uninitialized value $max_number

[chaoyanggu]

Professor Li， I used the pneumo-typer to predict the serotypes of 500 Streptococcus pneumoniae, but there were nearly 100 which I could not get the results, the error showed that the uninitialized value $max_number in concatenation (.) or string at /datapool/software/anaconda3/envs/serotyper/share/pneumo-typer/lib/PTyper.pm line 916, line 2. In my running task, all 500 strains of Streptococcus pneumoniae were downloaded from the NCBI, the 400 strains of them I ran at the same time all had normal predictions, but the 100 except, I don't know why this happened. The strains that failed to run were as follows: GCA_000411735 GCA_000412955 GCA_000506605 GCA_000506625 GCA_000506645 GCA_000692035 GCA_000762425 GCA_000762445 GCA_000762465 …..

The error showed as follows:

Tue Aug 13 16:47:28 2024: pneumo-typer.pl start...

STEP-1: Dealing with genomes extract genome sequence, gene sequences and gene feature table (TFT); annotate genome which has no annotation information using prodigal> Genomenucleotide_extract_percent: 100%...done Genenucleotide_TFT_extract_percent: 100%...done

STEP-2: Determining the sequence type (ST/cgST)

STEP-2.1: MLST analysis Blastn_percent: 100%...done

STEP-3: Predicting serotype Blastn_percent: 100%...done Process data and obtain serotype...Use of uninitialized value $max_number in concatenation (.) or string at /datapool/software/anaconda3/envs/serotyper/share/pneumo-typer/lib/PTyper.pm line 916, line 2. Use of uninitialized value $max_number in concatenation (.) or string at /datapool/software/anaconda3/envs/serotyper/share/pneumo-typer/lib/PTyper.pm line 916, line 1. done

STEP-4: Output sequence type and serotype results Use of uninitialized value $array[0] in split at /datapool/software/anaconda3/envs/serotyper/share/pneumo-typer/script/ser_join_ST.pl line 62, line 1. Use of uninitialized value in hash element at /datapool/software/anaconda3/envs/serotyper/share/pneumo-typer/script/ser_join_ST.pl line 62, line 1.

STEP-5: Heatmaping the cps gene distribution in genomes Argument "" isn't numeric in foreach loop entry at /datapool/software/anaconda3/envs/serotyper/share/pneumo-typer/script/lib/SVG_heatmap.pm line 905, line 1. Use of uninitialized value in multiplication () at /datapool/software/anaconda3/envs/serotyper/share/pneumo-typer/script/lib/SVG_heatmap.pm line 48, line 1. Use of uninitialized value in subtraction (-) at /datapool/software/anaconda3/envs/serotyper/share/pneumo-typer/script/lib/process.pm line 986. Use of uninitialized value in subtraction (-) at /datapool/software/anaconda3/envs/serotyper/share/pneumo-typer/script/lib/process.pm line 986. Use of uninitialized value $tab_width in addition (+) at /datapool/software/anaconda3/envs/serotyper/share/pneumo-typer/script/lib/SVG_heatmap.pm line 159. Argument "" isn't numeric in foreach loop entry at /datapool/software/anaconda3/envs/serotyper/share/pneumo-typer/script/lib/SVG_heatmap.pm line 905, line 1. Use of uninitialized value in multiplication () at /datapool/software/anaconda3/envs/serotyper/share/pneumo-typer/script/lib/SVG_heatmap.pm line 48, line 1. Use of uninitialized value in multiplication (*) at /datapool/software/anaconda3/envs/serotyper/share/pneumo-typer/script/lib/SVG_heatmap.pm line 50, line 1. Use of uninitialized value in subtraction (-) at /datapool/software/anaconda3/envs/serotyper/share/pneumo-typer/script/lib/process.pm line 986. Use of uninitialized value in subtraction (-) at /datapool/software/anaconda3/envs/serotyper/share/pneumo-typer/script/lib/process.pm line 986. Use of uninitialized value $tab_width in addition (+) at /datapool/software/anaconda3/envs/serotyper/share/pneumo-typer/script/lib/SVG_heatmap.pm line 159.

STEP-6: Visualizing the cps gene cluster for genomes Use of uninitialized value $tab_width in addition (+) at /datapool/software/anaconda3/envs/serotyper/share/pneumo-typer/script/lib/SVG_image.pm line 142. Use of uninitialized value $SVG_image::array_image[1] in addition (+) at /datapool/software/anaconda3/envs/serotyper/share/pneumo-typer/script/lib/SVG_image.pm line 147. Use of uninitialized value $SVG_image::array_image[0] in addition (+) at /datapool/software/anaconda3/envs/serotyper/share/pneumo-typer/script/lib/SVG_image.pm line 147. Use of uninitialized value $SVG_image::array_image[5] in addition (+) at /datapool/software/anaconda3/envs/serotyper/share/pneumo-typer/script/lib/SVG_image.pm line 147.

Tue Aug 13 16:32:04 2024: done!

I am looking forward to hearing from you. Thank you very much.

[Xiangyang1984]

Dear Dr. Chaoyang Gu,

pneumo-typer requires at least one matching cps gene to predict the serotype. The reason for the error is that these 100 genomes cannot match any cps genes. We tested the nine genomes you submitted and confirmed that they indeed cannot match any cps genes.

Previously, we performed serotype predictions on all 21,260 S. pneumoniae genomes in the NCBI database. Among them, 20,760 genomes could obtain predicted serotype results, while only 500 genomes could not.

We will modify pneumo-typer to ensure that if there is no serotype prediction result, it will output as NA instead of displaying an error message. Thank you for using the pneumo-typer.

Xiangyang Li lixiangyang@fudan.edu.cn Kaili University

[Xiangyang1984]

Given that low quality of genome sequence could be one of the reasons why cps genes are unable to be detected, it is recommended to utilize checkm and quast software to filter out low-quality genomes. @chaoyanggu

[chaoyanggu]

Thank you for your reply, which is very helpful for our later research.