-
Notifications
You must be signed in to change notification settings - Fork 30
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
IndexError: sequence length is not enough in R1 read #285
Comments
It looks like the R1 fastq file is truncated, which causes an error when automatically detecting chemistry. Chemistry can be specified explicitly to skip automatic detection of chemistry:
|
Hi, I tried yesterday to specifically define chemistry as that and I obtained an error that was a bit different but it was saying the same about R1 reads.
…----- Original Message -----
From: Tony Zhou ***@***.***>
To: singleron-RD/CeleScope ***@***.***>
Cc: calcaidecabello ***@***.***>, Author ***@***.***>
Sent: Wed, 15 May 2024 06:11:03 +0200 (CEST)
Subject: Re: [singleron-RD/CeleScope] IndexError: sequence length is not enough in R1 read (Issue #285)
It looks like the R1 fastq file is truncated, which causes an error when automatically detecting chemistry. Chemistry can be specified explicitly to skip automatic detection of chemistry:
```
multi_rna \
--chemistry scopeV3.0.1 \
..
```
--
Reply to this email directly or view it on GitHub:
#285 (comment)
You are receiving this because you authored the thread.
Message ID: ***@***.***>
|
Hi,
I repeated to copy the error, and this is what I obtained:
2024-05-15 09:15:12,797 - celescope.tools.sample.sample - INFO - start...
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='rna', outdir='.//Bnsortednuclei1/00.sample', sample='Bnsortednuclei1', thread='16', debug=False, fq1='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/00_rawdata/Bnsortednuclei_R1.fastq.gz', chemistry='scopeV3.0.1', wells=384, func=<function sample at 0x7efc807f6820>)
2024-05-15 09:15:12,896 - celescope.tools.sample.run - INFO - start...
Sample ID: Bnsortednuclei1
Assay: rna
Chemistry: scopeV3.0.1 (kit V2)
Software Version: 2.0.7
2024-05-15 09:15:12,897 - celescope.tools.sample.run - INFO - done. time used: 0:00:00.000273
2024-05-15 09:15:12,898 - celescope.tools.step._clean_up - INFO - start...
2024-05-15 09:15:12,929 - celescope.tools.step._render_html - INFO - start...
2024-05-15 09:15:14,182 - celescope.tools.step._render_html - INFO - done. time used: 0:00:01.252553
2024-05-15 09:15:14,182 - celescope.tools.step._clean_up - INFO - done. time used: 0:00:01.284344
2024-05-15 09:15:14,182 - celescope.tools.sample.sample - INFO - done. time used: 0:00:01.384928
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='rna', chemistry='scopeV3.0.1', pattern=None, whitelist=None, adapter_3p='AAAAAAAAAAAA', genomeDir='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/ZS11/', outFilterMatchNmin='50', soloCellFilter='EmptyDrops_CR 3000 0.99 10 45000 90000 500 0.01 20000 0.001 10000', starMem='32', STAR_param='', SAM_attributes='', soloFeatures='Gene GeneFull_Ex50pAS', fq1='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/00_rawdata/Bnsortednuclei_R1.fastq.gz', fq2='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/00_rawdata/Bnsortednuclei_R2.fastq.gz', outdir='.//Bnsortednuclei1/01.starsolo', sample='Bnsortednuclei1', thread='16', debug=False, func=<function starsolo at 0x7fd387e0dee0>)
STAR \
--genomeDir /netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/ZS11/ \
--readFilesIn /netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/00_rawdata/Bnsortednuclei_R2.fastq.gz /netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/00_rawdata/Bnsortednuclei_R1.fastq.gz \
--readFilesCommand zcat \
--soloCBwhitelist /netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist1 /netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist2 /netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/data/chemistry/scopeV3.0.1/bclist3 \
--soloCellFilter EmptyDrops_CR 3000 0.99 10 45000 90000 500 0.01 20000 0.001 10000 \
--outFileNamePrefix .//Bnsortednuclei1/01.starsolo/Bnsortednuclei1_ \
--runThreadN 16 \
--clip3pAdapterSeq AAAAAAAAAAAA \
--outFilterMatchNmin 50 \
--soloFeatures Gene GeneFull_Ex50pAS \
--outSAMattributes NH HI nM AS CR UR CB UB GX GN \
--soloType CB_UMI_Complex \
--soloCBposition 0_0_0_8 0_25_0_33 0_50_0_58 \
--soloUMIposition 0_60_0_71 --soloUMIlen 12 \
--soloCBmatchWLtype 1MM \
--outSAMtype BAM SortedByCoordinate \
--soloCellReadStats Standard \
--soloBarcodeReadLength 0 \
chmod: cannot access './/Bnsortednuclei1/01.starsolo/Bnsortednuclei1_Solo.out/': No such file or directory
chmod -R 755 .//Bnsortednuclei1/01.starsolo/Bnsortednuclei1_Solo.out/Traceback (most recent call last):
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/bin/celescope", line 8, in <module>
sys.exit(main())
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/celescope.py", line 54, in main
args.func(args)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/starsolo.py", line 186, in starsolo
q30_cb, q30_umi, chemistry = runner.run()
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/starsolo.py", line 177, in run
self.run_starsolo()
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/starsolo.py", line 136, in run_starsolo
subprocess.check_call(cmd, shell=True)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/subprocess.py", line 373, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'chmod -R 755 .//Bnsortednuclei1/01.starsolo/Bnsortednuclei1_Solo.out/' returned non-zero exit status 1.
2024-05-15 09:15:24,667 - celescope.rna.analysis.analysis - INFO - start...
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='rna', genomeDir='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/ZS11/', matrix_file='.//Bnsortednuclei1/outs/filtered', outdir='.//Bnsortednuclei1/02.analysis', sample='Bnsortednuclei1', thread='16', debug=False, func=<function analysis at 0x7f0d5bb184c0>)
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='rna', genomeDir='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/ZS11/', matrix_file='.//Bnsortednuclei1/outs/filtered', outdir='.//Bnsortednuclei1/02.analysis', sample='Bnsortednuclei1', thread='16', debug=False, func=<function analysis at 0x7f0d5bb184c0>)
Traceback (most recent call last):
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/bin/celescope", line 8, in <module>
sys.exit(main())
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/celescope.py", line 54, in main
args.func(args)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/rna/analysis.py", line 64, in analysis
runner.run()
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/rna/analysis.py", line 38, in run
with analysis_wrapper.Scanpy_wrapper(self.args, display_title=self.display_title) as scanpy_wrapper:
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/analysis_wrapper.py", line 59, in __init__
self.adata = sc.read_10x_mtx(
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/scanpy/readwrite.py", line 490, in read_10x_mtx
adata = read(
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/scanpy/readwrite.py", line 554, in _read_v3_10x_mtx
adata = read(
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/scanpy/readwrite.py", line 112, in read
return _read(
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/scanpy/readwrite.py", line 737, in _read
raise FileNotFoundError(f'Did not find file {filename}.')
FileNotFoundError: Did not find file Bnsortednuclei1/outs/filtered/matrix.mtx.gz.
Best,
Cristina.
From: "Tony Zhou" ***@***.***>
To: "singleron-RD/CeleScope" ***@***.***>
Cc: "Cristina Alcaide" ***@***.***>, "Author" ***@***.***>
Sent: Wednesday, 15 May, 2024 06:11:03
Subject: Re: [singleron-RD/CeleScope] IndexError: sequence length is not enough in R1 read (Issue #285)
It looks like the R1 fastq file is truncated, which causes an error when automatically detecting chemistry. Chemistry can be specified explicitly to skip automatic detection of chemistry:
multi_rna \
--chemistry scopeV3.0.1 \
..
—
Reply to this email directly, [ #285 (comment) | view it on GitHub ] , or [ https://github.com/notifications/unsubscribe-auth/BIPNUQUQGXPNQ2KR2IWSAX3ZCLN5PAVCNFSM6AAAAABHWDQIM6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJRGU2DINRSGQ | unsubscribe ] .
You are receiving this because you authored the thread. Message ID: <singleron-RD/CeleScope/issues/285/2111544624 @ github . com>
|
Would you please check the length read of R1 fastq reads? Are their lengths 61bp like the read in the error report?
|
Hi,
I have been talking with Khalil from technical support, we have checked the FASTQC files and the reads are 150pb in length. We haven't been able to identify the error.
Best,
Cristina.
From: "Tony Zhou" ***@***.***>
To: "singleron-RD" ***@***.***>
Cc: "Cristina Alcaide" ***@***.***>, "Author" ***@***.***>
Sent: Wednesday, 15 May, 2024 09:59:56
Subject: Re: [singleron-RD/CeleScope] IndexError: sequence length is not enough in R1 read (Issue #285)
Would you please check the length read of R1 fastq reads? Are their lengths 61bp like the read in the error report?
scopeV3.0.1 requires a minimum R1 read length of 72bp
It seems that the main error is "IndexError: sequence length is not enough in R1 read: TGCCTGATCCGAACATGTAGGTCTCTGTCGGTGTGACTACGTATTAGCATGTGTCTGAACT"
—
Reply to this email directly, [ #285 (comment) | view it on GitHub ] , or [ https://github.com/notifications/unsubscribe-auth/BIPNUQUNAWMJI32SULMKXLTZCMIXZAVCNFSM6AAAAABHWDQIM6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJRHAZTGMBWGM | unsubscribe ] .
You are receiving this because you authored the thread. Message ID: <singleron-RD/CeleScope/issues/285/2111833063 @ github . com>
|
It seems that at least one R1 read is 61bp in length, which does not meet the minimum requirement of 72bp. In theory, the length of each read of the raw data should be the same. Why does this short read appear? Maybe
While it may be important to find the reason for the short read length, here are some ways to bypass this error:
|
您好,请问当测序R1 pattern 是这样的 C9L16C9L16C9U12=71bp,该如何正确运行celescope呢? 回复: 参考#276 这里。设置 以下参数 :--chemistry customized --pattern --whitelist |
Hi,
I am trying to run celescope. I built the reference genome and I have created the shell scripts, but I obtain this error:
sh Bnsortednuclei1.sh
2024-05-14 14:13:14,148 - celescope.tools.sample.sample - INFO - start...
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='rna', outdir='.//Bnsortednuclei1/00.sample', sample='Bnsortednuclei1', thread='16', debug=False, fq1='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/00_rawdata/Bnsortednuclei_R1.fastq.gz', chemistry='auto', wells=384, func=<function sample at 0x7fa2b78e0820>)
2024-05-14 14:13:14,209 - celescope.tools.sample.run - INFO - start...
2024-05-14 14:13:14,872 - celescope.tools.barcode.check_chemistry - INFO - start...
2024-05-14 14:13:14,872 - celescope.tools.barcode.check_chemistry - INFO - /netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/00_rawdata/Bnsortednuclei_R1.fastq.gz
2024-05-14 14:13:14,872 - celescope.tools.barcode.get_chemistry - INFO - start...
Traceback (most recent call last):
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/bin/celescope", line 8, in
sys.exit(main())
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/celescope.py", line 54, in main
args.func(args)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/sample.py", line 68, in sample
runner.run()
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/sample.py", line 36, in run
chemistry = ch.check_chemistry()
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 56, in check_chemistry
chemistry = self.get_chemistry(fastq1)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 131, in get_chemistry
chemistry = self.seq_chemistry(seq)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 87, in seq_chemistry
linker_flv_rna = Barcode.get_seq_str(seq, self.pattern_dict_flv_rna["L"])
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 276, in get_seq_str
raise IndexError(f"sequence length is not enough in R1 read: {seq}")
IndexError: sequence length is not enough in R1 read: TGCCTGATCCGAACATGTAGGTCTCTGTCGGTGTGACTACGTATTAGCATGTGTCTGAACT
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='rna', chemistry='auto', pattern=None, whitelist=None, adapter_3p='AAAAAAAAAAAA', genomeDir='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/ZS11/', outFilterMatchNmin='50', soloCellFilter='EmptyDrops_CR 3000 0.99 10 45000 90000 500 0.01 20000 0.001 10000', starMem='32', STAR_param='', SAM_attributes='', soloFeatures='Gene GeneFull_Ex50pAS', fq1='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/00_rawdata/Bnsortednuclei_R1.fastq.gz', fq2='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/00_rawdata/Bnsortednuclei_R2.fastq.gz', outdir='.//Bnsortednuclei1/01.starsolo', sample='Bnsortednuclei1', thread='16', debug=False, func=<function starsolo at 0x7fc688421ee0>)
2024-05-14 14:13:21,219 - celescope.tools.barcode.check_chemistry - INFO - start...
2024-05-14 14:13:21,220 - celescope.tools.barcode.check_chemistry - INFO - /netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/00_rawdata/Bnsortednuclei_R1.fastq.gz
2024-05-14 14:13:21,220 - celescope.tools.barcode.get_chemistry - INFO - start...
Traceback (most recent call last):
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/bin/celescope", line 8, in
sys.exit(main())
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/celescope.py", line 54, in main
args.func(args)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/starsolo.py", line 185, in starsolo
with Starsolo(args) as runner:
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/starsolo.py", line 41, in init
chemistry_list = ch.check_chemistry()
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 56, in check_chemistry
chemistry = self.get_chemistry(fastq1)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 131, in get_chemistry
chemistry = self.seq_chemistry(seq)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 87, in seq_chemistry
linker_flv_rna = Barcode.get_seq_str(seq, self.pattern_dict_flv_rna["L"])
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 276, in get_seq_str
raise IndexError(f"sequence length is not enough in R1 read: {seq}")
IndexError: sequence length is not enough in R1 read: TGCCTGATCCGAACATGTAGGTCTCTGTCGGTGTGACTACGTATTAGCATGTGTCTGAACT
2024-05-14 14:13:26,722 - celescope.rna.analysis.analysis - INFO - start...
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='rna', genomeDir='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/ZS11/', matrix_file='.//Bnsortednuclei1/outs/filtered', outdir='.//Bnsortednuclei1/02.analysis', sample='Bnsortednuclei1', thread='16', debug=False, func=<function analysis at 0x7fc0797f64c0>)
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='rna', genomeDir='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/ZS11/', matrix_file='.//Bnsortednuclei1/outs/filtered', outdir='.//Bnsortednuclei1/02.analysis', sample='Bnsortednuclei1', thread='16', debug=False, func=<function analysis at 0x7fc0797f64c0>)
Traceback (most recent call last):
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/bin/celescope", line 8, in
sys.exit(main())
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/celescope.py", line 54, in main
args.func(args)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/rna/analysis.py", line 64, in analysis
runner.run()
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/rna/analysis.py", line 38, in run
with analysis_wrapper.Scanpy_wrapper(self.args, display_title=self.display_title) as scanpy_wrapper:
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/analysis_wrapper.py", line 59, in init
self.adata = sc.read_10x_mtx(
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/scanpy/readwrite.py", line 490, in read_10x_mtx
adata = read(
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/scanpy/readwrite.py", line 554, in _read_v3_10x_mtx
adata = read(
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/scanpy/readwrite.py", line 112, in read
return _read(
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/scanpy/readwrite.py", line 737, in _read
raise FileNotFoundError(f'Did not find file {filename}.')
FileNotFoundError: Did not find file Bnsortednuclei1/outs/filtered/matrix.mtx.gz.
(Cris_singleron_snseq) calcaide@dell-node-4:/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/shell$ cd ../
(Cris_singleron_snseq) calcaide@dell-node-4:/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460$ sh ./shell/Bnsortednuclei1.sh
2024-05-14 14:20:03,762 - celescope.tools.sample.sample - INFO - start...
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='rna', outdir='.//Bnsortednuclei1/00.sample', sample='Bnsortednuclei1', thread='16', debug=False, fq1='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/00_rawdata/Bnsortednuclei_R1.fastq.gz', chemistry='auto', wells=384, func=<function sample at 0x7fe755b11820>)
2024-05-14 14:20:03,835 - celescope.tools.sample.run - INFO - start...
2024-05-14 14:20:04,488 - celescope.tools.barcode.check_chemistry - INFO - start...
2024-05-14 14:20:04,489 - celescope.tools.barcode.check_chemistry - INFO - /netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/00_rawdata/Bnsortednuclei_R1.fastq.gz
2024-05-14 14:20:04,489 - celescope.tools.barcode.get_chemistry - INFO - start...
Traceback (most recent call last):
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/bin/celescope", line 8, in
sys.exit(main())
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/celescope.py", line 54, in main
args.func(args)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/sample.py", line 68, in sample
runner.run()
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/sample.py", line 36, in run
chemistry = ch.check_chemistry()
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 56, in check_chemistry
chemistry = self.get_chemistry(fastq1)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 131, in get_chemistry
chemistry = self.seq_chemistry(seq)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 87, in seq_chemistry
linker_flv_rna = Barcode.get_seq_str(seq, self.pattern_dict_flv_rna["L"])
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 276, in get_seq_str
raise IndexError(f"sequence length is not enough in R1 read: {seq}")
IndexError: sequence length is not enough in R1 read: TGCCTGATCCGAACATGTAGGTCTCTGTCGGTGTGACTACGTATTAGCATGTGTCTGAACT
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='rna', chemistry='auto', pattern=None, whitelist=None, adapter_3p='AAAAAAAAAAAA', genomeDir='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/ZS11/', outFilterMatchNmin='50', soloCellFilter='EmptyDrops_CR 3000 0.99 10 45000 90000 500 0.01 20000 0.001 10000', starMem='32', STAR_param='', SAM_attributes='', soloFeatures='Gene GeneFull_Ex50pAS', fq1='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/00_rawdata/Bnsortednuclei_R1.fastq.gz', fq2='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/00_rawdata/Bnsortednuclei_R2.fastq.gz', outdir='.//Bnsortednuclei1/01.starsolo', sample='Bnsortednuclei1', thread='16', debug=False, func=<function starsolo at 0x7fb7396a1ee0>)
2024-05-14 14:20:10,529 - celescope.tools.barcode.check_chemistry - INFO - start...
2024-05-14 14:20:10,530 - celescope.tools.barcode.check_chemistry - INFO - /netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/00_rawdata/Bnsortednuclei_R1.fastq.gz
2024-05-14 14:20:10,530 - celescope.tools.barcode.get_chemistry - INFO - start...
Traceback (most recent call last):
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/bin/celescope", line 8, in
sys.exit(main())
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/celescope.py", line 54, in main
args.func(args)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/starsolo.py", line 185, in starsolo
with Starsolo(args) as runner:
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/starsolo.py", line 41, in init
chemistry_list = ch.check_chemistry()
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 56, in check_chemistry
chemistry = self.get_chemistry(fastq1)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 131, in get_chemistry
chemistry = self.seq_chemistry(seq)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 87, in seq_chemistry
linker_flv_rna = Barcode.get_seq_str(seq, self.pattern_dict_flv_rna["L"])
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 276, in get_seq_str
raise IndexError(f"sequence length is not enough in R1 read: {seq}")
IndexError: sequence length is not enough in R1 read: TGCCTGATCCGAACATGTAGGTCTCTGTCGGTGTGACTACGTATTAGCATGTGTCTGAACT
2024-05-14 14:20:15,806 - celescope.rna.analysis.analysis - INFO - start...
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='rna', genomeDir='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/ZS11/', matrix_file='.//Bnsortednuclei1/outs/filtered', outdir='.//Bnsortednuclei1/02.analysis', sample='Bnsortednuclei1', thread='16', debug=False, func=<function analysis at 0x7f3cca87e4c0>)
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='rna', genomeDir='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/ZS11/', matrix_file='.//Bnsortednuclei1/outs/filtered', outdir='.//Bnsortednuclei1/02.analysis', sample='Bnsortednuclei1', thread='16', debug=False, func=<function analysis at 0x7f3cca87e4c0>)
Traceback (most recent call last):
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/bin/celescope", line 8, in
sys.exit(main())
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/celescope.py", line 54, in main
args.func(args)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/rna/analysis.py", line 64, in analysis
runner.run()
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/rna/analysis.py", line 38, in run
with analysis_wrapper.Scanpy_wrapper(self.args, display_title=self.display_title) as scanpy_wrapper:
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/analysis_wrapper.py", line 59, in init
self.adata = sc.read_10x_mtx(
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/scanpy/readwrite.py", line 490, in read_10x_mtx
adata = read(
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/scanpy/readwrite.py", line 554, in _read_v3_10x_mtx
adata = read(
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/scanpy/readwrite.py", line 112, in read
return _read(
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/scanpy/readwrite.py", line 737, in _read
raise FileNotFoundError(f'Did not find file {filename}.')
FileNotFoundError: Did not find file Bnsortednuclei1/outs/filtered/matrix.mtx.gz.
It seems that the main error is "IndexError: sequence length is not enough in R1 read: TGCCTGATCCGAACATGTAGGTCTCTGTCGGTGTGACTACGTATTAGCATGTGTCTGAACT"
I don't know if it is related with a sequencing problem or I should change some parameters.
Can you help me, please?
Thank you in advance!
The text was updated successfully, but these errors were encountered: