cufflinks_gtf_to_bed.pl
x TransDecoder-2.0.1/util/ffindex_resume.pl
x TransDecoder-2.0.1/util/gene_list_to_gff.pl
x TransDecoder-2.0.1/util/get_top_longest_fasta_entries.pl
x TransDecoder-2.0.1/util/gff3_file_to_bed.pl
x TransDecoder-2.0.1/util/gff3_file_to_proteins.pl
x TransDecoder-2.0.1/util/index_gff3_files_by_isoform.pl
x TransDecoder-2.0.1/util/nr_ORFs_gff3.pl
x TransDecoder-2.0.1/util/pfam_mpi.pbs
x TransDecoder-2.0.1/util/pfam_runner.pl
x TransDecoder-2.0.1/util/remove_eclipsed_ORFs.pl
x TransDecoder-2.0.1/util/score_CDS_liklihood_all_6_frames.pl
x TransDecoder-2.0.1/util/seq_n_baseprobs_to_logliklihood_vals.pl
dyld: Library not loaded: /usr/local/lib/gcc/x86_64-apple-darwin13.3.0/4.8.3/libgomp.1.dylib
  Referenced from: /usr/local/bin/makeblastdb
  Reason: image not found
lincRNA_pipeline.sh: line 41: 74333 Trace/BPT trap: 5       makeblastdb -in $blastfile -dbtype nucl -out $blastfile.blast.out
dyld: Library not loaded: /usr/local/lib/gcc/x86_64-apple-darwin13.3.0/4.8.3/libgomp.1.dylib
  Referenced from: /usr/local/bin/makeblastdb
  Reason: image not found
lincRNA_pipeline.sh: line 43: 74335 Trace/BPT trap: 5       makeblastdb -in $referenceCDS -dbtype nucl -out $referenceCDS.blast.out
lincRNA_pipeline.sh: line 46: gffread: command not found
sed: transcripts_u_filter.fa: No such file or directory
lincRNA_pipeline.sh: line 53: cd: transcripts_u_filter.fa.transdecoder_dir: No such file or directory
sed: longest_orfs.cds: No such file or directory
/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can't open file '../extract_sequences.py': [Errno 2] No such file or directory
sed: longest_orfs.cds.genes.not.genes.fa: No such file or directory
dyld: Library not loaded: /usr/local/lib/gcc/x86_64-apple-darwin13.3.0/4.8.3/libgomp.1.dylib
  Referenced from: /usr/local/bin/blastn
  Reason: image not found
lincRNA_pipeline.sh: line 70: 74348 Trace/BPT trap: 5       blastn -query longest_orfs.cds.genes.not.genes.fa -db ../$blastfile.blast.out -out longest_orfs.cds.genes.not.genes.fa.blast.out -outfmt 6
/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can't open file '../filter_sequences.py': [Errno 2] No such file or directory
grep: longest_orfs.cds.genes.not.genes.fa: No such file or directory
/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can't open file '../fasta_remove.py': [Errno 2] No such file or directory
sed: lincRNA.genes: No such file or directory
/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can't open file '../extract_sequences-1.py': [Errno 2] No such file or directory
lincRNA_pipeline.sh: line 83: cap3: command not found
cat: lincRNA.genes.fa.cap.singlets: No such file or directory
cat: lincRNA.genes.fa.cap.contigs: No such file or directory
dyld: Library not loaded: /usr/local/lib/gcc/x86_64-apple-darwin13.3.0/4.8.3/libgomp.1.dylib
  Referenced from: /usr/local/bin/blastn
  Reason: image not found
lincRNA_pipeline.sh: line 92: 74358 Trace/BPT trap: 5       blastn -query lincRNA_genes_non_redundant.fa -db ../$referenceCDS.blast.out -out lincRNA_non_redundant.fa_cds_blast.out -evalue 1e-30 -outfmt 6
/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can't open file '../linc_RNA_filter.py': [Errno 2] No such file or directory
grep: lincRNA_non_redundant.fa_cds_blast.out.filtered: No such file or directory
/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can't open file '../extract_sequences-1.py': [Errno 2] No such file or directory
grep: lincRNA_non_redundant_filtered.genes.fa: No such file or directory
dyld: Library not loaded: /usr/local/lib/gcc/x86_64-apple-darwin13.3.0/4.8.3/libgomp.1.dylib
  Referenced from: /usr/local/bin/makeblastdb
  Reason: image not found
lincRNA_pipeline.sh: line 104: 74363 Trace/BPT trap: 5       makeblastdb -in lincRNA_non_redundant_filtered.genes.fa -dbtype nucl -out lincRNA_non_redundant_filtered_blast.out
dyld: Library not loaded: /usr/local/lib/gcc/x86_64-apple-darwin13.3.0/4.8.3/libgomp.1.dylib
  Referenced from: /usr/local/bin/blastn
  Reason: image not found
lincRNA_pipeline.sh: line 106: 74364 Trace/BPT trap: 5       blastn -query lincRNA_non_redundant_filtered.genes.fa -db lincRNA_non_redundant_filtered_blast.out -out lincRNA_non_redundant_filtered_blast.out.blast.out -evalue 1e-30 -outfmt 6
/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can't open file '../linc_RNA_filter-1.py': [Errno 2] No such file or directory
grep: lincRNA_non_redundant_filtered_blast.out.blast.out.uniq: No such file or directory
/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can't open file '../extract_sequences-1.py': [Errno 2] No such file or directory
/usr/local/Cellar/python/2.7.8_2/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can't open file '../fasta_header_rename.py': [Errno 2] No such file or directory

real    0m54.186s
user    0m0.319s
sys 0m0.534s

A few things that should probably be done:

mfcovington commented 9 years ago

@jkhta13

Dependencies are:

ghost commented 9 years ago

@mfcovington Thanks.

upendrak commented 9 years ago

@jkhta13 thanks for helping me out. Hope you can fix the pipeline. Good luck and let me know if you need further information....

ghost commented 9 years ago

I never said it was for free.

On Fri, Mar 20, 2015 at 3:06 PM, Upendra Kumar Devisetty < notifications@github.com> wrote:

@jkhta13 https://github.com/jkhta13 thanks for helping me out. Hope you can fix the pipeline. Good luck and let me know if you need further information....

— Reply to this email directly or view it on GitHub https://github.com/upendrak/lincRNA_pipeline/issues/2#issuecomment-84166499 .

upendrak commented 9 years ago

@jkhta13 how about i offer you authorship?

ghost commented 9 years ago

No I meant a million bucks.

On Fri, Mar 20, 2015 at 3:22 PM, Upendra Kumar Devisetty < notifications@github.com> wrote:

@jkhta13 https://github.com/jkhta13 how about i offer you authorship?

— Reply to this email directly or view it on GitHub https://github.com/upendrak/lincRNA_pipeline/issues/2#issuecomment-84169227 .

upendrak commented 9 years ago

this pipeline is not that worth...

On Mar 20, 2015, at 3:23 PM, jkhta13 notifications@github.com wrote:

No I meant a million bucks.

On Fri, Mar 20, 2015 at 3:22 PM, Upendra Kumar Devisetty < notifications@github.com> wrote:

@jkhta13 https://github.com/jkhta13 how about i offer you authorship?

— Reply to this email directly or view it on GitHub https://github.com/upendrak/lincRNA_pipeline/issues/2#issuecomment-84169227 .

— Reply to this email directly or view it on GitHub https://github.com/upendrak/lincRNA_pipeline/issues/2#issuecomment-84169325.

mfcovington commented 9 years ago

It will be once he's finished with it! He's going to embed real diamonds in the code.

ghost commented 9 years ago

You mean bitcoins.

On Fri, Mar 20, 2015 at 4:15 PM, Mike Covington notifications@github.com wrote:

It will be once he's finished with it! He's going to embed real diamonds in the code.

— Reply to this email directly or view it on GitHub https://github.com/upendrak/lincRNA_pipeline/issues/2#issuecomment-84186072 .