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maiziex / Aquila_stLFR

Human haplotype-resolved assembly and variant detection for stLFR, hybrid assembly for linked-reads
MIT License
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Error msg for Aquila_stLFR_fastq_preprocess.py #2

Open victor0104 opened 2 years ago

victor0104 commented 2 years ago

Dear Sir,

I was used Aquila_stLFR_fastq_preprocess.py to generate fastq file for step1. Unfortunately, following error messages were appeared with command "/tools/Aquila_stLFR/bin/Aquila_stLFR_fastq_preprocess.py -1 ecoli_S1_L001_R1_001.fastq.gz -2 ecoli_S1_L001_R2_001.fastq.gz -o ecoli.fastq".How can i fix this problem? Thank you.

Error msg Traceback (most recent call last): File "/tools/Aquila_stLFR/bin/Aquila_stLFR_fastq_preprocess.py", line 54, in main() File "/tools/Aquila_stLFR/bin/Aquila_stLFR_fastq_preprocess.py", line 50, in main merge_paired_reads(fastq_1,fastq_2,out_file) File "/tools/Aquila_stLFR/bin/Aquila_stLFR_fastq_preprocess.py", line 21, in merge_paired_reads barcode1 = data1[0].split("#")[1].split("/")[0] IndexError: list index out of range

maiziex commented 2 years ago

Hi, ecoli_S1_L001_R1_001.fastq.gz and ecoli_S1_L001_R2_001.fastq.gz are paired-end reads from stLFR? Can you print the first two reads from both files that I can take a look ? Best Maizie

victor0104 commented 2 years ago

Hi,Maizie All data were generated from tell-seq data and transform to 10x genomics data format. Can Aquila_stLFR process those data from different linked read platforms?Here are the first two reads from both files.Thank you. ecoli_S1_L001_R1_001.fastq.gz @MN00867:58:000H2TH3V:1:11101:25722:1140 AAAAAAAAAAAAAAAANNNNNNNGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATGTTGGTGATTACAGGCTGAACGGGGAGGATAACGCAAGAATTGA + FFFF6FFFFFFFFFFFJJJJJJJA/FAFFFAFFFFFFFFFFAAFFFFFFF//FFFFF/FFFFFAF/=AFFFFFFFFFFFFFFFF/=FF/FFF/FAFFFFFAFFFFFFFFFFFFF/FFFF/FFFFFFFFAFFFFFFFFFAFFFFFFFFFF/FF=FF/FFFFF=F/FFFFF @MN00867:58:000H2TH3V:1:11101:23413:1140 AAACAAACAAACAAACNNNNNNNCTGATTGAGCAACGCCACCAGTTGTGCTTTTTTTTGCGGCGTTAAGGTAAATCCGAGTGGATTCTGGCTATTAGTCATCAGCCAGCACGCTTTCACCGGATACTCCTGCTACGCCAGTTCCAGCGCCTGAAGATCTATCCCTTCTT + FFFFFFFFFFFFFFFFJJJJJJJFFFFFFFAFFFFFFFFFFFFFFFFFFFFFFFFFAFFFFAFFFFFFFFAFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFAAFFFFFFFAFFFFFFFFFFFFFFFFFFFFFFFAFFFFFFF ecoli_S1_L001_R2_001.fastq.gz @MN00867:58:000H2TH3V:1:11101:25722:1140 GTCGTANATAATCAACAAATCCACCGGANTGCACAATGTCGCTATATATNCGATNTNAACCCTNGNANNNCTGTNACCGNNTNCCANNACGGCNNNTTTTTCACAGTTATCATNANCGNCTGATTCAATTCTTGCGTTATCCTCCC + AFFFFF#FFFFFAF//FFF6//F/A/=/#F/AFFAAFFFF==FFF=FFF#/=FF#F#FF//FF#/#F###/FAF#FF=/##A#=AF##FF/A/###FFFFFF/FFFFA=F=F/#F#F/#/FFFFFFFFFF/FAFF/6FFF//F/FF @MN00867:58:000H2TH3V:1:11101:23413:1140 ACCGGGNGATTGGGTGATAGTAGAGAATNCTTGTTTCTACGGTGCGTTGNAGGCNCNGGAGCGNCNANNNCTGANGGCGNNANCGGNNGCGACNNNTGTTAAAGAAGGGATAGNTNTTNAGGCGCTGGAACTGGCGTAGCAGGAGT + AAFFFF#FFFFFFFFFFFFFFFFFFFFF#/FFFFFFFFFFAFFFFFFFA#FFFF#A#FFFFFF#F#F###FFFF#AFFF##F#FAF##FFFFF###FFFFFFFAFFFF=FFF/#F#FF#FFFFFFFFFFFFFF=FFFFFFFFFFFF

Regards, Victor

maiziex commented 2 years ago

Hi Victor, If it is converted to the 10x linked-read format, you can use Aquila (https://github.com/maiziex/Aquila) instead of Aquila_stLFR. I checked your reads, the barcode is still inside of read1 (the length is 169)? To run Aquila, you need to move the barcode out and put it at the read name line. For example: @A00741:47:HCM53DRXX:1:1105:10556:25598 BX:Z:GTTCATGTCTATATTAGT-1 ATGGAATCGTTGAGTTTACTCTAATGGGATAATCATTGAATGGAATTGAATGCAATCATTGAATGGAATAGAATGGAATCATCATTGAATGGAATCAAATGGAAACCTCAATGAATGGAATCGAATGGAATCATCATCGAATGGAA + FFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF @A00741:47:HCM53DRXX:1:1105:10592:25598 BX:Z:GAAACCATAAGTACCCGA-1 GTAGAATCTGCAAGTGGATATTTGGACTGCTTTGAGGCCTTCGTCGGAAACGGGAATATCTTCACATAAGAACTAGACAGAAGAATTCTGGGAAATTTCTTTGTGATGTGTGCATTCAACACACAGAGTTGAACCTTTCTGTTGAT + FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Best Maizie