yangjywhu
commented
3 years ago I have the same problem：
[Mon Aug 31 19:42:08 2020]
rule viraltrack:
input: result/viraltrack/umi_tools/p1_R2_extraced.fastq.gz, ref/hg38_WIV04/STARindex/STARindex, script/Viral-Track/Viral_Track_scanning.R, script/Viral-Track/Virusite_annotation_file.txt
output: result/viraltrack/scanning/p1_R2/Parameters.txt, result/viraltrack/scanning/p1_R2/Files_to_process.txt, result/viraltrack/scanning/p1_R2/outs
jobid: 1
wildcards: sample=p1, read=R2
Loading of the libraries.... ... done ! Warning message:
Output directory does not exist ! Creating it !
1 Fastq files are going to be processed !
Mapping p1_R2_extraced.fastq file
Aug 31 19:42:40 ..... started STAR run
Aug 31 19:42:40 ..... loading genome
Aug 31 20:19:08 ..... started 1st pass mapping
Mapping ofp1_R2_extraced.fastq done !
All fastq files have been mapped successfully
Starting the BAM file analysis
samtools index: "result/viraltrack/scanning/p1_R2/outs/p1_R2_extraced//p1_R2_extraced_Aligned.sortedByCoord.out.bam" is in a format that cannot be usefully indexed
Indexing of the bam file for p1_R2_extraced is done
samtools idxstats: fail to load index for "result/viraltrack/scanning/p1_R2/outs/p1_R2_extraced//p1_R2_extraced_Aligned.sortedByCoord.out.bam"
Computing stat file for the bam file for p1_R2_extraced is done
Error in read.table(temp_chromosome_count_path, header = F, row.names = 1) :
no lines available in input
Execution halted
[Mon Aug 31 20:19:37 2020]
Error in rule viraltrack:
jobid: 1
output: result/viraltrack/scanning/p1_R2/Parameters.txt, result/viraltrack/scanning/p1_R2/Files_to_process.txt, result/viraltrack/scanning/p1_R2/outs
shell:
echo 'N_thread=1
Output_directory="result/viraltrack/scanning/p1_R2/outs"
Index_genome="ref/hg38_WIV04/STARindex/STARindex"
Viral_annotation_file="script/Viral-Track/Virusite_annotation_file.txt"
Name_run="cov2sc_p1_R2"
Load_STAR_module=FALSE
Load_samtools_module=FALSE
Load_stringtie_module=FALSE
Minimal_read_mapped=5
Single_cell_metadata="script/config.yaml"
' > result/viraltrack/scanning/p1_R2/Parameters.txt
echo "result/viraltrack/umi_tools/p1_R2_extraced.fastq.gz" > result/viraltrack/scanning/p1_R2/Files_to_process.txt
set +u; source ~/miniconda3/bin/activate viraltrack; set -u
Rscript script/Viral-Track/Viral_Track_scanning.R result/viraltrack/scanning/p1_R2/Parameters.txt result/viraltrack/scanning/p1_R2/Files_to_process.txt
set +u; conda deactivate; set -u
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Removing output files of failed job viraltrack since they might be corrupted:
result/viraltrack/scanning/p1_R2/Parameters.txt, result/viraltrack/scanning/p1_R2/Files_to_process.txt, result/viraltrack/scanning/p1_R2/outs
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
PierreBSC
Hi Pierre Bost,
I downloaded the nine FASTQ files for series GSE145926, via SRA in the original format, conform reported from paper. So I end up with two files the each sample. Did you use the 18 FASTQ files of COVID-19 samples to analysis? if so, after doing all the preparation of the files, how long did it take to run the scripts? When I run Viral-Track Scanning.R script, reported me the error:
samtools index: "/home/vanessa/star_cv/output_viral_track//SRR11181955_2//SRR11181955_2Aligned.sortedByCoord.out.bam" is in a format that cannot be usefully indexed Indexing of the bam file for SRR11181955_2 is done samtools idxstats: fail to load index for "/home/vanessa/star_cv/output_viral_track//SRR11181955_2//SRR11181955_2Aligned.sortedByCoord.out.bam" Computing stat file for the bam file for SRR11181955_2 is done Error in read.table(temp_chromosome_count_path, header = F, row.names = 1) : no lines available in input Execution halted
What am I doing wrong? What solution do you suggest?
Another question, about the analysis with MetaCell, this analysis was carried out separated of the scripts, correct?
Best regards, Vanessa