probleam in cutadapt with Ipyrad in Conda

[cavdberg]

I have recently updated my conda, in which I had Ipyrad running since 2021. Then, ipyrad started to give errors in step 2, appararently some incompatibility with cutadapt. The error occurs for each sample, when trying to trim:

IPyradError( error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_68.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_68_R1_.fastq.gz Anyone have an idea how to solve this? I tried changing versions of cutadapt, without success.

[isaacovercast]

Can you post the version of cutadapt? I'll take a look.

On Fri, Oct 27, 2023, 17:55 Cássio van den Berg @.***> wrote:

I have recently updated my conda, in which I had Ipyrad running since

2021. Then, ipyrad started to give errors in step 2, appararently some incompatibility with cutadapt. The error occurs for each sample, when trying to trim:

IPyradError( error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_68.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_68_R1_.fastq.gz Anyone have an idea how to solve this? I tried changing versions of cutadapt, without success. — Reply to this email directly, view it on GitHub , or unsubscribe . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[cavdberg]

HI Isaac, by now none is working, I will have to reinstall the whole environment that got messed up when I tried to change versions of cutatapt. But the one with that error was 2.6. Do you have a recommended compatible version of cutadapt? The version is not specified in the dependencies of ipyrad.

Regards Cassio

On Fri, Oct 27, 2023 at 7:08 PM Isaac Overcast @.***> wrote:

Can you post the version of cutadapt? I'll take a look.

On Fri, Oct 27, 2023, 17:55 Cássio van den Berg @.***> wrote:

I have recently updated my conda, in which I had Ipyrad running since

2021. Then, ipyrad started to give errors in step 2, appararently some incompatibility with cutadapt. The error occurs for each sample, when trying to trim:

IPyradError( error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_68.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_68_R1_.fastq.gz Anyone have an idea how to solve this? I tried changing versions of cutadapt, without success. — Reply to this email directly, view it on GitHub , or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABNSXP7KMZ6VM3IXDLZNVHDYBQUTJAVCNFSM6AAAAAA6TNHP56VHI2DSMVQWIX3LMV43ASLTON2WKOZRHE3DMMRTGYZTGNY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

— Reply to this email directly, view it on GitHub https://github.com/dereneaton/ipyrad/issues/532#issuecomment-1783562343, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFXMBR7ACIXPIF6ABRUTMDYBQWF3AVCNFSM6AAAAAA6TNHP56VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOBTGU3DEMZUGM . You are receiving this because you authored the thread.Message ID: @.***>

--

---

Cássio van den Berg Full Professor Univ. Estadual de Feira de Santana Dept. Ciências Biológicas Av. Transnordestina, s/n 44036-900 Feira de Santana-BA Brazil Phone: +5575 34885745 mobile +5575 91999331 Lattes http://lattes.cnpq.br/2129963760543898 Personal Homepage http://www.cassiovandenberg.com/d/?q=node/2 Google Scholar https://scholar.google.com.br/citations?user=zX7H1gwAAAAJ&hl=pt-BR Pesquisador CNPQ 1A

---

[cavdberg]

Dear Isaac.

This is an Update.

Here running on Ubuntu 22.04

I removed conda completely. Installed the new conda 23.9.0 with Python 3.10. Then installed the libmamba solver. The created a env.

Conda installed ipyrad with Py. 3.10 smoothly.

I verified cutadapter. Version 4.5.

Tried to go on in the samples that I had already demultiplexed in step 1. Same error, in all the 120 samples. I am attaching the error log for s2.txt.

My impression checking the log, is that there is an extra blank space in the beginning of the filename path, that is making cutapadt not to find the file.

Regards Cassio

On Fri, Oct 27, 2023 at 7:15 PM Cássio van den Berg @.***> wrote:

HI Isaac, by now none is working, I will have to reinstall the whole environment that got messed up when I tried to change versions of cutatapt. But the one with that error was 2.6. Do you have a recommended compatible version of cutadapt? The version is not specified in the dependencies of ipyrad.

Regards Cassio

On Fri, Oct 27, 2023 at 7:08 PM Isaac Overcast @.***> wrote:

Can you post the version of cutadapt? I'll take a look.

On Fri, Oct 27, 2023, 17:55 Cássio van den Berg @.***> wrote:

I have recently updated my conda, in which I had Ipyrad running since

2021. Then, ipyrad started to give errors in step 2, appararently some incompatibility with cutadapt. The error occurs for each sample, when trying to trim:

IPyradError( error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_68.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_68_R1_.fastq.gz Anyone have an idea how to solve this? I tried changing versions of cutadapt, without success. — Reply to this email directly, view it on GitHub , or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABNSXP7KMZ6VM3IXDLZNVHDYBQUTJAVCNFSM6AAAAAA6TNHP56VHI2DSMVQWIX3LMV43ASLTON2WKOZRHE3DMMRTGYZTGNY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

— Reply to this email directly, view it on GitHub https://github.com/dereneaton/ipyrad/issues/532#issuecomment-1783562343, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFXMBR7ACIXPIF6ABRUTMDYBQWF3AVCNFSM6AAAAAA6TNHP56VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOBTGU3DEMZUGM . You are receiving this because you authored the thread.Message ID: @.***>

--

---

Cássio van den Berg Full Professor Univ. Estadual de Feira de Santana Dept. Ciências Biológicas Av. Transnordestina, s/n 44036-900 Feira de Santana-BA Brazil Phone: +5575 34885745 mobile +5575 91999331 Lattes http://lattes.cnpq.br/2129963760543898 Personal Homepage http://www.cassiovandenberg.com/d/?q=node/2 Google Scholar https://scholar.google.com.br/citations?user=zX7H1gwAAAAJ&hl=pt-BR Pesquisador CNPQ 1A

---

--

---

Cássio van den Berg Full Professor Univ. Estadual de Feira de Santana Dept. Ciências Biológicas Av. Transnordestina, s/n 44036-900 Feira de Santana-BA Brazil Phone: +5575 34885745 mobile +5575 91999331 Lattes http://lattes.cnpq.br/2129963760543898 Personal Homepage http://www.cassiovandenberg.com/d/?q=node/2 Google Scholar https://scholar.google.com.br/citations?user=zX7H1gwAAAAJ&hl=pt-BR Pesquisador CNPQ 1A

---

[12:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_68.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_68_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_68.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_68_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_68_R1_.fastq.gz'\n" [0:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_121.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_121_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_121.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_121_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_121_R1_.fastq.gz'\n" [4:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_171.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_171_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_171.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_171_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_171_R1_.fastq.gz'\n" [6:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_186b.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_186b_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_186b.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_186b_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_186b_R1_.fastq.gz'\n" [14:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_57.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_57_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_57.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_57_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_57_R1_.fastq.gz'\n" [2:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_56.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_56_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_56.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_56_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_56_R1_.fastq.gz'\n" [10:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_67.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_67_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_67.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_67_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_67_R1_.fastq.gz'\n" [8:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_SP_191.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_SP_191_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_SP_191.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_SP_191_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_SP_191_R1_.fastq.gz'\n" [6:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_MG_22.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_MG_22_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_MG_22.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_MG_22_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_MG_22_R1_.fastq.gz'\n" [14:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_36.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_36_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_36.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_36_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_36_R1_.fastq.gz'\n" [8:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_148.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_148_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_148.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_148_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_148_R1_.fastq.gz'\n" [8:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_109.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_109_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_109.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_109_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_109_R1_.fastq.gz'\n" [2:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_RJ_17.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_17_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_RJ_17.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_17_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_17_R1_.fastq.gz'\n" [0:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_153.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_153_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_153.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_153_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_153_R1_.fastq.gz'\n" [6:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_146.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_146_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_146.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_146_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_146_R1_.fastq.gz'\n" [4:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_170.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_170_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_170.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_170_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_170_R1_.fastq.gz'\n" [14:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_180.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_180_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_180.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_180_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_180_R1_.fastq.gz'\n" [12:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_SP_196.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_SP_196_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_SP_196.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_SP_196_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_SP_196_R1_.fastq.gz'\n" [10:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_46.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_46_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_46.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_46_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_46_R1_.fastq.gz'\n" [0:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_RJ_20.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_20_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_RJ_20.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_20_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_20_R1_.fastq.gz'\n" [12:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_161.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_161_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_161.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_161_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_161_R1_.fastq.gz'\n" [12:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_62.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_62_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_62.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_62_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_62_R1_.fastq.gz'\n" [0:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_RJ_19.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_19_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_RJ_19.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_19_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_19_R1_.fastq.gz'\n" [4:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_173.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_173_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_173.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_173_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_173_R1_.fastq.gz'\n" [6:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_RJ_29.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_29_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_RJ_29.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_29_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_29_R1_.fastq.gz'\n" [4:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_187.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_187_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_187.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_187_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_187_R1_.fastq.gz'\n" [14:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_PA_107.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_PA_107_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_PA_107.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_PA_107_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_PA_107_R1_.fastq.gz'\n" [2:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_61.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_61_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_61.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_61_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_61_R1_.fastq.gz'\n" [6:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_72.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_72_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_72.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_72_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_72_R1_.fastq.gz'\n" [10:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_178.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_178_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_178.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_178_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_178_R1_.fastq.gz'\n" [12:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_83.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_83_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_83.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_83_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_83_R1_.fastq.gz'\n" [10:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_179.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_179_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_179.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_179_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_179_R1_.fastq.gz'\n" [4:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_RJ_15.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_15_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_RJ_15.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_15_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_15_R1_.fastq.gz'\n" [6:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_64.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_64_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_64.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_64_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_64_R1_.fastq.gz'\n" [2:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_169.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_169_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_169.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_169_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_169_R1_.fastq.gz'\n" [0:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_63.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_63_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_63.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_63_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_63_R1_.fastq.gz'\n" [14:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_76.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_76_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_76.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_76_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_76_R1_.fastq.gz'\n" [8:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_RS_100.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RS_100_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_RS_100.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RS_100_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RS_100_R1_.fastq.gz'\n" [12:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_SP_198.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_SP_198_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_SP_198.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_SP_198_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_SP_198_R1_.fastq.gz'\n" [10:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_53.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_53_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_53.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_53_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_53_R1_.fastq.gz'\n" [14:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_77.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_77_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_77.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_77_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_77_R1_.fastq.gz'\n" [4:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_73.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_73_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_73.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_73_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_73_R1_.fastq.gz'\n" [0:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_38.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_38_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_38.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_38_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_38_R1_.fastq.gz'\n" [8:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_55.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_55_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_55.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_55_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_55_R1_.fastq.gz'\n" [2:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_147.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_147_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_147.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_147_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_147_R1_.fastq.gz'\n" [6:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_78.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_78_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_78.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_78_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_78_R1_.fastq.gz'\n" [12:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_RJ_26.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_26_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_RJ_26.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_26_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_26_R1_.fastq.gz'\n" [10:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_SP_199.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_SP_199_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_SP_199.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_SP_199_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_SP_199_R1_.fastq.gz'\n" [14:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_RJ_24.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_24_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_RJ_24.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_24_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_24_R1_.fastq.gz'\n" [4:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_69.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_69_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_69.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_69_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_69_R1_.fastq.gz'\n" [0:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_177.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_177_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_177.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_177_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_177_R1_.fastq.gz'\n" [8:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_82.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_82_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_82.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_82_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_82_R1_.fastq.gz'\n" [2:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_50.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_50_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_50.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_50_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_50_R1_.fastq.gz'\n" [6:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_84.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_84_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_84.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_84_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_84_R1_.fastq.gz'\n" [12:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_52.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_52_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_52.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_52_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_52_R1_.fastq.gz'\n" [10:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_41.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_41_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_41.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_41_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_41_R1_.fastq.gz'\n" [14:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_135.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_135_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_135.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_135_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_135_R1_.fastq.gz'\n" [4:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_SP_197.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_SP_197_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_SP_197.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_SP_197_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_SP_197_R1_.fastq.gz'\n" [0:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_97.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_97_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_97.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_97_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_97_R1_.fastq.gz'\n" [8:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_MG_30.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_MG_30_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_MG_30.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_MG_30_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_MG_30_R1_.fastq.gz'\n" [2:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_75.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_75_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_75.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_75_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_75_R1_.fastq.gz'\n" [6:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_154.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_154_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_154.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_154_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_154_R1_.fastq.gz'\n" [12:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_96.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_96_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_96.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_96_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_96_R1_.fastq.gz'\n" [10:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_66.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_66_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_66.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_66_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_66_R1_.fastq.gz'\n" [14:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_120.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_120_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_120.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_120_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_120_R1_.fastq.gz'\n" [4:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_SP_194.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_SP_194_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_SP_194.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_SP_194_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_SP_194_R1_.fastq.gz'\n" [0:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_162.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_162_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_162.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_162_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_162_R1_.fastq.gz'\n" [8:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_47.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_47_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_47.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_47_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_47_R1_.fastq.gz'\n" [2:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_RJ_25.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_25_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_RJ_25.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_25_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_25_R1_.fastq.gz'\n" [6:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_81.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_81_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_81.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_81_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_81_R1_.fastq.gz'\n" [12:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_95.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_95_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_95.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_95_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_95_R1_.fastq.gz'\n" [10:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_186.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_186_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_186.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_186_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_186_R1_.fastq.gz'\n" [14:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_RJ_09.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_09_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_RJ_09.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_09_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_RJ_09_R1_.fastq.gz'\n" [4:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_60.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_60_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_60.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_60_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_60_R1_.fastq.gz'\n" [0:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_54.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_54_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_54.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_54_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_54_R1_.fastq.gz'\n" [8:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_71.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_71_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_71.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_71_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_71_R1_.fastq.gz'\n" [2:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_165.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_165_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_165.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_165_R1_.fastq.gz\nProcessing single-end reads on 1 core ...\nERROR: [Errno 2] No such file or directory: ' /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_165_R1_.fastq.gz'\n" [6:apply] IPyradError: error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_79.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_79_R1_.fastq.gz b"This is cutadapt 4.5 with Python 3.10.13\nCommand line parameters: -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --o

[cavdberg]

I managed to make a temporary fix in it here by inserting an lstrip() to remove that space on the name of the file for cutadapt on rawedits.py line 435,436 as in

data.dirs.edits, sname + ".trimmedR1.fastq.gz"), sample.files.concat[0][0].lstrip(),

That might be useful if it gives the same problems for other users.

Regards Cassio

On Sat, Oct 28, 2023 at 6:43 AM Cássio van den Berg @.***> wrote:

Dear Isaac.

This is an Update.

Here running on Ubuntu 22.04

I removed conda completely. Installed the new conda 23.9.0 with Python 3.10. Then installed the libmamba solver. The created a env.

Conda installed ipyrad with Py. 3.10 smoothly.

I verified cutadapter. Version 4.5.

Tried to go on in the samples that I had already demultiplexed in step 1. Same error, in all the 120 samples. I am attaching the error log for s2.txt.

My impression checking the log, is that there is an extra blank space in the beginning of the filename path, that is making cutapadt not to find the file.

Regards Cassio

On Fri, Oct 27, 2023 at 7:15 PM Cássio van den Berg @.***> wrote:

HI Isaac, by now none is working, I will have to reinstall the whole environment that got messed up when I tried to change versions of cutatapt. But the one with that error was 2.6. Do you have a recommended compatible version of cutadapt? The version is not specified in the dependencies of ipyrad.

Regards Cassio

On Fri, Oct 27, 2023 at 7:08 PM Isaac Overcast @.***> wrote:

Can you post the version of cutadapt? I'll take a look.

On Fri, Oct 27, 2023, 17:55 Cássio van den Berg @.***> wrote:

I have recently updated my conda, in which I had Ipyrad running since

2021. Then, ipyrad started to give errors in step 2, appararently some incompatibility with cutadapt. The error occurs for each sample, when trying to trim:

IPyradError( error in cutadapt -a AGATCGGAAGAGC --quality-base 33 -q 20 --minimum-length 50 --max-n 5 --trim-n --output /home/cavdberg/analises_ipyrad/crotalus_edits/Cd_BA_68.trimmed_R1_.fastq.gz /home/cavdberg/analises_ipyrad/corrida2_tudo_fastqs/Cd_BA_68_R1_.fastq.gz Anyone have an idea how to solve this? I tried changing versions of cutadapt, without success. — Reply to this email directly, view it on GitHub , or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABNSXP7KMZ6VM3IXDLZNVHDYBQUTJAVCNFSM6AAAAAA6TNHP56VHI2DSMVQWIX3LMV43ASLTON2WKOZRHE3DMMRTGYZTGNY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

— Reply to this email directly, view it on GitHub https://github.com/dereneaton/ipyrad/issues/532#issuecomment-1783562343, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFXMBR7ACIXPIF6ABRUTMDYBQWF3AVCNFSM6AAAAAA6TNHP56VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOBTGU3DEMZUGM . You are receiving this because you authored the thread.Message ID: @.***>

--

---

Cássio van den Berg Full Professor Univ. Estadual de Feira de Santana Dept. Ciências Biológicas Av. Transnordestina, s/n 44036-900 Feira de Santana-BA Brazil Phone: +5575 34885745 mobile +5575 91999331 Lattes http://lattes.cnpq.br/2129963760543898 Personal Homepage http://www.cassiovandenberg.com/d/?q=node/2 Google Scholar https://scholar.google.com.br/citations?user=zX7H1gwAAAAJ&hl=pt-BR Pesquisador CNPQ 1A

---

--

---

Cássio van den Berg Full Professor Univ. Estadual de Feira de Santana Dept. Ciências Biológicas Av. Transnordestina, s/n 44036-900 Feira de Santana-BA Brazil Phone: +5575 34885745 mobile +5575 91999331 Lattes http://lattes.cnpq.br/2129963760543898 Personal Homepage http://www.cassiovandenberg.com/d/?q=node/2 Google Scholar https://scholar.google.com.br/citations?user=zX7H1gwAAAAJ&hl=pt-BR Pesquisador CNPQ 1A

---

--

---

Cássio van den Berg Full Professor Univ. Estadual de Feira de Santana Dept. Ciências Biológicas Av. Transnordestina, s/n 44036-900 Feira de Santana-BA Brazil Phone: +5575 34885745 mobile +5575 91999331 Lattes http://lattes.cnpq.br/2129963760543898 Personal Homepage http://www.cassiovandenberg.com/d/?q=node/2 Google Scholar https://scholar.google.com.br/citations?user=zX7H1gwAAAAJ&hl=pt-BR Pesquisador CNPQ 1A

---

[isaacovercast]

Hi Cassio,

Glad you got it figured out. It's unusual there is the hanging space in the filename. Were these fastq files demultiplexed by ipyrad or were they pre-demultiplexed before you ran step 1? The fix you propose seems good, but it will only fix R1 and not R2 for paired-end data. If we can figure out what the upstream problem is I can fix it in the code where it should crop up.

Can you send me the results of ls -l on the directory with the raw fastq files? And can you attach here the .json file of this assembly? I'll check it out.

Thanks! -isaac

[cavdberg]

The samples were demultiplexed in step 1 with ipyrad. In fact, these were old projects that I had done in 2021, and wanted to repeat only passes 2-7 with different parameters, and then they started to give the issue.

Then I have run demultiplexing step1 with the current version again, but the same bug happened in step2 with the filenames, even done with the current version from step1.

Best wishes, Cassio

On Sat, Oct 28, 2023 at 10:28 AM Isaac Overcast @.***> wrote:

Hi Cassio,

Glad you got it figured out. It's unusual there is the hanging space in the filename. Were these fastq files demultiplexed by ipyrad or were they pre-demultiplexed before you ran step 1? The fix you propose seems good, but it will only fix R1 and not R2 for paired-end data. If we can figure out what the upstream problem is I can fix it in the code where it should crop up.

Can you send me the results of ls -l on the directory with the raw fastq files? And can you attach here the .json file of this assembly? I'll check it out.

Thanks! -isaac

— Reply to this email directly, view it on GitHub https://github.com/dereneaton/ipyrad/issues/532#issuecomment-1783810384, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFXMBWV4QAYBMBFXLFS2ALYBUB7ZAVCNFSM6AAAAAA6TNHP56VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOBTHAYTAMZYGQ . You are receiving this because you authored the thread.Message ID: @.***>

--

---

Cássio van den Berg Full Professor Univ. Estadual de Feira de Santana Dept. Ciências Biológicas Av. Transnordestina, s/n 44036-900 Feira de Santana-BA Brazil Phone: +5575 34885745 mobile +5575 91999331 Lattes http://lattes.cnpq.br/2129963760543898 Personal Homepage http://www.cassiovandenberg.com/d/?q=node/2 Google Scholar https://scholar.google.com.br/citations?user=zX7H1gwAAAAJ&hl=pt-BR Pesquisador CNPQ 1A

---

[cavdberg]

Ah, I failed to tell you that there are no spaces in the file names in the fastqs folder , the problems are arising somewhere else in the sample objects.

On Sat, Oct 28, 2023 at 11:05 AM Cássio van den Berg @.***> wrote:

The samples were demultiplexed in step 1 with ipyrad. In fact, these were old projects that I had done in 2021, and wanted to repeat only passes 2-7 with different parameters, and then they started to give the issue.

Then I have run demultiplexing step1 with the current version again, but the same bug happened in step2 with the filenames, even done with the current version from step1.

Best wishes, Cassio

On Sat, Oct 28, 2023 at 10:28 AM Isaac Overcast @.***> wrote:

Hi Cassio,

Glad you got it figured out. It's unusual there is the hanging space in the filename. Were these fastq files demultiplexed by ipyrad or were they pre-demultiplexed before you ran step 1? The fix you propose seems good, but it will only fix R1 and not R2 for paired-end data. If we can figure out what the upstream problem is I can fix it in the code where it should crop up.

Can you send me the results of ls -l on the directory with the raw fastq files? And can you attach here the .json file of this assembly? I'll check it out.

Thanks! -isaac

— Reply to this email directly, view it on GitHub https://github.com/dereneaton/ipyrad/issues/532#issuecomment-1783810384, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFXMBWV4QAYBMBFXLFS2ALYBUB7ZAVCNFSM6AAAAAA6TNHP56VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOBTHAYTAMZYGQ . You are receiving this because you authored the thread.Message ID: @.***>

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Cássio van den Berg Full Professor Univ. Estadual de Feira de Santana Dept. Ciências Biológicas Av. Transnordestina, s/n 44036-900 Feira de Santana-BA Brazil Phone: +5575 34885745 mobile +5575 91999331 Lattes http://lattes.cnpq.br/2129963760543898 Personal Homepage http://www.cassiovandenberg.com/d/?q=node/2 Google Scholar https://scholar.google.com.br/citations?user=zX7H1gwAAAAJ&hl=pt-BR Pesquisador CNPQ 1A

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Cássio van den Berg Full Professor Univ. Estadual de Feira de Santana Dept. Ciências Biológicas Av. Transnordestina, s/n 44036-900 Feira de Santana-BA Brazil Phone: +5575 34885745 mobile +5575 91999331 Lattes http://lattes.cnpq.br/2129963760543898 Personal Homepage http://www.cassiovandenberg.com/d/?q=node/2 Google Scholar https://scholar.google.com.br/citations?user=zX7H1gwAAAAJ&hl=pt-BR Pesquisador CNPQ 1A

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[cavdberg]

I also forgot to send you the files.

corrida2 is the whole plate (384 sample) run crotalus.json is the branching

I checked them, there is the damn spaces, in some lines of the .json but not in the others.... I suppose I could FIND nad REPLACE rather than put the lstrip(), though, the lstrip() is more universal to remove the trailing species, when needed.

Regards Cassio

On Sat, Oct 28, 2023 at 11:06 AM Cássio van den Berg @.***> wrote:

Ah, I failed to tell you that there are no spaces in the file names in the fastqs folder , the problems are arising somewhere else in the sample objects.

On Sat, Oct 28, 2023 at 11:05 AM Cássio van den Berg @.***> wrote:

The samples were demultiplexed in step 1 with ipyrad. In fact, these were old projects that I had done in 2021, and wanted to repeat only passes 2-7 with different parameters, and then they started to give the issue.

Then I have run demultiplexing step1 with the current version again, but the same bug happened in step2 with the filenames, even done with the current version from step1.

Best wishes, Cassio

On Sat, Oct 28, 2023 at 10:28 AM Isaac Overcast @.***> wrote:

Hi Cassio,

Glad you got it figured out. It's unusual there is the hanging space in the filename. Were these fastq files demultiplexed by ipyrad or were they pre-demultiplexed before you ran step 1? The fix you propose seems good, but it will only fix R1 and not R2 for paired-end data. If we can figure out what the upstream problem is I can fix it in the code where it should crop up.

Can you send me the results of ls -l on the directory with the raw fastq files? And can you attach here the .json file of this assembly? I'll check it out.

Thanks! -isaac

— Reply to this email directly, view it on GitHub https://github.com/dereneaton/ipyrad/issues/532#issuecomment-1783810384, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFXMBWV4QAYBMBFXLFS2ALYBUB7ZAVCNFSM6AAAAAA6TNHP56VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOBTHAYTAMZYGQ . You are receiving this because you authored the thread.Message ID: @.***>

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Cássio van den Berg Full Professor Univ. Estadual de Feira de Santana Dept. Ciências Biológicas Av. Transnordestina, s/n 44036-900 Feira de Santana-BA Brazil Phone: +5575 34885745 mobile +5575 91999331 Lattes http://lattes.cnpq.br/2129963760543898 Personal Homepage http://www.cassiovandenberg.com/d/?q=node/2 Google Scholar https://scholar.google.com.br/citations?user=zX7H1gwAAAAJ&hl=pt-BR Pesquisador CNPQ 1A

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Cássio van den Berg Full Professor Univ. Estadual de Feira de Santana Dept. Ciências Biológicas Av. Transnordestina, s/n 44036-900 Feira de Santana-BA Brazil Phone: +5575 34885745 mobile +5575 91999331 Lattes http://lattes.cnpq.br/2129963760543898 Personal Homepage http://www.cassiovandenberg.com/d/?q=node/2 Google Scholar https://scholar.google.com.br/citations?user=zX7H1gwAAAAJ&hl=pt-BR Pesquisador CNPQ 1A

---

--

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Cássio van den Berg Full Professor Univ. Estadual de Feira de Santana Dept. Ciências Biológicas Av. Transnordestina, s/n 44036-900 Feira de Santana-BA Brazil Phone: +5575 34885745 mobile +5575 91999331 Lattes http://lattes.cnpq.br/2129963760543898 Personal Homepage http://www.cassiovandenberg.com/d/?q=node/2 Google Scholar https://scholar.google.com.br/citations?user=zX7H1gwAAAAJ&hl=pt-BR Pesquisador CNPQ 1A

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total 18605152 -rw-r--r-- 1 cavdberg cavdberg 6147823 out 27 12:35 12_neocardimii_34R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 3053089 out 27 12:35 12_neocardimii_35R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 12708820 out 27 12:35 12_neocardimii_36R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 13275919 out 27 12:36 12_neocardimii_37R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 10116308 out 27 12:36 12_neocardimii_38R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 17895487 out 27 12:36 12_neocardimii_39R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 296028 out 27 12:36 12_neocardimii_41R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 10891757 out 27 12:36 12_ssp_10R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 9641729 out 27 12:36 12_ssp_11R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 11553424 out 27 12:36 12_ssp_12R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 10371848 out 27 12:36 12_ssp_13R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 17221926 out 27 12:37 12_ssp_14R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 8765282 out 27 12:37 12_ssp_16R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 15268895 out 27 12:37 12_ssp_24R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 10724041 out 27 12:37 12_ssp_25R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 16161216 out 27 12:37 12_ssp_26R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 14506657 out 27 12:38 12_ssp_27R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 8531960 out 27 12:38 12_ssp_4R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 8208534 out 27 12:38 12_ssp_5bR1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 12174146 out 27 12:38 12_ssp_5R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 9271674 out 27 12:38 12_ssp_6R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 7031266 out 27 12:38 12_ssp_8R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 12079098 out 27 12:38 12_ssp_9R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 18507193 out 27 12:39 13_bradei_40R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 21034549 out 27 12:39 13_bradei_41R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 13518009 out 27 12:39 13_bradei_42R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 20526352 out 27 12:39 13_bradei_43R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 15210663 out 27 12:39 13_bradei_44R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 12225232 out 27 12:40 13_bradei_45R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 13172246 out 27 12:40 13_bradei_46R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 10028317 out 27 12:40 13_guaicuhyensis_25R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 17296523 out 27 12:41 13_guaicuhyensis_26R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 17905668 out 27 12:41 13_guaicuhyensis_27R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 11338476 out 27 12:41 13_guaicuhyensis_28R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 8524260 out 27 12:41 13_guaicuhyensis_29R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 9685367 out 27 12:41 13_guaicuhyensis_30R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 18920522 out 27 12:42 13_guaicuhyensis_32R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 17361086 out 27 12:42 13_ssp_17R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 12808998 out 27 12:42 13_ssp_18R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 10317080 out 27 12:42 13_ssp_19R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 5622800 out 27 12:42 13_ssp_20R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 22311666 out 27 12:42 13_ssp_21R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 15583992 out 27 12:43 13_ssp_22R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 11777457 out 27 12:43 13_ssp_2R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 17031609 out 27 12:43 13_ssp_4R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 14326364 out 27 12:43 13_ssp_5R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 13036454 out 27 12:43 13_ssp_6R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 15840549 out 27 12:44 13_ssp_7R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 17383400 out 27 12:44 13_ssp_8R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 8609733 out 27 12:44 13_ssp_9R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 6476002 out 27 12:44 14_cruziana_10R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 11062428 out 27 12:44 14_cruziana_11R1.fastq.gz 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12:46 16_bradei_4R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 9621271 out 27 12:46 16_bradei_5R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 14948533 out 27 12:46 16_bradei_6R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 8483413 out 27 12:46 16_bradei_7R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 12301654 out 27 12:46 16_ssp_10R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 14875194 out 27 12:47 16_ssp_11R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 12954795 out 27 12:47 16_ssp_12R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 11721839 out 27 12:47 16_ssp_13R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 3542145 out 27 12:47 16_ssp_14R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 12552474 out 27 12:47 16_ssp_22R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 10599798 out 27 12:47 16_ssp_24R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 12074372 out 27 12:47 16_ssp_25R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 9059457 out 27 12:48 16_ssp_26R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 11441233 out 27 12:48 16_ssp_28R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 21492311 out 27 12:48 16_ssp_29R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 16065603 out 27 12:48 16_ssp_30R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 12574199 out 27 12:48 16_ssp_9R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 13311852 out 27 12:48 17_aromatica_10R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 13589256 out 27 12:49 17_aromatica_11R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 15477355 out 27 12:49 17_aromatica_4R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 18968356 out 27 12:49 17_aromatica_5R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 14251720 out 27 12:49 17_aromatica_6R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 13992569 out 27 12:49 17_aromatica_7R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 13733060 out 27 12:50 17_aromatica_9R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 13717474 out 27 12:50 17_briegeri_35R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 16109477 out 27 12:50 17_briegeri_36R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 13721100 out 27 12:50 17_novyi_23R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 20433783 out 27 12:50 17_novyi_24R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 15364526 out 27 12:51 17_novyi_25R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 9971832 out 27 12:51 17_novyi_26R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 16195846 out 27 12:51 17_novyi_27R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 21221838 out 27 12:51 17_novyi_28R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 13733489 out 27 12:51 17_novyi_29R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 15761108 out 27 12:52 18_briegeri_11R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 17824962 out 27 12:52 18_briegeri_13R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 9825978 out 27 12:52 18_briegeri_16R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 19446527 out 27 12:52 18_briegeri_17R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 18455116 out 27 12:52 18_briegeri_18R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 12163498 out 27 12:52 18_briegeri_19R1.fastq.gz -rw-r--r-- 1 cavdberg cavdberg 11610787 out 27 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[isaacovercast]

Hey Cassio,

Hm, that is interesting. I tried adding spaces to a barcodes file and we are stripping spaces from sample names. I can't get the issue you're seeing to reproduce. Can you email me the barcodes file and the .json file that you are seeing this problem with? Can you email them to me directly, the attachments aren't coming through when attached to a reply to a github issue message.

-isaac

[cavdberg]

Oh, I need your non-github email to do that. But notice, the trailing spaces are not coming from the barcode file, because the space is placed before the full path in the .json file, therefore it is being inserted somehow before the path string on writing the .json. I have tried to examine previous steps of the process, but I could not figure out well where the code for writing the .json is located. There are no spaces at all in my barcode file, only tabs and LF.

Another thing to notice is that I have done many analyses for which the step1 was performed in 2021, they were all working back then, when I made several different parameter files, with different clustering and min-samples specs.

Then I decided recently to run additional steps 2 to 7 in the same projects with new parameter files, changing only clustering threshold and min_samples, after I updated conda and ipyrad, and this is when this trailing space thing started.

My impression is that the trailing spaces have always been there in the JSONs, but the version of cutadapt back in 2021 could deal with them and find the files and now the current version doesn't.

Finally, all the 2021 files were in an HPC cluster at the university. I copied them now to my pc, to try steps 2-7 here, but the problem replicated there and here, I had to edit the code for ipyrad both in the HPC and in Ubuntu.

Note: I deleted and reinstalled Miniconda and ipyrad with py 3.10 in the HPC cluster today as well, to make a new test, instead of the "updated" version. I am demultiplexing another dataset to see whether I am still getting spaces in the .json file, and I let you know. The "updated" version was in Python 3.10, and gave an error in cutadapt that I had to reinstall it separately. I will updated you on this new attempt.

But please leave your email if I can send you some files, if the problems persist.

Regards Cassio

On Sat, Oct 28, 2023 at 4:59 PM Isaac Overcast @.***> wrote:

Hey Cassio,

Hm, that is interesting. I tried adding spaces to a barcodes file and we are stripping spaces from sample names. I can't get the issue you're seeing to reproduce. Can you email me the barcodes file and the .json file that you are seeing this problem with? Can you email them to me directly, the attachments aren't coming through when attached to a reply to a github issue message.

-isaac

— Reply to this email directly, view it on GitHub https://github.com/dereneaton/ipyrad/issues/532#issuecomment-1783909792, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFXMBXUPOHQOWAND353AADYBVP3NAVCNFSM6AAAAAA6TNHP56VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOBTHEYDSNZZGI . You are receiving this because you authored the thread.Message ID: @.***>

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Cássio van den Berg Full Professor Univ. Estadual de Feira de Santana Dept. Ciências Biológicas Av. Transnordestina, s/n 44036-900 Feira de Santana-BA Brazil Phone: +5575 34885745 mobile +5575 91999331 Lattes http://lattes.cnpq.br/2129963760543898 Personal Homepage http://www.cassiovandenberg.com/d/?q=node/2 Google Scholar https://scholar.google.com.br/citations?user=zX7H1gwAAAAJ&hl=pt-BR Pesquisador CNPQ 1A

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