Error with reading input files

[o k]

Hello,

I am new to transcriptomics and am trying to use transabyss for the first time, but running into error with input files (error listed below).

Here is the command I use (with four input files):

transabyss --pe Cyto_92_1M_S7_R1_001.fastq.gz Cyto_92_1M_S7_R2_001.fastq.gz Cyto_92_1P_S8_R1_001.fastq.gz Cyto_92_1P_S8_R2_001.fastq.gz

I get the following error:

Reading `/Users/.../RNAseq/Cyto_92_1M_S7_R1_001.fastq.gz'...
/Users/.../RNAseq/Cyto_92_1M_S7_R1_001.fastq.gz:1: error: Expected either `>' or `@' or 11 fields
and saw `' and 1 fields near
?BC?>ŝ?r?J?l??S??s?#?`l
                       n??͉}刽??I??Ȓ,~$ٽz}?ڍ?T*\?̙?J??O??z???\=?V??????????}}z}\-_?O???r????????x???:||?סi??ph???9?k??}ծd??ڗ?W??????????V?4???ᚪ??.??G?v`}?q?????j??vS????_????};?5?6WN?+?2???zE_??O·~l??>>??'2b?/???jw8`???5y???%?}=??z?6?z???????\W??n_???b_????Ǐ??z?ǧͶe?j1$??h??H???[y??$\?`'v?hwn??
make: *** [transabyss-1.fa] Error 1
ERROR: CMD ended with status code 2

It seems to me that the program cannot read input files properly. When I open the files the reads look as follows (and have "@" in the beginning):

File 1:

@D00635:134:C95LWANXX:4:2312:1436:1874 1:N:0:CGCTCATT+AGGCGAAG
NGGACATCGGCCAGGAGGCTGGACTGGGGAACACCCTTCCAGAAGTCGGTGGAGGAAGCGGCCTTGGTGGCAACGGTCAGGATGTCGGTGATGGCCTCGATCTTGGGAGCAATGTTGACGAGATCG
+
#=A@BFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGG
@D00635:134:C95LWANXX:4:2312:1626:1922 1:N:0:CGCTCATT+AGGCGAAG
NCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGA
+
#:3<AEFGGGGGGGGGGFGGGFGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGFGGGGGFGGGBGGGGGEGGGGFEGGGGEGGBGC>BGBF0@>FBE>@BEFC0<<@FE0800@C@F<<../86
@D00635:134:C95LWANXX:4:2312:2489:1830 1:N:0:CGCTCATT+AGGCGAAG
NATCGTTAGTGCCTCGGTCCAAGGGTGCTTGTGGAGGTTCATCAACATATTCTCCTCAAGGGCTGTCTTGCGGTAGTTGATGCCAATGGAGTAGTAGTGTCGGTTCAGGCCATGAATCAGCGCTTG
+

......

File 2:

@D00635:134:C95LWANXX:4:2312:1436:1874 2:N:0:CGCTCATT+AGGCGAAG
CGTCAACATTGCTCCCAAGATCGAGGCCATCACCGACATCCTGACCGTTGCCACCAAGGCCGCTTCCTCCACCGACTTCTGGAAGGGTGTTCCCCAGTCCAGCCTCCTGGCCGATGTCCTAGATCG
+
CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGEGGGGGGGGGGGGGGGGGGGGGGBGGGGGGGGGGG
@D00635:134:C95LWANXX:4:2312:1626:1922 2:N:0:CGCTCATT+AGGCGAAG
CTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTTGCCCTGG
+
CCCCCGGGGGGGGGGGGGFFGGGGGGGGGGD>CFGGGGGGGGG@@FGGGFC@DDC11@GGC@1CFE>1:F:F11=<CD11111D11CB100=0<@00=:0F0008>0<000C0000000000880<
@D00635:134:C95LWANXX:4:2312:2489:1830 2:N:0:CGCTCATT+AGGCGAAG
CCTCAACAAGCCCTCTATTCAAGCGCTGATTCATGGCCTGAACCGACACTACTACTCCATTGGCATCAACTACCGCAAGACAGCCCTTGAGGAGAATATGTTGATGAACCTCCACAAGCACCCTTG
+

......

I went through older messages in the group regarding similar problems with input files. I see in my files there is 1 and 2 indicated in reads names, but not in the format /1, /2 (as was mentioned in older conversations). Can this format be the issue? If so, what should I do about it? Will be grateful for any suggestions.

Thanks,

Olga

[Ka Ming Nip]

Hi Olga,

The read names look fine to me.

The error message indicates that one line within your read file `Cyto_92_1M_S7_R1_001.fastq.gz` is not in the correct format.

There shouldn't be anything wrong with Trans-ABySS in terms of reading FASTQ files. You can test it out using these read files:

https://github.com/bcgsc/pavfinder/blob/master/pavfinder/test/transcriptome/test_1.fastq.gz

https://github.com/bcgsc/pavfinder/blob/master/pavfinder/test/transcriptome/test_2.fastq.gz

Ka Ming

--
Ka Ming Nip, PhD
Collaborator | Dr. Inanc Birol Lab
Canada's Michael Smith Genome Sciences Centre

---

From: trans...@googlegroups.com <trans...@googlegroups.com> on behalf of o k <oko...@gmail.com>
Sent: September 6, 2023 2:04:44 PM
To: Trans-ABySS
Subject: Error with reading input files

 

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[Olga Kozhar]

Hello Ka Ming,

thank you for your quick response. I just tried the test files you referenced and I am getting the same error message, as well as with the test dataset that comes with the software (referenced in read.me file). This tells me the problem is not in input files.

Can it be the incompatibility in software versions? I am running ABySS 2.3.7 and Python 3.10.

Thank you,

Olga

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[Ka Ming Nip]

Hi Olga,

You need to use ABySS versions 2.0.x, e.g.

https://github.com/bcgsc/abyss/releases/tag/2.0.3

If you installed Trans-ABySS via conda, it should install the correct version of ABySS.

Ka Ming

--
Ka Ming Nip, PhD
Collaborator | Dr. Inanc Birol Lab
Canada's Michael Smith Genome Sciences Centre

---

From: trans...@googlegroups.com <trans...@googlegroups.com> on behalf of Olga Kozhar <oko...@gmail.com>
Sent: September 7, 2023 7:49:51 AM
To: trans...@googlegroups.com
Subject: Re: Error with reading input files

 

To view this discussion on the web visit https://groups.google.com/d/msgid/trans-abyss/CAFvnCw9cT_CbSgw5tgbCKUrtRkCoqEoO2MvbOvfxF4Og2T0oGw%40mail.gmail.com.

[o k]

Thank you for suggestion, Ka Ming.

I cannot install transabyss with conda because my computer does not support python v.3.x. or v.2.x.

I will try to find a different machine compatible with older versions of python.

Olga