C3POa.py: AttributeError: 'tuple' object has no attribute 'append'

[PingpingZheng]

I've tried C3POa.py to process the preprocessed R2C2 fastq data: python3 ./C3POa.py --reads splint_reads/R2C2_raw_reads.fastq --path ./consensus --matrix ./NUC.4.4.mat --config config --slencutoff 1000 --groupSize 1000 --numThreads 16

It returns the AttributeError(see below)

Traceback (most recent call last):
  File "./C3POa.py", line 708, in <module>
    main()
  File "./C3POa.py", line 683, in main
    read_list = read_fastq_file(input_file)
  File "./C3POa.py", line 610, in read_fastq_file
    read_list[-1].append(line)
AttributeError: 'tuple' object has no attribute 'append'

• the input file (R2C2_raw_reads.fastq) is output file of C3POa_preprocessing.py, with the splint position in the header.

• config file is in tab format:

poa     /data/analysis/bio-pipeline/poaV2/poa
racon   /data/analysis/racon/bin/racon
gonk    /data/analysis/gonk/gonk
minimap2        /data/analysis/minimap2/minimap2
consensus       /data/analysis/C3POa/consensus.py
racon   /data/analysis/racon/bin/racon
blat    /data/analysis/blat

Is there anything wrong with my settings? How to fix it? Thank you.

PingPing

[rvolden]

I took out the part where I make the list it's trying to append to a tuple, so hopefully this should be fixed now

[PingpingZheng]

Thanks. The AttributeError is fixed with the updated C3POa.py. But it gave IndexError from read_fastq_file

Traceback (most recent call last):
  File "./C3POa.py", line 709, in <module>
    main()
  File "./C3POa.py", line 684, in main
    read_list = read_fastq_file(input_file)
  File "./C3POa.py", line 604, in read_fastq_file
    root, seed = splitLine[0]+'_'+splitLine[1], int(splitLine[2])
IndexError: list index out of range

[rvolden]

That's weird. Can you post a couple of reads from the R2C2_raw_reads.fastq file? The header for each seq should look something like this: @c87143c2-4d88-4365-b501-2ec06b5f9d16_7498

[PingpingZheng]

Sure, see below:

@70fbb8c7-aec1-4e54-a8ce-29b5d4dd8a75_739
GCAGAGATCCTGCCACGGTTCCGTCGCCGCCCACCCGTCGGACTCTGCTTTGAACCAGCGGCGACATCGCAGGCTCCTCCGTAAGTGGAGGAGACGATGCCGGTGCCTCGGTCGTCCCATTGCCAGTCTTCGTTCAGGGTATAGACCTTCACTCGCCTGCGTATCCGACATGGTGGCTGCTGTTATCCACCGCTCCAGCCGCCGCCTCCTCGCTTACCTCGTCCGCGCTCCTCACTCTTAGGAGACGGTAAAGGCAGTGGCGGTGGCGGCGGCGGCTGGCTTCGGAGGCCCAGATTACCATGGCTCCCAAAGGGTTCGGCGCGAGAGGGTGACAACAGGCCGCACGAGGCCTCTCCGCCCGGAGAACCCGTTACCTCTCACTTCACCCGCGCATACACTTACTCTGCCTACGATCTCTTTTGCCCCACGGGGCTCGCGCTCTCCGCCGCGCGGTGCTGCTACAGATCATACCATCTCCAGCAACCCGACTCTCTCTGCCTTTCTCTTCCTCCTCAACAGGCTCACGAACTATCTAGCGAGGCTACGGCGGCAAACAAGTCCATGAGCAGCACCTCCGCTTCTGCGCTTTGAGCCGGAATGCTCGGCGCTCTCCCCATGTACTCTGCGTTGATACCCTGCGCCAAAGGAGATATTTTCGATCGCGTCATATAATTTATTTAGTGCATTGATCCTTTACTCCTCTAAAGGAACAACTGACCCAGCAAAAGGTACACAATACTTTTACTGCCAGCAAAGAGAAAGACAACTCTGGCTTGAAGCTATCAAAGAAAACTAGTAGTGATACATAGCCATACCTCTATGGAACTCATCAGCCTCACTACACGACATCTTCAGGTCTACTTCGCAGAGGTAGTCCCAATAGTTTACAAAACACTCGGAAAGAAAGTTTCCCTAAACCGTTTTTGTACTAGACGTATAATGGATAAGTAAATAGGGGAGGAAGGTGTCAGCTCCTGAGGCAGCATCAGTACCTAGTCTCTCACTACTTCCTCCCTTCTCTCTCACACCTCCCCTCTTCAAAGAGGAGGGACTGGAAAGGAAGGAGTCAATCCTTAAGAAGATGGGAGAAGGACAGAAGTCTCGGTCTCTGAGGACCCAAGTCCCAGTCAAGAAGTACAGTACTTGTTTTTGCCGTACACAAGAGCCAGTTCCAGAACCGCTGTCGAAGGGAGTAGCAACGGTAACAGACCCAAGGGCCCTAAACCCAAGCTTCCCCAGCCTTTAACCAGGGCACTATCCCCTGTCTACAGTTCCGATAACCGTCGGACTCTGCCCGAACCAGCAGCGACATCCCCTTGAGCTCCTCCACGTAGAGTGGAGGAGACGTGCCAATGCCCCTCGGTCG
+
$"##$#'-,*&$$$#(&-544++/()/35963&''(147044=?9&%%%%)*'&%$%$#$(**(',0.#$$&*=>83;8*03425776-+*%/%*+%***-/-/42355),30+1048667468&8>>;?>6??;3;559.**,,.2214%666.)'&(325=@;;559;..033676-+,)#%%-./&&'&).2-))--/10.0,24,34.--10478:4895**+7=:3C<9;>989%58*-1%%,')76/*%#'&'+%%)<8;**,''*&&+##%%))*+*0&)+*.+%)&#&#','116=<:4&$&&%)1..1'+-0++&'()'644,*&$%&&++*$'''%&.32356'022786551.-*,-/37>489=9(<-..398983911431(&%))*+6773&'(%,-.*2216??@):::7-.)&*/0137''+<;;<=9;<=4-+-..$$(,*17+/0116,')').+86130'$&%%%%%1:BG?%*+;?98867/364==:9>;5:6+&++03675&&'$&$+$30-'%(*'(///-01/../300%4646=;8*%%'&*)466%(9=3//0210-''(**+&'55948=999,8:.--/7;80;;>::52*,5:9:01188'&%#'*()(',++.)%('$&,006752/)(3149:HF-5300'&'&%)+4+/9/475477B@<CB>,<@:6@<;52,&8:3<A-6%)1+,*+$,+,-,.6:><B?E2,-::;:64445568$19:-350;@76<<=8BD:@-.----169;C:8;85&('+;)671(//,0/020.(%%$$$&2+,+667*+'0./--23532*310('(.'$$%+*(('#..+&)/@;<288:0&')),%*((72295('%%+4.,)-0795449;5'+/0+%4-++3:4%667:96:;/;-+)'',-.2--5)'((*+(,)17:;62;=91,3%',252($(,,*/6;0$5:<90%$(+&'#(***&/.,1:+)/3-:;A@722323532;9827898::<6;%''(+48///26=?=+/*)%>@<77:B=;<>><68>><71)5373165*(*,',+'4:3359>0>94:2//-**4::79/3;7;<=///31((')(%,&')()272*$-3)/)'').&**+3@@C=(-46369;846'2275948=@;<10./.-$%3,45%$*)&&&,..082*%%+89,++2+89:=0316??=;:81-.,,%%'')''%%&%$%%##%,'('&&,..0314950.*$,+++*/0;?6954662.))0,-:?AC<<*3($,,01:32//01248998+'&&&%%(+/01585$1+((%&,707>)/-340.-,'(4510-6667:,0:4&
@5ed61936-7ca9-49f0-a9e6-e74c09f91362_1119
GAATAAGAGTTGTCTTTTTCTCTTTGCTGGCAGTAGAAGTGTTGTGTACCTTTTGCTAGGTCAGGTTGTTCTTTGGGAGGTAAAAGGATCAAATGCACTAAAACTCTATATAATAGGCGATCGAAAATATCCCTTTAAGCAGTGGTATCAACGCAGAGTACATGGGGGCCGGCAGGGCCTCACGTTCCTTTACCAGCGGCTTCCGCCTGCTACGGTCTGAAGCACCTCAGGATCATTCCTTCACAGGGACCCTAGCCAGGCAGCGCGCGCCTCACTGTACCGGAGAGCTCCAAGCACGCGCTTGGTCTGGGGCAGACGCTACATCTGGGAAGGGGTGGGTGGCTGGGTAGATGGGCGAGGAAGGATCGTCTCTACCCTCTCTCAAGTAGCTGAGGCCTCCGAAACCTTCCCTAGCTGGATTTGGGGACAGAGGAGCGCTGGTATTGATAAAATAACTCTCTTTGCTATTCCTTTAGGAGCCCAAATGAGGATTGAAAGTGAGAAGAATGGGACCTGGGCTTGGGGTGGGAGGTGGGAAAGCAGAACCCCGTGTGCCTGTTTCTGCGTCGTCTGGAGAAAAAGCTTTTCAAGATGTCTGATAGACCTTATTCGGTTCAAAGCTCTCTAAAGTCCTCCCACCTTTTTTTTAAACTTCATGGAAAATGAAACATTTCAGAGAAGTTACTTGCCTAGAGGCAACCTTTAAGTCACCTAATGGCTAAGTAGGAAAGCAAGTCAGTTCCAACATAGTGGAAATGGAGTGGAAATGCATGGCATACAATGAGCTATATTAGAAGGTTCCCATTTAGACAGTTTTCATGTTGTATTCCATGTTGGCTTCTACAGGGAAAAAAAGTGTTAAGAGCATCTTAAGCAACTGTTTTTGCTTCTTTCCATAGTGACTAGTAATATCAGCAGGTGTCAGGTCTAAACCGAAGTGCATTGAAAAAAAAAAAAAAAAAAAAAAAAAAATTAGCTAGGACTTACCATACCCCAGTGAGATCGGAAGAGCGTCGTGTAGTGAGGCTGATGAGTTCCATAGGGTTATATTTCCAAATCACTACTTAGTTTTTGATAGCTTCAAGCCAGAGTTGTCTTTTCTCTTTGCTGGCAGTAAGAAGTATTGTGTACCTTTTGCTGGGTCAGGTTGTTCTTTAGGAGGTAAAAGAGTCAAGTGCTGCTAAACTCTATGCTGTAACAGATCGAACCACACTGGTGGTGGTGTCAACATGATACGTAAGGTGAGGAACACTCCAGTTCATATGCATGTTCGCCTTCCAGTCTGGTGAGCTGCCAGGATCTCATTCCTTCACAGGGACCCTAATAAACAAGCATGAA
(base) prom@PC48A011:/data/analysis/20200825_R2C2_VISTA/splint_reads/splint_10xUMI_2020$ tail R2C2_raw_reads.fastq
+
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
@6dc91ee8-c1bf-4fdf-b5ef-f116f8f34f3a_772
TTGTACTTCGTTCAGTTACGTATTGCTCTGATTTTAAATATACAATACATCATACATACACTTTACAAGCAAGTTAAATGGAGATAAGGAGGATTGAAATCATAGAAGATGCAAATGACCTTTCAAATCAACACAATGTGTTCTGAAACTTTCGTGACTAATACCATGCATCTGTGATCAATGAACTATGTGGTTTTGAATCGGATATGAACCATTAGTACTACTACTTGAGCTAAACTTCTGCATGGTTCATAATTTTTTAAAATTAATGTAGTTAATATGCATGTTATCGTCCTTTCTTCCATTCTTACCAGTATGTGCCATTTGCAAAACAAAAATGCTAATAATCAGTAATAGTCCTATAAAAGATGTTAACTCTGTTTAGTCATTATTTGATCTTGCTCTAACCTTAAAATTTTGCTTGATTATTGACCTCTGTTGCATTTATTCTAAAGCCCCCAAAAAATTATCTAGCCGTTTCGAATATCAACATTACCCTGGTGTATTCACTGCTGTATGCATTATTGTTCTTTGTTGCTGTTTTATGCCTTCATATTAGCAAATATGAAATTCTGTGAAAAAACCCTTTGATCCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATCCTATCTGTCAGAAAACATACGCCAAGATCAGAGAAGCGTCATTAGTGAGGCTGATGAGTTCCATAGGAGCTATATTACTCATCACTACTTAGTTTTTCGATGACCAAGCCAGAGTTGTCTTTTTCTCTTTGCTGGCAGTAAAAGTATTGTGTACCTTTTGCTGGGTCAGGTGTTCTTTAGGAGGAGTAAAGGATCAAATGCACTAAAGGACTATATCCGGAGCGATCGAAAATATCCCTTTAAGCAGTGGTATCAACGCAGAGTACATGGGGAACGGGAGCACGGAGCAGCGCCAGGGCCCCCAGCCACTCTGAAAGTGCGCTTGAATAATGACTCATTGTGCAATACAAATCCTCATTTAAATGCACTAAGTACAGACACAACTTGCCGCAGAGAAGCTGCTCTGGGGCAGGCTGTCTTAAATAAGAAGAGTAAACTTATTTTTTATGAGGGTGAAGGATGCTGGAAGGGAGTAAAGTTTAGGAATATCTGGAGAGAAAGAGAGCCTGCAGTTATGTACATTTTGTCCTTTTTCCGTAAGGAAAAAATGAGGACTTTGGAAATTCAGATCCCTCTTTGATATCAGAGATTTAAACAACACATTTTTAGTTTTAACCAGTTGTAGTCAAAATGCTACAATAAAACAAAAAAGAGAAGAAAATGAAGAGCATTTGACTCCCGCACTTAAAATGAAGTACACATAAAGTTTAAACTGGTTATGACAAAAGCCTATAGTTGTGTTTCTTGAACTATAAAGAAAACAAATTTTGGCAGTCTTTAAGTATATATAGCTTAAAATATAATTTTAGCATTTGGCACCATATGTGTGCCATTATGTTTGATTTTGCATTACTGTTTCACAATGAAGCTTTACTTTAAGGCTTTGATTTTTATGATTATGAAAGAAATAAGGCACAACCTGGTTTTTCTTTCTTAGAGATTTCATCACTGTTGATGTGGTTCTTTTGTGTTAAAAAA
+
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email protected]'#+-6625235:98<@;4???==>;LMFC479B?;;+<;-=?ALKAFC>BD>?:=>?:+C8FA>CCFFIF@1445<;5;7*''$./42.*&&.*++.AA>>>>@ADD@8)::<>@<+*(()+++,-+&'*)//7<<8''8;?:@FF:*%+,051:AA<=28/8=:43,-2245*%9:<=.77:55:.5=FEEA,066?DE=333739=B4178199;8C=72/.(5;B;:6;??8681%'#457>777744:,(*79:8785BFBCD@71:=<@A?=67*

[PingpingZheng]

I cat all raw fastq file from fastq_pass into one big fastq file for preprocessing. R2C2_raw_reads.fastq is the output from C3POa_preprocessing.py.

[rvolden]

Can you post the output of grep -c '^$' R2C2_raw_reads.fastq? I'm trying to see if there are blank entries that could be messing up the fastq parser

[PingpingZheng]

It is 0. No blank lines in fastq.

[rvolden]

Weird. Pull the new code and try again. I took out the hairpin check. I don't think this is going to fix it, but it's the only thing that's changed from my stable version.

[PingpingZheng]

It still has the IndexError:

Traceback (most recent call last):
  File "./C3POa.py", line 710, in <module>
    main()
  File "./C3POa.py", line 685, in main
    read_list = read_fastq_file(input_file)
  File "./C3POa.py", line 600, in read_fastq_file
    root, seed = splitLine[0], int(splitLine[1])
IndexError: list index out of range

[rvolden]

Can you change that portion of code to

splitLine = line[1:].split('_')
print(splitLine)
root, seed = splitLine[0], splitLine[1]

And rerun and post the printed lines? If I can't figure it out after that, I'll change the fastq parsing api to something more reliable

[PingpingZheng]

['fb110236-8253-41de-a81f-93679e30bcd3', '3138']
['7ffe2ed5-2680-449a-8372-07c186cd3457', '1734']
['7d9b5c11-8859-4ae7-afb2-841654369af5', '2793']
['939e77ce-2ab6-4a4b-9564-3371900328f1', '1381']
['1459c103-2368-414b-bac0-695ed525456f', '1074']
['5662a3d3-2df8-4ccd-afee-a35cfb2c9f80', '871']
['14396e56-5cf1-4d7c-a392-4f80d1c22ed2', '875']
['0b9011dc-dfe0-4a5c-8ea3-fe98854c2c79', '3167']
['b0858a2f-f099-437f-a45a-55a610f6a7f6', '4133']
['121dc77f-f9b2-4389-acae-b791dea36283', '2725']
.....

[rvolden]

What about when it gets to the index error? What's the last printed splitLine?
Try

splitLine = line[1:].split('_')
if len(splitLine) != 2:
    print(splitLine)
root, seed = splitLine[0], splitLine[1]

[PingpingZheng]

After change the code to:

splitLine = line[1:].split('_')
print(splitLine)
root, seed = splitLine[0], splitLine[1]

It returns:

['fb110236-8253-41de-a81f-93679e30bcd3', '3138']
['7ffe2ed5-2680-449a-8372-07c186cd3457', '1734']
['7d9b5c11-8859-4ae7-afb2-841654369af5', '2793']
['939e77ce-2ab6-4a4b-9564-3371900328f1', '1381']
['1459c103-2368-414b-bac0-695ed525456f', '1074']
['5662a3d3-2df8-4ccd-afee-a35cfb2c9f80', '871']
['14396e56-5cf1-4d7c-a392-4f80d1c22ed2', '875']
['0b9011dc-dfe0-4a5c-8ea3-fe98854c2c79', '3167']
['b0858a2f-f099-437f-a45a-55a610f6a7f6', '4133']
['121dc77f-f9b2-4389-acae-b791dea36283', '2725']
.....

Traceback (most recent call last):
  File "./C3POa.py", line 711, in <module>
    main()
  File "./C3POa.py", line 686, in main
    read_list = read_fastq_file(input_file)
  File "./C3POa.py", line 601, in read_fastq_file
    root, seed = splitLine[0], splitLine[1]
IndexError: list index out of range

[rvolden]

But what's the header that it prints right before it errors out?

[PingpingZheng]

Tried:

splitLine = line[1:].split('_')
if len(splitLine) != 2:
    print(splitLine)
root, seed = splitLine[0], splitLine[1]

It did return something weird:

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email protected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email protected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Traceback (most recent call last):
  File "./C3POa.py", line 713, in <module>
    main()
  File "./C3POa.py", line 688, in main
    read_list = read_fastq_file(input_file)
  File "./C3POa.py", line 603, in read_fastq_file
    root, seed = splitLine[0], splitLine[1]
IndexError: list index out of range

[rvolden]

Yeah that's a quality line, something's going wrong with the parser. Can you email me ([email protected]) so I can send you a modified version of C3POa.py? I'm going to add a dependency that I don't want to get pushed just yet.

[PingpingZheng]

Sure. Many thanks.