Star Fusion error with FusionMap Test data

ninn...@gmail.com

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Mar 23, 2016, 7:45:31 AM3/23/16

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Dear all,

I am successfully running star fusion (the newest version 7) on all kinds of data. But I cannot get it to run on the sample data from the fusion map publication (http://omicsoft.com/fusionmap/Software/FusionMap_2014-10-17.zip).

I get the following error:

ReadAlignChunk_processChunks.cpp:115:processChunks EXITING because of FATAL ERROR in input reads: unknown file format: the read ID

should start with @ or >

Call

STAR-Fusion_v0.7.0_FULL/STAR-Fusion --genome_lib_dirSTAR-Fusion/GRCh38_gencode_v23_CTAT_lib --left_fq DatasetP2_SimulatedReads_R1.fastq.gz --right_fq

DatasetP2_SimulatedReads_R2.fastq.gz --output_dir results

I have checked the files and there is no problem with the @.

This is how the file looks like:

head <(zcat DatasetP2_SimulatedReads_R1.fastq.gz)
@R_1:1
TCATTGGAGACGGTTTGGTGAAACCAGAGGCCCTAAATAAGAAAGCTATCCAGATTATTAACAGGGTTCGAGATA
+R_1:1
777757754272652746323822816991872468715875136993134287398628988653887661181
@R_2:1
GAGCAGATCCGCGCGCACGACCAGCCCGGCGACAAGTGGCTGGTCATCGAGCGCCGCGTCTACGACATCAGCCGC
+R_2:1
777757754272652746323822816991872468715875136993134287398628988653887661181
@R_3:1
AAACAGGGTTCGAGATAAGCTCACTGGTCGGGACTTCTCTCATGATGACACTTTGGATGTTCCAACGCAAGTTGA

Thanks for any help!

Alexander Dobin

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Mar 23, 2016, 10:51:48 AM3/23/16

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Hi @ninninahm

the most likely reason is that the files are not being unzipped.

Do you see the STAR log file, Log.out - please send it to me.

I have also forwarded your e-mail to Brian Haas.

Cheers

Alex

Ilario De Toma

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Nov 17, 2016, 11:25:58 AM11/17/16

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Hi! I am having the same problem, how did you solved it? Usually I have no problems with fq.gz file in STAR because you can set the option --readFilesCommand zcat
However I have some reads that give me the same error, even though they start with @

Ilario

Alexander Dobin

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Nov 17, 2016, 4:23:28 PM11/17/16

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Hi Ilario,

please send me the Log.out file of the failed run.

Cheers

Alex

Javier Simón-Sánchez

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Jun 8, 2017, 11:20:35 AM6/8/17

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Hello, I am getting exactly the same errors and read names seem to be OK. Attached the log.out file I am getting.

Thanks!

Log.out

Alexander Dobin

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Jun 9, 2017, 5:13:57 PM6/9/17

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Hi Javier,

for gzipped files you need an extra option

--readFilesCommand zcat

Cheers

Alex

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