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sunzhengCDNM / MAP2B

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ERROR: sample has no reads #2

Open agavriilidou opened 7 months ago

agavriilidou commented 7 months ago

Hi,

I am trying to run MAP2B like this:

python3 /tools/MAP2B/bin/MAP2B.py \
-i /annotation/map2b/data.list \
-o /annotation/map2b/map2b.out

after I have MAP2B environment activated.

My data list looks like this:

SC_DM_F5B_10-15_I_II /processed/clean_human/done/SC_DM_F5B_10-15_I_II_nophix_nohuman_1.fastq.gz /processed/clean_human/done/SC_DM_F5B_10-15_I_II_nophix_nohuman_2.fastq.gz

The error I get is that the files have no reads. I tried it with unzipped files as well and got the same error.

I would appreciate your help!

sunzhengCDNM commented 7 months ago

Hi,

Could you please verify whether "data.list" utilizes tabs as separators instead of spaces? If tabs are indeed used and an error persists, could you share the specific error message that occurs?

Best, Zheng

meniaG @.***> 于2024年4月5日周五 10:25写道：

Hi,

I am trying to run MAP2B like this:

python3 /tools/MAP2B/bin/MAP2B.py \ -i /annotation/map2b/data.list \ -o /annotation/map2b/map2b.out

after I have MAP2B environment activated.

My data list looks like this:

SC_DM_F5B_10-15_I_II /processed/clean_human/done/SC_DM_F5B_10-15_I_II_nophix_nohuman_1.fastq.gz /processed/clean_human/done/SC_DM_F5B_10-15_I_II_nophix_nohuman_2.fastq.gz

The error I get is that the files have no reads. I tried it with unzipped files as well and got the same error.

I would appreciate your help!

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agavriilidou commented 7 months ago

Hi,

I did use tabs as separators in the data.list file. Does it accept the complete path to the fastq file?

python3 tools/MAP2B/bin/MAP2B.py -i /annotation/map2b/data.list \
-o /projects/0/prjs0956/annotation/map2b/map2b_out 
2024-04-05 21:55:32 - MAP2B.py - INFO - mkdir: /annotation/map2b/map2b_out
2024-04-05 21:55:32 - MAP2B.py - ERROR - Sample SC_DM_F5B_10-15_I_II    /processed/clean_human/done/SA_DK_F7.2_0-2cm_I_nophix_nohuman_1.fastq   /processed/clean_human/done/SA_DK_F7.2_0-2cm_I_nophix_nohuman_2.fastq has no Reads

I just ran it again using unzipped fastq files and I got this.

Best, Menia

sunzhengCDNM commented 7 months ago

Hi Menia,

Could you please show me a few lines of your fastq file?

Best, Zheng

On Fri, Apr 5, 2024 at 15:58 meniaG @.***> wrote:

Hi,

I did use tabs as separators in the data.list file. Does it accept the complete path to the fastq file?

python3 tools/MAP2B/bin/MAP2B.py -i /annotation/map2b/data.list \ -o /projects/0/prjs0956/annotation/map2b/map2b_out 2024-04-05 21:55:32 - MAP2B.py - INFO - mkdir: /annotation/map2b/map2b_out 2024-04-05 21:55:32 - MAP2B.py - ERROR - Sample SC_DM_F5B_10-15_I_II /processed/clean_human/done/SA_DK_F7.2_0-2cm_I_nophix_nohuman_1.fastq /processed/clean_human/done/SA_DK_F7.2_0-2cm_I_nophix_nohuman_2.fastq has no Reads

I just ran it again using unzipped fastq files and I got this.

Best, Menia

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agavriilidou commented 7 months ago

Hi Zheng,

Sure.


@A00627:764:H2WFLDSXC:1:1101:23041:10551 1:N:0:GTATTCACCG+GTATGCAAGG
CCCGACATGCGGACCGCCCGGACGCAGCAGCTCTCGGATGGCGAGTTGTTCTCGATCATCGAGCACGGGATTCGGCTCACCGGCATGCCCGCATGGGGAACGGGGACGCCAGAG
GGCGAACGCGGGAGCTGGGCATTGGTCCACTACCTC
+
FFF,FFF::FFFFFF:FFFF,FF:F::F,FF,FFF:FFFF:::F::FF:F:::F:F:FF::::FFFFFF,F,FFFF::F:F:,FFF:FFF:FF::FFFF,FFFFFFF,FFFFF:
FFFFF,FFFFFFFFF:F,FFF,F::FF,FFF,FFFF
@A00627:764:H2WFLDSXC:1:1101:11840:10567 1:N:0:GTATTCACCG+GTATGCAAGG
ACGCATCTACCAGGGTGTCACCATCAATCAAAATGGCGGAAATTTTATTGGCCGAGCCGACGACGATGCCCAAGAGGCCGAAGAAGAACTTCGGTCTCAACTGCACAGCCTGAA
CCACCATTTGCTAGAAGTCTGGGACGTCGATGACTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F
FFFFFF,FFFFF:FFFFFFFFFFFFFFFFFFFFFFF
@A00627:764:H2WFLDSXC:1:1101:15510:10567 1:N:0:GTATTCACCG+GTATGCAAGG
CCTTCCTTTTCTATCTGACTGTAGTTAGCCTCGGCTTTATTAAGGCGTCTGGATGCGTATGCGATGGGCCTTTCCGAACCGTTGATCCTATGCTGTAACACCGCTCCTATACCC
TATACCGTAGGGTGACGCGTCACAACACAACAATAG
+
,FFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF
@A00627:764:H2WFLDSXC:1:1101:23556:10567 1:N:0:GTATTCACCG+GTATGCAAGG
GCCCCCAGCATCCGCCGGACTTCGCGGTTCCGCCCTTCTTTGAGCACGACCCGGTACCAGTGGTTGCGGCCCCGCCCGCCGGCGTCCTCGATCGTCTCGAACCGGGCCTGCCCG
TCCTCAAGCAGAAGAAGGCAACGAGATCGGAAGAGC
+
F,,FFFFFFFF:FFFF,FFFFF::FFFFF::F:,,,FFFFF:::FFF:FFF:FFF:FFFF::FFFF:FFFFFFFFFFFFFFFFFFFFFFFF,FFFF:FFFFFFFF,::,F:FFF
F,F:F:,,::,FF:,,:::,F,,F,:F::,,:,,:,
@A00627:764:H2WFLDSXC:1:1101:16794:10598 1:N:0:GTATTCACCG+GTATGCAAGG
CACCATGCTCGATGCAAACGCCAACGTCAGTACGGCCGAGCAGGGGAATAATAGGCGACTTCGCATGCGATGCTTCCTCGCGGAGGGGGCGATGGCGCCATGCCGCTTGCCGAC
GCCGCCCATGATGATGGACAACGCACTGGGGTCCGT
+
sunzhengCDNM commented 7 months ago

Please also send me the data.list so I can try on my end. Thanks. Best, Zheng

meniaG @.***> 于2024年4月8日周一 04:11写道：

Hi Zheng,

Sure.

@A00627:764:H2WFLDSXC:1:1101:23041:10551 1:N:0:GTATTCACCG+GTATGCAAGG CCCGACATGCGGACCGCCCGGACGCAGCAGCTCTCGGATGGCGAGTTGTTCTCGATCATCGAGCACGGGATTCGGCTCACCGGCATGCCCGCATGGGGAACGGGGACGCCAGAG GGCGAACGCGGGAGCTGGGCATTGGTCCACTACCTC + FFF,FFF::FFFFFF:FFFF,FF:F::F,FF,FFF:FFFF:::F::FF:F:::F:F:FF::::FFFFFF,F,FFFF::F:F:,FFF:FFF:FF::FFFF,FFFFFFF,FFFFF: FFFFF,FFFFFFFFF:F,FFF,F::FF,FFF,FFFF @A00627:764:H2WFLDSXC:1:1101:11840:10567 1:N:0:GTATTCACCG+GTATGCAAGG ACGCATCTACCAGGGTGTCACCATCAATCAAAATGGCGGAAATTTTATTGGCCGAGCCGACGACGATGCCCAAGAGGCCGAAGAAGAACTTCGGTCTCAACTGCACAGCCTGAA CCACCATTTGCTAGAAGTCTGGGACGTCGATGACTG + FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F FFFFFF,FFFFF:FFFFFFFFFFFFFFFFFFFFFFF @A00627:764:H2WFLDSXC:1:1101:15510:10567 1:N:0:GTATTCACCG+GTATGCAAGG CCTTCCTTTTCTATCTGACTGTAGTTAGCCTCGGCTTTATTAAGGCGTCTGGATGCGTATGCGATGGGCCTTTCCGAACCGTTGATCCTATGCTGTAACACCGCTCCTATACCC TATACCGTAGGGTGACGCGTCACAACACAACAATAG + ,FFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF @A00627:764:H2WFLDSXC:1:1101:23556:10567 1:N:0:GTATTCACCG+GTATGCAAGG GCCCCCAGCATCCGCCGGACTTCGCGGTTCCGCCCTTCTTTGAGCACGACCCGGTACCAGTGGTTGCGGCCCCGCCCGCCGGCGTCCTCGATCGTCTCGAACCGGGCCTGCCCG TCCTCAAGCAGAAGAAGGCAACGAGATCGGAAGAGC + F,,FFFFFFFF:FFFF,FFFFF::FFFFF::F:,,,FFFFF:::FFF:FFF:FFF:FFFF::FFFF:FFFFFFFFFFFFFFFFFFFFFFFF,FFFF:FFFFFFFF,::,F:FFF F,F:F:,,::,FF:,,:::,F,,F,:F::,,:,,:, @A00627:764:H2WFLDSXC:1:1101:16794:10598 1:N:0:GTATTCACCG+GTATGCAAGG CACCATGCTCGATGCAAACGCCAACGTCAGTACGGCCGAGCAGGGGAATAATAGGCGACTTCGCATGCGATGCTTCCTCGCGGAGGGGGCGATGGCGCCATGCCGCTTGCCGAC GCCGCCCATGATGATGGACAACGCACTGGGGTCCGT +

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sunzhengCDNM commented 7 months ago

It might be caused by the difference in the ending character (at each line) between Windows and Linux. Before sending me the file, could you please make sure the data.list you used is with the LF character as the ending character for each line? (please see here https://www.editpadpro.com/tricklinebreak.html#:~:text=Line%20Breaks%20in%20Windows%2C%20UNIX%20%26%20Macintosh%20Text%20Files&text=Windows%2C%20and%20DOS%20before%20it,CR%20character%20for%20line%20breaks. for details) Best, Zheng

Zheng Sun @.***> 于2024年4月8日周一 08:18写道：

Please also send me the data.list so I can try on my end. Thanks. Best, Zheng

meniaG @.***> 于2024年4月8日周一 04:11写道：

Hi Zheng,

Sure.

@A00627:764:H2WFLDSXC:1:1101:23041:10551 1:N:0:GTATTCACCG+GTATGCAAGG CCCGACATGCGGACCGCCCGGACGCAGCAGCTCTCGGATGGCGAGTTGTTCTCGATCATCGAGCACGGGATTCGGCTCACCGGCATGCCCGCATGGGGAACGGGGACGCCAGAG GGCGAACGCGGGAGCTGGGCATTGGTCCACTACCTC + FFF,FFF::FFFFFF:FFFF,FF:F::F,FF,FFF:FFFF:::F::FF:F:::F:F:FF::::FFFFFF,F,FFFF::F:F:,FFF:FFF:FF::FFFF,FFFFFFF,FFFFF: FFFFF,FFFFFFFFF:F,FFF,F::FF,FFF,FFFF @A00627:764:H2WFLDSXC:1:1101:11840:10567 1:N:0:GTATTCACCG+GTATGCAAGG ACGCATCTACCAGGGTGTCACCATCAATCAAAATGGCGGAAATTTTATTGGCCGAGCCGACGACGATGCCCAAGAGGCCGAAGAAGAACTTCGGTCTCAACTGCACAGCCTGAA CCACCATTTGCTAGAAGTCTGGGACGTCGATGACTG + FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F FFFFFF,FFFFF:FFFFFFFFFFFFFFFFFFFFFFF @A00627:764:H2WFLDSXC:1:1101:15510:10567 1:N:0:GTATTCACCG+GTATGCAAGG CCTTCCTTTTCTATCTGACTGTAGTTAGCCTCGGCTTTATTAAGGCGTCTGGATGCGTATGCGATGGGCCTTTCCGAACCGTTGATCCTATGCTGTAACACCGCTCCTATACCC TATACCGTAGGGTGACGCGTCACAACACAACAATAG + ,FFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF @A00627:764:H2WFLDSXC:1:1101:23556:10567 1:N:0:GTATTCACCG+GTATGCAAGG GCCCCCAGCATCCGCCGGACTTCGCGGTTCCGCCCTTCTTTGAGCACGACCCGGTACCAGTGGTTGCGGCCCCGCCCGCCGGCGTCCTCGATCGTCTCGAACCGGGCCTGCCCG TCCTCAAGCAGAAGAAGGCAACGAGATCGGAAGAGC + F,,FFFFFFFF:FFFF,FFFFF::FFFFF::F:,,,FFFFF:::FFF:FFF:FFF:FFFF::FFFF:FFFFFFFFFFFFFFFFFFFFFFFF,FFFF:FFFFFFFF,::,F:FFF F,F:F:,,::,FF:,,:::,F,,F,:F::,,:,,:, @A00627:764:H2WFLDSXC:1:1101:16794:10598 1:N:0:GTATTCACCG+GTATGCAAGG CACCATGCTCGATGCAAACGCCAACGTCAGTACGGCCGAGCAGGGGAATAATAGGCGACTTCGCATGCGATGCTTCCTCGCGGAGGGGGCGATGGCGCCATGCCGCTTGCCGAC GCCGCCCATGATGATGGACAACGCACTGGGGTCCGT +

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agavriilidou commented 7 months ago

Hi Zheng,

It was indeed the ending character. I made the data.list using nano on Linux and it worked. Thanks a lot for your help!

Cheers! Menia