CMD ERROR: stringtie

[shanmugavadivelps]

I am using funannotate to annotate genome of plant with following command

funannotate train -i cicar.CDCFrontier_Cook_v3_cleaned_sorted_masked.fa -o funn --left /media/shanmu/Shanmu_IIPR5/Senthil_Nitrate/C1/C1_forward_paired.fq.gz --right /media/shanmu/Shanmu_IIPR5/Senthil_Nitrate/C1/C1_reverse_paired.fq.gz --stranded no --strain "Cicer arietinum" --isolate CDC_Frontier --cpus 30-------------------------------------------------------
[Jul 08 07:42 PM]: OS: Ubuntu 22.04, 52 cores, ~ 196 GB RAM. Python: 3.8.19
[Jul 08 07:42 PM]: Running 1.8.17
[Jul 08 07:42 PM]: Adapter and Quality trimming PE reads with Trimmomatic
[Jul 08 07:44 PM]: Running read normalization with Trinity
[Jul 08 09:15 PM]: Building Hisat2 genome index
[Jul 08 09:20 PM]: Aligning reads to genome using Hisat2
[Jul 08 09:23 PM]: Running genome-guided Trinity, logfile: funn/training/Trinity-gg.log
[Jul 08 09:23 PM]: Clustering of reads from BAM and preparing assembly commands
[Jul 08 09:44 PM]: Assembling 44,873 Trinity clusters using 29 CPUs
Progress: 44873 complete, 0 failed, 0 remaining
[Jul 09 12:56 AM]: 124,547 transcripts derived from Trinity
[Jul 09 12:56 AM]: Running StringTie on Hisat2 coordsorted BAM
[Jul 09 12:56 AM]: CMD ERROR: stringtie -p 30 funn/training/hisat2.coordSorted.bam
[Jul 09 12:56 AM]: Error creating output file ./tmp_mry87R/stdout.07_09_00:56:23.tmp

Also i could find "###################################################################

Stopping here due to --no_distributed_trinity_exec in effect ##" at end of Trinity log file.

I am getting same error even if i increase CPUs. pls help me to solve the issue.

[hyphaltip]

it looks like a stringtie error not about cpus, is the funannotate-train.log in the logfiles folder have any other error message and I assume you aren't running out of space as to why the writing is failing?

[shanmugavadivelps]

Thanks for the reply sir. I could detect at end of Trinity.log as follows, MD: touch Dir_hisat2.coordSorted.bam.norm_200.bam.minC1.gff.ok ## Done ## Tuesday, July 8, 2025: 21:44:38 CMD: touch partitions.ok Tuesday, July 8, 2025: 21:44:38 CMD: find Dir_* -name '*reads' > read_files.list Tuesday, July 8, 2025: 21:44:39 CMD: touch read_files.list.ok Tuesday, July 8, 2025: 21:44:39 CMD: /home/shanmu/anaconda3/envs/funannotate/opt/trinity-2.15.2/util/support_scripts/ write_partitioned_trinity_cmds.pl --reads_list_file read_files.list --CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --full_cleanup --no_distributed_trinity_exec > trinity_GG.cmds Tuesday, July 8, 2025: 21:44:39 CMD: touch trinity_GG.cmds.ok Tuesday, July 8, 2025: 21:44:39 CMD: touch trinity_GG.cmds.ok ################################################################### ## Stopping here due to --no_distributed_trinity_exec in effect ## ################################################################### Also i am attaching the funannotate log files. The command i used funannotate train -i cicar.CDCFrontier_Cook_v3_cleaned_sorted_masked.fa -o funn_1 --left /media/shanmu/Shanmu_IIPR5/Senthil_Nitrate/C1/C1_forward_paired.fq.gz --right /media/shanmu/Shanmu_IIPR5/Senthil_Nitrate/C1/C1_reverse_paired.fq.gz --stranded no --strain "Cicer arietinum" --isolate CDC_Frontier --cpus 30 pls help me to solve the issue sir