missing output file - Githubissues

Rob-murphys commented 2 years ago

I am running the script as follows:

perl /programmes/NCyc/NCycProfiler.pl c -d /prepost/final_assemblies/matriline_assembly/contig_500bp_filt/cd-hit_dereplication_output/metaProdigal_output -m diamond -f faa -s prot -si seqnum.txt -o /prepost/final_assemblies/matriline_assembly/contig_500bp_filt/cd-hit_dereplication_output/metaProdigal_output/ncyc_output/ncyc_profiles.txt

yet I am getting no output to ncyc_profiles.txt. The run is executing correctly it seems and I do get the raw diamond output.

Any idea what I am doing wrong?

qichao1984 commented 2 years ago

weird issue, cannot tell what’s going on. Any on screen errors?

发件人: @.> 发送时间: 2021年12月17日 23:56 收件人: @.> 抄送: @.***> 主题: [qichao1984/NCyc] missing output file (Issue #29)

I am running the script as follows:

perl /programmes/NCyc/NCycProfiler.pl c -d /prepost/final_assemblies/matriline_assembly/contig_500bp_filt/cd-hit_dereplication_output/metaProdigal_output -m diamond -f faa -s prot -si seqnum.txt -o /prepost/final_assemblies/matriline_assembly/contig_500bp_filt/cd-hit_dereplication_output/metaProdigal_output/ncyc_output/ncyc_profiles.txt

yet I am getting no output to ncyc_profiles.txt. The run is executing correctly it seems and I do get the raw diamond output.

Any idea what I am doing wrong?

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Rob-murphys commented 2 years ago

No from what I can see. I can send the full log file if you wish?

Rob-murphys commented 2 years ago

ncyc-call.sh.e33993390.zip

Here is the STDERR output for a run showing just the stuff diamond normally prints.

This is the exact output of the run using this command: perl /programmes/NCyc/NCycProfiler.pl c -d /prepost/final_assemblies/matriline_assembly/contig_500bp_filt/cd-hit_dereplication_output/metaProdigal_output -m diamond -f faa -s prot -si seqnum.txt -o /prepost/final_assemblies/matriline_assembly/contig_500bp_filt/cd-hit_dereplication_output/metaProdigal_output/ncyc_output/ncyc_profiles.txt

Unless the output is being saved somewhere else I am at a loss.

Rob-murphys commented 2 years ago

Would you have any insight as to why there is no output?

qichao1984 commented 2 years ago

I’m not sure. But I would suggest to give absolute path for the sampleinfo file option (-si). It might be due to the script failing to find the sample info file in the current directory.

On Jan 3, 2022, at 8:04 PM, Lamm-a @.**@.>> wrote:

Would you have any insight as to why there is no output?

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Rob-murphys commented 2 years ago

Fixed it. I missed off $path when directing the tool to the sample info!

Rob-murphys commented 2 years ago

Is there any way to get the output by contig?

My metagenomes are co assemblies so I would like a by contig breakdown of what genes were found where. Is that possible?

qichao1984 commented 2 years ago

Contigs are not recommended. Use predicted genes/proteins instead.

On Jan 3, 2022, at 10:41 PM, Lamm-a @.**@.>> wrote:

Would it "break" the tool to submit a single gene at a time? That being a single protein sequence such as:

k119_359118_1 # 110 # 1420 # -1 # ID=987811_1;partial=00;start_type=ATG;rbs_motif=TAAA;rbs_spacer=9bp;gc_cont=0.368 MGCISAKEEIHVPSNKTEPTAFNSSTIESDLSSITNQYTFKGVIGHGRFGQVFLADSLEG KQVAIKVISKENFPNCFLTEEVEILSEVDHPNIIKYLKHYESKRYLYVVTEYCAGGDLFQ KIIDQGKFNEDEAVIAMEELLRAINHCHHLGIIHRDLKPENILYTSKRTLKLIDFGISVK SNSTVNEKLAGTAQYIAPEVFVDEIYTTACDVWSLGVIMHVLLSSHLPISGDSLGQIELR VMRYGGPTFKLKVWEKVSEEAKDLLKKMLDPDHKTRITAAEALKHPWFISRTTRAVISYS GIIGALKNYSEFSKDKKSELELVVKHMNEEELDKFRKAFLKLDKEMNGLLTSNGLEEILN GTQEVISGKEMEELIRRVNLNGQAFINYSSFLAALISADKFLTGEKLNPETIAVEWNSKQ NIVYIEENNRHSKIIQ*

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Rob-murphys commented 2 years ago

so the tool would work it i submitted a fasta with just the below in it?

>k119_359118_1 # 110 # 1420 # -1 # ID=987811_1;partial=00;start_type=ATG;rbs_motif=TAAA;rbs_spacer=9bp;gc_cont=0.368
MGCISAKEEIHVPSNKTEPTAFNSSTIESDLSSITNQYTFKGVIGHGRFGQVFLADSLEG
KQVAIKVISKENFPNCFLTEEVEILSEVDHPNIIKYLKHYESKRYLYVVTEYCAGGDLFQ
KIIDQGKFNEDEAVIAMEELLRAINHCHHLGIIHRDLKPENILYTSKRTLKLIDFGISVK
SNSTVNEKLAGTAQYIAPEVFVDEIYTTACDVWSLGVIMHVLLSSHLPISGDSLGQIELR
VMRYGGPTFKLKVWEKVSEEAKDLLKKMLDPDHKTRITAAEALKHPWFISRTTRAVISYS
GIIGALKNYSEFSKDKKSELELVVKHMNEEELDKFRKAFLKLDKEMNGLLTSNGLEEILN
GTQEVISGKEMEELIRRVNLNGQAFINYSSFLAALISADKFLTGEKLNPETIAVEWNSKQ
NIVYIEENNRHSKIIQ*

qichao1984 / NCyc

missing output file #29