Error: reads file does not look like a FASTQ file - failed! Plase check if you provide correct parameters/options for the pipeline! #6
Description
Hello guys,
I have 2 (de novo) transcriptomes to which I'm trying to assess the assembly quality. My data is paired-end and strand-specific.
This is the command I'm trying to run:
nohup /home/gabriel/sw/DETONATE_v1.8.1/detonate/rsem-eval/rsem-eval-calculate-score -p 16 \ --transcript-length-parameters /home/gabriel/sw/DETONATE_v1.8.1/detonate/rsem-eval/true_transcript_length_distribution/human.txt \ --forward-prob 0 \ --paired-end B1_RMC13_Paired_1.fq.gz,B1_RMC14_Paired_1.fq.gz,B1_RMC15_Paired_1.fq.gz,B1_RMC16_Paired_1.fq.gz,B2_RMC21_Paired_1.fq.gz,B2_RMC22_Paired_1.fq.gz,B2_RMC23_Paired_1.fq.gz,B2_RMC24_Paired_1.fq.gz,B3_RMC31_Paired_1.fq.gz,B3_RMC32_Paired_1.fq.gz,B3_RMC33_Paired_1.fq.gz,B3_RMC34_Paired_1.fq.gz B1_RMC13_Paired_2.fq.gz,B1_RMC14_Paired_2.fq.gz,B1_RMC15_Paired_2.fq.gz,B1_RMC16_Paired_2.fq.gz,B2_RMC21_Paired_2.fq.gz,B2_RMC22_Paired_2.fq.gz,B2_RMC23_Paired_2.fq.gz,B2_RMC24_Paired_2.fq.gz,B3_RMC31_Paired_2.fq.gz,B3_RMC32_Paired_2.fq.gz,B3_RMC33_Paired_2.fq.gz,B3_RMC34_Paired_2.fq.gz /media/raid/raperez/transcriptomes151/data-rafaela/trinityOUT-RMC/Trinity.fasta RMCassembly_rsem_eval 150 > log_rsem_eval_RMC.txt 2>&1 &
And this is the error I'm getting:
bowtie -q --phred33-quals -n 2 -e 99999999 -l 25 -I 1 -X 1000 --nofw -p 16 -a -m 200 -S RMCassembly_rsem_eval.temp/RMCassembly_rsem_eval -1 B1_RMC13_Paired_1.fq.gz,B1_RMC14_Paired_1.fq.gz,B1_RMC15_Paired_1.fq.gz,B1_RMC16_Paired_1.fq.gz,B2_RMC21_Paired_1.fq.gz,B2_RMC22_Paired_1.fq.gz,B2_RMC23_Paired_1.fq.gz,B2_RMC24_Paired_1.fq.gz,B3_RMC31_Paired_1.fq.gz,B3_RMC32_Paired_1.fq.gz,B3_RMC33_Paired_1.fq.gz,B3_RMC34_Paired_1.fq.gz -2 B1_RMC13_Paired_2.fq.gz,B1_RMC14_Paired_2.fq.gz,B1_RMC15_Paired_2.fq.gz,B1_RMC16_Paired_2.fq.gz,B2_RMC21_Paired_2.fq.gz,B2_RMC22_Paired_2.fq.gz,B2_RMC23_Paired_2.fq.gz,B2_RMC24_Paired_2.fq.gz,B3_RMC31_Paired_2.fq.gz,B3_RMC32_Paired_2.fq.gz,B3_RMC33_Paired_2.fq.gz,B3_RMC34_Paired_2.fq.gz | samtools view -S -b -o RMCassembly_rsem_eval.temp/RMCassembly_rsem_eval.bam -
Error: reads file does not look like a FASTQ file
terminate called after throwing an instance of 'int'
Aborted (core dumped)
[samopen] SAM header is present: 3679486 sequences.
[sam_read1] reference 'ID:Bowtie VN:1.1.2 CL:"bowtie --wrapper basic-0 -q --phred33-quals -n 2 -e 99999999 -l 25 -I 1 -X 1000 --nofw -p 16 -a -m 200 -S RMCassembly_rsem_eval.temp/RMCassembly_rsem_eval -1 B1_RMC13_Paired_1.fq.gz,B1_RMC14_Paired_1.fq.gz,B1_RMC15_Paired_1.fq.gz,B1_RMC16_Paired_1.fq.gz,B2_RMC21_Paired_1.fq.gz,B2_RMC22_Paired_1.fq.gz,B2_RMC23_Paired_1.fq.gz,B2_RMC24_Paired_1.fq.gz,B3_RMC31_Paired_1.fq.gz,B3_RMC32_Paired_1.fq.gz,B3_RMC33_Paired_1.fq.gz,B3_RMC34_Paired_1.fq.gz -2 B1_RMC13_Paired_2.fq.gz,B1_RMC14_Paired_2.fq.gz,B1_RMC15_Paired_2.fq.gz,B1_RMC16_Paired_2.fq.gz,B2_RMC21_Paired_2.fq.gz,B2_RMC22_Paired_2.fq.gz,B2_RMC23_Paired_2.fq.gz,B2_RMC24_Paired_2.fq.gz,B3_RMC31_Paired_2.fq.gz,B3_RMC32_Paired_2.fq.gz,B3_RMC33_Paired_2.fq.gz,B3_RMC34_Paired_2.fq.gz"
DN0_c0_g1_i9 LN:515
@sq SN:TRINITY_DN0_c10_g1_i1 LN:235
@sq SN:TRINITY_DN0_c11_g1_i3 LN:543
@sq SN:TRINITY_DN0_c11_g1_i4 LN:1525
@sq SN:TRINITY_DN0_c11_g1_i5 LN:1390
@sq SN:TRINITY_DN0_c11_g1_i6 LN:542
@sq SN:TRINITY_DN0_c121_g1_i1 LN:213
@sq SN:TRINITY_DN0_c12_g1_i10 LN!' is recognized as '*'.
[main_samview] truncated file.
"bowtie -q --phred33-quals -n 2 -e 99999999 -l 25 -I 1 -X 1000 --nofw -p 16 -a -m 200 -S RMCassembly_rsem_eval.temp/RMCassembly_rsem_eval -1 B1_RMC13_Paired_1.fq.gz,B1_RMC14_Paired_1.fq.gz,B1_RMC15_Paired_1.fq.gz,B1_RMC16_Paired_1.fq.gz,B2_RMC21_Paired_1.fq.gz,B2_RMC22_Paired_1.fq.gz,B2_RMC23_Paired_1.fq.gz,B2_RMC24_Paired_1.fq.gz,B3_RMC31_Paired_1.fq.gz,B3_RMC32_Paired_1.fq.gz,B3_RMC33_Paired_1.fq.gz,B3_RMC34_Paired_1.fq.gz -2 B1_RMC13_Paired_2.fq.gz,B1_RMC14_Paired_2.fq.gz,B1_RMC15_Paired_2.fq.gz,B1_RMC16_Paired_2.fq.gz,B2_RMC21_Paired_2.fq.gz,B2_RMC22_Paired_2.fq.gz,B2_RMC23_Paired_2.fq.gz,B2_RMC24_Paired_2.fq.gz,B3_RMC31_Paired_2.fq.gz,B3_RMC32_Paired_2.fq.gz,B3_RMC33_Paired_2.fq.gz,B3_RMC34_Paired_2.fq.gz | samtools view -S -b -o RMCassembly_rsem_eval.temp/RMCassembly_rsem_eval.bam -" failed! Plase check if you provide correct parameters/options for the pipeline!
Based on all the digging I was able to do (specially here: https://groups.google.com/forum/#!forum/detonate-users) with the very limited answers I could find, I think that either there is a problem on the assembly step that could be caused by a faulty detonate installation (https://groups.google.com/forum/#!searchin/detonate-users/upstream$20read%7Csort:date/detonate-users/6dJWgs7VZ5k/c93Q5K2gFAAJ), OR, detonate cannot understand .fq.gz files as fastq files (which it does not sound very obvious...it does not make much sense to unzip all the reads files so they can be .fq so detonate can understand them as fastq files... I mean, .fq.gz are pretty standard - someone actually asked about it and never got a reply: https://groups.google.com/forum/#!searchin/detonate-users/fq.gz%7Csort:date/detonate-users/JtorPELgoys/7y6333g9AgAJ).
So please, if any of you have had this problem and could give me a hand on solving it, I would be very grateful.