How can I fix this error even though the same samples I have analyzed using a different haplotype and the run was successful. What could be the problem?

executor >  slurm (71)
[60/9ace9e] NFC…NOME:GTF_FILTER (TL.fasta) | 1 of 1 ✔
[61/bca7c1] NFC…:GTF2BED (TL.filtered.gtf) | 1 of 1 ✔
[b5/6742cd] NFC…IPTS_FASTA (rsem/TL.fasta) | 1 of 1 ✔
[c8/75fb62] NFC…:SAMTOOLS_FAIDX (TL.fasta) | 1 of 1 ✔
[12/d24504] NFC…_GENOMEGENERATE (TL.fasta) | 1 of 1 ✔
[-        ] NFC…ASEQ:RNASEQ:SAMTOOLS_INDEX -
[2b/7ec55a] NFC…ANDEDNESS:CAT_FASTQ (T_24) | 4 of 4 ✔
[c0/c520c4] NFC…TRANDEDNESS:FQ_LINT (T_24) | 4 of 4 ✔
[0d/09d6a0] NFC…S_TRIMGALORE:FASTQC (T_24) | 4 of 4 ✔
[57/73ed56] NFC…IMGALORE:TRIMGALORE (T_24) | 4 of 4 ✔
[21/210dbf] NFC…LINT_AFTER_TRIMMING (T_24) | 4 of 4 ✔
[84/942ea3] NFC…EX (genome.transcripts.fa) | 1 of 1 ✔
[9b/865a29] NFC…SALMON:FQ_SUBSAMPLE (T_24) | 4 of 4 ✔
[99/2330e6] NFC…SALMON:SALMON_QUANT (T_24) | 4 of 4 ✔
[a4/446c4d] NFC…LIGN_STAR:STAR_ALIGN (T_0) | 2 of 4
[e7/aa7594] NFC…TOOLS:SAMTOOLS_SORT (T_12) | 2 of 2
[20/050650] NFC…OOLS:SAMTOOLS_INDEX (T_12) | 2 of 2
[4e/e7a83f] NFC…OOLS:SAMTOOLS_STATS (T_12) | 2 of 2
[17/5ea756] NFC…S:SAMTOOLS_FLAGSTAT (T_12) | 2 of 2
[6e/13822c] NFC…S:SAMTOOLS_IDXSTATS (T_12) | 2 of 2
[14/ad1bf3] NFC…SALMON:SALMON_QUANT (T_12) | 2 of 2
[a0/e7c850] NFC…MENT:CUSTOM_TX2GENE (null) | 1 of 1 ✔
[f9/3cc07e] NFC…CARD_MARKDUPLICATES (T_12) | 2 of 2
[99/956773] NFC…CARD:SAMTOOLS_INDEX (T_12) | 2 of 2
[29/6f0077] NFC…OOLS:SAMTOOLS_STATS (T_12) | 2 of 2
[b2/4863cc] NFC…S:SAMTOOLS_FLAGSTAT (T_12) | 2 of 2
[55/bffae2] NFC…S:SAMTOOLS_IDXSTATS (T_12) | 2 of 2
[58/25afe8] NFC…STRINGTIE_STRINGTIE (T_12) | 2 of 2
[4a/63f07f] NFC…_QC:PRESEQ_LCEXTRAP (T_12) | 2 of 2
[0e/b0c43e] NFC…BREAD_FEATURECOUNTS (T_12) | 2 of 2
[23/15292a] NFC…TIQC_CUSTOM_BIOTYPE (T_12) | 2 of 2
[bf/70d199] NFC…IGNMENT_QC:DUPRADAR (T_12) | 2 of 2
Plus 5 more processes waiting for tasks…

ERROR ~ Error executing process > 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (T_0)'

Caused by:
  Missing output file(s) `*Log.final.out` expected by process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (T_0)`


Command executed:

  STAR \
      --genomeDir star \
      --readFilesIn input1/T_0_trimmed_1_val_1.fq.gz input2/T_0_trimmed_2_val_2.fq.gz \
      --runThreadN 12 \
      --outFileNamePrefix T_0. \
       \
      --sjdbGTFfile TL.filtered.gtf \
       \
      --quantMode TranscriptomeSAM --outSAMtype BAM Unsorted --outSAMattributes NH HI AS NM MD --readFilesCommand zcat --twopassMode Basic --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMstrandField intronMotif --quantTranscriptomeSAMoutput BanSingleEnd --outSAMattrRGline 'ID:T_0' 'SM:T_0' 'PL:ILLUMINA'



  if [ -f T_0.Unmapped.out.mate1 ]; then
      mv T_0.Unmapped.out.mate1 T_0.unmapped_1.fastq
      gzip T_0.unmapped_1.fastq
  fi
  if [ -f T_0.Unmapped.out.mate2 ]; then
      mv T_0.Unmapped.out.mate2 T_0.unmapped_2.fastq
      gzip T_0.unmapped_2.fastq
  fi

Command exit status:
  0

Command output:
  	/opt/conda/bin/STAR-avx2 --genomeDir star --readFilesIn input1/T_0_trimmed_1_val_1.fq.gz input2/T_0_trimmed_2_val_2.fq.gz --runThreadN 12 --outFileNamePrefix T_0. --sjdbGTFfile TL.filtered.gtf --quantMode TranscriptomeSAM --outSAMtype BAM Unsorted --outSAMattributes NH HI AS NM MD --readFilesCommand zcat --twopassMode Basic --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMstrandField intronMotif --quantTranscriptomeSAMoutput BanSingleEnd --outSAMattrRGline ID:T_0 SM:T_0 PL:ILLUMINA
  	STAR version: 2.7.11b   compiled: 2025-01-09T12:32:06+0000 :/opt/conda/conda-bld/star_1736425784849/work/source
  Jun 11 11:08:01 ..... started STAR run
  Jun 11 11:08:01 ..... loading genome
  Jun 11 11:08:19 ..... processing annotations GTF
  Jun 11 11:08:26 ..... inserting junctions into the genome indices
  Jun 11 11:09:26 ..... started 1st pass mapping
  Jun 11 13:23:21 ..... finished 1st pass mapping
  Jun 11 13:23:23 ..... inserting junctions into the genome indices
  Jun 11 13:25:22 ..... started mapping
  Jun 11 17:00:09 ..... finished mapping
  Jun 11 17:00:11 ..... finished successfully

Command error:
  WARNING: Not virtualizing pid namespace by configuration
  [E::bgzf_flush] File write failed (wrong size)
  [E::bgzf_flush] File write failed (wrong size)
  [E::bgzf_flush] File write failed (wrong size)
  [E::bgzf_flush] File write failed (wrong size)
  [E::bgzf_flush] File write failed (wrong size)
  [E::bgzf_flush] File write failed (wrong size)
  [E::bgzf_flush] File write failed (wrong size)
  [E::bgzf_flush] File write failed (wrong size)
  [E::bgzf_flush] File write failed (wrong size)
  [E::bgzf_flush] File write failed (wrong size)
  [E::bgzf_flush] File write failed (wrong size)
  [E::bgzf_flush] File write failed (wrong size)
  [E::bgzf_flush] File write failed (wrong size)
  [E::bgzf_flush] File write failed (wrong size)
  [E::bgzf_flush] File write failed (wrong size)
  [E::bgzf_flush] File write failed (wrong size)
  [E::bgzf_flush] File write failed (wrong size)
  [E::bgzf_flush] File write failed (wrong size)
  [E::bgzf_flush] File write failed (wrong size)
  [E::bgzf_flush] File write failed (wrong size)
  [E::bgzf_flush] File write failed (wrong size)
  [E::bgzf_flush] File write failed (wrong size)
  [E::bgzf_flush] File write failed (wrong size)
  [E::bgzf_close] File write failed
  ls: cannot access '*Log.final.out': No such file or directory
  ls: cannot access 'T_0.sortedByCoord.out.bam': No such file or directory
  ls: cannot access 'T_0.Aligned.sortedByCoord.out.bam': No such file or directory
  ls: cannot access '*Aligned.unsort.out.bam': No such file or directory
  ls: cannot access '*fastq.gz': No such file or directory
  ls: cannot access '*.tab': No such file or directory
  ls: cannot access '*.SJ.out.tab': No such file or directory
  ls: cannot access '*.ReadsPerGene.out.tab': No such file or directory
  ls: cannot access '*.out.junction': No such file or directory
  ls: cannot access '*.out.sam': No such file or directory
  ls: cannot access '*.wig': No such file or directory
  ls: cannot access '*.bg': No such file or directory

Work dir:
 /hapgenequantification/tl/work/a4/446c4d917c302814d738dfc9bb66c5

Container:
  /fdb/nxf/singularity-images/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-26-268b4c9c6cbf8fa6606c9b7fd4fafce18bf2c931d1a809a0ce51b105ec06c89d-data.img

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

 -- Check '.nextflow.log' file for details

Hi, @Javan Okendo! Slack uses channels to organise discussions. Press the

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more option on the left sidebar. Then hover over Your organisation, and finally select Channels to browse. Each nf-core pipeline has it’s own channel (e.g. #CE8SSJV3N). Please post any questions about specific pipelines in the relevant channel. If you’re not sure where to post your message, please ask @Igor Trujnara for help.