Error 141 on installation test

[mb492]

Hello,

I have installed ORP according to the instructions but when running the 'Test the installation' section in the 'sampledata' folder I get this error:
Total time = 2.32095s
Reported 69 pairwise alignments, 69 HSPs.
15 queries aligned.
make: [/PROJECTS/Oyster_River_Protocol/sampledata/assemblies/diamond/test.list5] Error 141
make: Deleting file `/PROJECTS/Oyster_River_Protocol/sampledata/assemblies/diamond/test.list5'
Any thoughts on how to fix Error 141? Thanks, Matt

[rafaeltiveron]

A slightly different error for me:

Total time = 1.52642s
Reported 62 pairwise alignments, 65 HSPs.
17 queries aligned.
ERROR	Impossible to read /usr/local/bin/Oyster_River/sampledata/assemblies/test.ORP.fasta

test.ORP.fasta was not generated.

[macmanes]

Do you have write permission to /usr/local/bin/? On Aug 29, 2019, at 08:35, rafaeltiveron <[email protected]<mailto:[email protected]>> wrote: Caution - External Email

…

________________________________ A slightly different error for me: Total time = 1.52642s Reported 62 pairwise alignments, 65 HSPs. 17 queries aligned. ERROR Impossible to read /usr/local/bin/Oyster_River/sampledata/assemblies/test.ORP.fasta — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_macmanes-2Dlab_Oyster-5FRiver-5FProtocol_issues_32-3Femail-5Fsource-3Dnotifications-26email-5Ftoken-3DAABIHEC2EKT2237KYA2L2ODQG67ANA5CNFSM4HYX5772YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5OKF6Y-23issuecomment-2D526164731&d=DwMCaQ&c=c6MrceVCY5m5A_KAUkrdoA&r=lFmSBplGfvpPNKk6W2tN6-UcUrgjlsdpj7JuHtA6g_Y&m=_jd2aosvrtLhcLDj0dHOtOPCnMZ5d8ScIXP2rzqiV6k&s=xA_lOgZWmOmkZyds49mGE6BFw5O7SH4PzHvPP9XQY6A&e=>, or mute the thread<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AABIHEGLDKIHKISNSN6QVNLQG67ANANCNFSM4HYX577Q&d=DwMCaQ&c=c6MrceVCY5m5A_KAUkrdoA&r=lFmSBplGfvpPNKk6W2tN6-UcUrgjlsdpj7JuHtA6g_Y&m=_jd2aosvrtLhcLDj0dHOtOPCnMZ5d8ScIXP2rzqiV6k&s=4tyrFq6U_48KRH-55l6gLVRD7ggybRfe_9HpAkWQmlw&e=>.

[rafaeltiveron]

Yes. I have tested as local user and root. Same issue. All the other files were generated and recorded on that.

[rafaeltiveron]

I've solved. The problem is on "TPM_FILT = ". It doesn't recognize the input value. You need to fix to "TPM_FILT=".

Also, I defined "ifndef TPM_FILT" below what was stated on "oyster.mk", for purpose of output salmon comparison on DESeq2, which is my interest. I just take off awk step:

ifdef TPM_FILT
	cat ${DIR}/quants/salmon_orthomerged_${RUNOUT}/quant.sf| awk '$$4 > $(TPM_FILT)' | cut -f1 | sed 1d > ${DIR}/assemblies/working/${RUNOUT}.HIGHEXP.txt
	cat ${DIR}/quants/salmon_orthomerged_${RUNOUT}/quant.sf| awk '$$4 < $(TPM_FILT)' | cut -f1 | sed 1d > ${DIR}/assemblies/working/${RUNOUT}.LOWEXP.txt
	cp ${DIR}/assemblies/${RUNOUT}.ORP.intermediate.fasta ${DIR}/assemblies/working/${RUNOUT}.ORP_BEFORE_TPM_FILT.fasta
	python ${MAKEDIR}/scripts/filter.py ${DIR}/assemblies/${RUNOUT}.ORP.intermediate.fasta ${DIR}/assemblies/working/${RUNOUT}.HIGHEXP.txt > ${DIR}/assemblies/working/${RUNOUT}.ORP.HIGHEXP.fasta
	grep -Fwf ${DIR}/assemblies/working/${RUNOUT}.LOWEXP.txt ${DIR}/assemblies/${RUNOUT}.ORP.diamond.txt >> ${DIR}/assemblies/working/${RUNOUT}.blasted
	awk '{print $$1}' ${DIR}/assemblies/working/${RUNOUT}.blasted | sort | uniq | tee -a ${DIR}/assemblies/working/${RUNOUT}.donotremove.list
	python ${MAKEDIR}/scripts/filter.py ${DIR}/assemblies/${RUNOUT}.ORP.intermediate.fasta ${DIR}/assemblies/working/${RUNOUT}.donotremove.list > ${DIR}/assemblies/working/${RUNOUT}.saveme.fasta
	cat ${DIR}/assemblies/working/${RUNOUT}.saveme.fasta ${DIR}/assemblies/working/${RUNOUT}.ORP.HIGHEXP.fasta > ${DIR}/assemblies/${RUNOUT}.ORP.fasta
	touch ${DIR}/assemblies/${RUNOUT}.filter.done
else
	touch ${DIR}/assemblies/${RUNOUT}.filter.done
endif
ifndef TPM_FILT
	cat ${DIR}/quants/salmon_orthomerged_${RUNOUT}/quant.sf| cut -f1 | sed 1d > ${DIR}/assemblies/working/${RUNOUT}.HIGHEXP.txt
	cat ${DIR}/quants/salmon_orthomerged_${RUNOUT}/quant.sf| cut -f1 | sed 1d > ${DIR}/assemblies/working/${RUNOUT}.LOWEXP.txt
	cp ${DIR}/assemblies/${RUNOUT}.ORP.intermediate.fasta ${DIR}/assemblies/working/${RUNOUT}.ORP_BEFORE_TPM_FILT.fasta
	python ${MAKEDIR}/scripts/filter.py ${DIR}/assemblies/${RUNOUT}.ORP.intermediate.fasta ${DIR}/assemblies/working/${RUNOUT}.HIGHEXP.txt > ${DIR}/assemblies/working/${RUNOUT}.ORP.HIGHEXP.fasta
	grep -Fwf ${DIR}/assemblies/working/${RUNOUT}.LOWEXP.txt ${DIR}/assemblies/${RUNOUT}.ORP.diamond.txt >> ${DIR}/assemblies/working/${RUNOUT}.blasted
	awk '{print $$1}' ${DIR}/assemblies/working/${RUNOUT}.blasted | sort | uniq | tee -a ${DIR}/assemblies/working/${RUNOUT}.donotremove.list
	python ${MAKEDIR}/scripts/filter.py ${DIR}/assemblies/${RUNOUT}.ORP.intermediate.fasta ${DIR}/assemblies/working/${RUNOUT}.donotremove.list > ${DIR}/assemblies/working/${RUNOUT}.saveme.fasta
	cat ${DIR}/assemblies/working/${RUNOUT}.saveme.fasta ${DIR}/assemblies/working/${RUNOUT}.ORP.HIGHEXP.fasta > ${DIR}/assemblies/${RUNOUT}.ORP.fasta
	touch ${DIR}/assemblies/${RUNOUT}.filter.done
else
	touch ${DIR}/assemblies/${RUNOUT}.filter.done
endif

I'm learning about programming. So, please, review these changes. Any mistake, please tell me. I didn't send these changes to github.

[rafaeltiveron]

So, with these changes, I've got a new error:

/usr/local/bin/Oyster_River/oyster.mk transrate STRAND=RF MEM=15 CPU=32 READ1=test.1.fq.gz READ2=test.2.fq.gz RUNOUT=test
[ INFO] 2019-08-29 11:34:00 : Loading assembly: /usr/local/bin/Oyster_River/sampledata/assemblies/test.ORP.fasta
[ERROR] 2019-08-29 11:34:00 : Non unique fasta identifier found
[ERROR] 2019-08-29 11:34:00 : >NODE_48_length_164_cov_0.825688_g45_i0
[ERROR] 2019-08-29 11:34:00 : Please make sure there are no duplicate entries in the assembly
[ERROR] 2019-08-29 11:34:00 : Contig name is taken from before the first | or space
[ERROR] 2019-08-29 11:34:00 : If you used Trinity, there is a known bug that breakscontig names to make them non-unique.
[ERROR] 2019-08-29 11:34:00 : You can fix your Trinity assembly by replacing | with _
[ERROR] 2019-08-29 11:34:00 : Example commands to achieve this:
[ERROR] 2019-08-29 11:34:00 : On OSX:
[ERROR] 2019-08-29 11:34:00 : `sed 's/\|/_/' Trinity.fasta > Trinity.fixed.fa`
[ERROR] 2019-08-29 11:34:00 : On Linux:
[ERROR] 2019-08-29 11:34:00 : `sed 's_|_-_g' Trinity.fasta > Trinity.fixed.fa`
[ERROR] 2019-08-29 11:34:00 : Transrate::AssemblyError
/usr/local/bin/Oyster_River/oyster.mk:410: recipe for target '/usr/local/bin/Oyster_River/sampledata/reports/transrate_test/assemblies.csv' failed

test.ORP.fasta has just these sequence labels:

J547
NODE_1_length_2546_cov_122.433962_g0_i0
NODE_21_length_448_cov_12.764075_g16_i0
NODE_29_length_283_cov_84.372807_g26_i0
NODE_2_length_1624_cov_77.863607_g1_i0
NODE_48_length_164_cov_0.825688_g45_i0
NODE_5_length_1385_cov_59.174809_g2_i0
NODE_66_length_164_cov_0.561798_g61_i0
NODE_9_length_969_cov_60.111597_g7_i0
R541
R544
S203
S568
TRINITY_DN30_c0_g1_i1
TRINITY_DN6_c0_g1_i1
TRINITY_DN7_c0_g1_i1
TRINITY_DN9_c0_g1_i2

So, again I changed the added part, as it:

ifndef TPM_FILT
#	cat ${DIR}/quants/salmon_orthomerged_${RUNOUT}/quant.sf| cut -f1 | sed 1d > ${DIR}/assemblies/working/${RUNOUT}.HIGHEXP.txt
	cat ${DIR}/quants/salmon_orthomerged_${RUNOUT}/quant.sf| cut -f1 | sed 1d > ${DIR}/assemblies/working/${RUNOUT}.LOWEXP.txt
	cp ${DIR}/assemblies/${RUNOUT}.ORP.intermediate.fasta ${DIR}/assemblies/working/${RUNOUT}.ORP_BEFORE_TPM_FILT.fasta
#	python ${MAKEDIR}/scripts/filter.py ${DIR}/assemblies/${RUNOUT}.ORP.intermediate.fasta ${DIR}/assemblies/working/${RUNOUT}.HIGHEXP.txt > ${DIR}/assemblies/working/${RUNOUT}.ORP.HIGHEXP.fasta
	grep -Fwf ${DIR}/assemblies/working/${RUNOUT}.LOWEXP.txt ${DIR}/assemblies/${RUNOUT}.ORP.diamond.txt >> ${DIR}/assemblies/working/${RUNOUT}.blasted
	awk '{print $$1}' ${DIR}/assemblies/working/${RUNOUT}.blasted | sort | uniq | tee -a ${DIR}/assemblies/working/${RUNOUT}.donotremove.list
	python ${MAKEDIR}/scripts/filter.py ${DIR}/assemblies/${RUNOUT}.ORP.intermediate.fasta ${DIR}/assemblies/working/${RUNOUT}.donotremove.list > ${DIR}/assemblies/working/${RUNOUT}.saveme.fasta
#	cat ${DIR}/assemblies/working/${RUNOUT}.saveme.fasta ${DIR}/assemblies/working/${RUNOUT}.ORP.HIGHEXP.fasta > ${DIR}/assemblies/${RUNOUT}.ORP.fasta
	cat ${DIR}/assemblies/working/${RUNOUT}.saveme.fasta > ${DIR}/assemblies/${RUNOUT}.ORP.fasta
	touch ${DIR}/assemblies/${RUNOUT}.filter.done
else
	touch ${DIR}/assemblies/${RUNOUT}.filter.done
endif

The problem has been solved, but I don't know if it was expected after the modifications:

4| #          
 3| #          
 2| #     #    
 1| # #   #   #
   -----------

-----------------------
|       Summary       |
-----------------------
|   observations: 8   |
| min value: -1.000000|
|   mean : -0.998000  |
| max value: -0.993000|
-----------------------


*****  See the following link for interpretation ***** 
*****  https://oyster-river-protocol.readthedocs.io/en/latest/strandexamine.html ***** 

(orp) root@Turing:/usr/local/bin/Oyster_River/sampledata# /usr/local/bin/Oyster_River/oyster.mk report STRAND=RF MEM=15 CPU=32 READ1=test.1.fq.gz READ2=test.2.fq.gz RUNOUT=test


*****  QUALITY REPORT FOR: test using the ORP version 2.2.7 ****
*****  THE ASSEMBLY CAN BE FOUND HERE: /usr/local/bin/Oyster_River/sampledata/assemblies/test.ORP.fasta **** 

*****  BUSCO SCORE ~~~~~~~~~~~~~~~~~~~~~~>	C:0.0%[S:0.0%,D:0.0%],F:0.3%,M:99.7%,n:303
*****  TRANSRATE SCORE ~~~~~~~~~~~~~~~~~~>      0.15058
*****  TRANSRATE OPTIMAL SCORE ~~~~~~~~~~>      0.26496
*****  UNIQUE GENES ORP ~~~~~~~~~~~~~~~~~>      40
*****  UNIQUE GENES TRINITY ~~~~~~~~~~~~~>      31
*****  UNIQUE GENES SPADES55 ~~~~~~~~~~~~>      22
*****  UNIQUE GENES SPADES75 ~~~~~~~~~~~~>      23
*****  UNIQUE GENES TRANSABYSS ~~~~~~~~~~>      35
*****  READS MAPPED AS PROPER PAIRS ~~~~~>      40.04%

Let me know if it is correct. Thank you.