Fail to find evidence.gff in GeneMark-ETP.stderr of braker3 run

[Dooozy]

Hello! Thank you for providing and updating the excellent tool. I tested my data with braker3 braker.pl --threads 48 --genome=genome.sfmsk.fa --prot_seq=proteins.fa --species=${sp} --gff3 --bam=${bams} while this run encountered an error (errors/GeneMark-ETP.stderr):

error, file/folder not found: evidence.gff.`
Here was reported to stdout/stderr.
 `ERROR in file /data/bebe/2_biosw/braker3/BRAKER-3.0.2/scripts/braker.pl at line 5470
Failed to execute: /data/bebe/anaconda3/envs/braker3f2/bin/perl /data/bebe/2_biosw/GeneMark/GeneMark-ETP/bin/gmetp.pl --cfg /data/bebe/5_project/prediction/braker3/mydata/GeneMark-ETP/etp_config.yaml --workdir /data/bebe/5_project/prediction/braker3/mydata/GeneMark-ETP --bam /data/bebe/5_project/prediction/braker3/mydata/GeneMark-ETP/etp_data/ --cores 48 --softmask  1>/data/bebe/5_project/prediction/braker3/mydata/errors/GeneMark-ETP.stdout 2>/data/bebe/5_project/prediction/braker3/mydata/errors/GeneMark-ETP.stderr
Failed to execute: /data/bebe/anaconda3/envs/braker3f2/bin/perl /data/bebe/2_biosw/GeneMark/GeneMark-ETP/bin/gmetp.pl --cfg /data/bebe/5_project/prediction/braker3/mydata/GeneMark-ETP/etp_config.yaml --workdir /data/bebe/5_project/prediction/braker3/mydata/GeneMark-ETP --bam /data/bebe/5_project/prediction/braker3/mydata/GeneMark-ETP/etp_data/ --cores 48 --softmask  1>/data/bebe/5_project/prediction/braker3/mydata/errors/GeneMark-ETP.stdout 2>/data/bebe/5_project/prediction/braker3/mydata/errors/GeneMark-ETP.stderr
The most common problem is an expired or not present file ~/.gm_key!

The bams were generated by STAR with --outSAMstrandField intronMotif (as disscussed in #582) and they cooperated well with braker2. Installation has been tested smoothly with running test3. the STAR run:

STAR --runMode alignReads --runThreadN 36 --readFilesIn ${id}_R1_clean.fq.gz ${id}_R2_clean.fq.gz --readFilesCommand zcat --genomeDir /data/bebe/species/trans/star/star_idx --outFileNamePrefix /data/bebe/species/trans/star/out/${id} --outFilterType BySJout --outSAMattributes NH HI AS NM MD \
       --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 \
       --alignIntronMin 20 --alignIntronMax ${max_intron_size}  \
                --alignMatesGapMax ${max_intron_size} --chimSegmentMin 20 \
                --outFilterMatchNminOverLread 0.66 --outFilterScoreMinOverLread 0.66 \
                --winAnchorMultimapNmax 70 --seedSearchStartLmax 45 \
                --outSAMattrIHstart 0 --outSAMstrandField intronMotif \
                --outSAMtype BAM SortedByCoordinate --outBAMsortingThreadN 36 --quantMode TranscriptomeSAM GeneCounts

Please let me know if you have any leads. Thanks!

[JohnUrban]

@Dooozy Check out the error messages I received when using STAR BAMs (even after including --outSAMstrandField intronMotif ) posted on issue #589

Do you think we are dealing with the same thing? Can you post the entire contents of errors/GeneMark-ETP.stderr?

[Dooozy]

I got this in my errors/GeneMark-ETP.stderr

FASTA index file /data/bebe/5_project/prediction/braker3/mydata/GeneMark-ETP/data/genome.softmasked.fasta.fai created.
error, file/folder not found: evidence.gff

(a rather short error message) And I run the task in local with 200 GB RAM.