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Failed run: Error: cannot open input file genome.fasta.masked.u.cds.gff! #4

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KatharinaHoff opened this issue Dec 18, 2023 · 4 comments
Closed

Failed run: Error: cannot open input file genome.fasta.masked.u.cds.gff! #4

KatharinaHoff opened this issue Dec 18, 2023 · 4 comments

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@KatharinaHoff
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KatharinaHoff commented Dec 18, 2023 •
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Dear Aleksey & Team,

I wanted to test EviAnn on Mus musculus. I used Mus caroli data as reference input. My job died. Here are the details:

prepare fasta files:

gffread -W -y mus_caroli_prot.faa -w mus_caroli_transc.fa -g ../tx_ncbi/GCF_900094665.1_CAROLI_EIJ_v1.1_genomic.fna ../tx_ncbi/GCF_900094665.1_CAROLI_EIJ_v1.1_genomic.gff

run eviann.sh:

eviann.sh -t 72 -g ../data/genome.fasta.masked -e ${PWD}/mus_caroli_transc.fa -r ${PWD}/mus_caroli_prot.faa

The input files exist:

ls -alht ../data/genome.fasta.masked
-rw-r--r-- 1 foo users 2.6G Mar 21  2023 ../data/genome.fasta.masked

ls -alht ${PWD}/mus_caroli_transc.fa
-rw-r--r-- 1 foo users 190M Dec 18 12:43 /home/nas-hs/users/katharina/galba/Mus_musculus/eviann/mus_caroli_transc.fa

ls -alht ${PWD}/mus_caroli_prot.faa
-rw-r--r-- 1 foo users 40M Dec 18 12:43 /home/nas-hs/users/katharina/galba/Mus_musculus/eviann/mus_caroli_prot.faa

Here is the STDERR output:

[samopen] SAM header is present: 21 sequences.
ls: cannot access 'tblastn.mus_caroli_prot.faa.*.batch.out': No such file or directory
[bam_header_read] EOF marker is absent. The input is probably truncated.
[samopen] SAM header is present: 21 sequences.
[samopen] SAM header is present: 21 sequences.
/home/foo/bin/EviAnn-1.0.7/bin/eviann.sh: line 346: genome.fasta.masked.mus_caroli_prot.faa.palign.gff: No such file or directory
  0 reference transcripts loaded.
  51504 query transfrags loaded.
mv: cannot stat 'genome.fasta.masked.protref.annotated.gtf': No such file or directory
Error: cannot open input file genome.fasta.masked.u.cds.gff!
mv: cannot stat 'genome.fasta.masked.k.gff': No such file or directory

Here is STDOUT:

Checking for ufasta on the PATH... /home/foo/bin/EviAnn-1.0.7/bin/ufasta
Checking for hisat2 on the PATH... /home/foo/bin/hisat2/hisat2
Checking for minimap2 on the PATH... /home/foo/bin/minimap2/minimap2
Checking for stringtie on the PATH... /home/foo/bin/EviAnn-1.0.7/bin/stringtie
Checking for gffread on the PATH... /home/foo/bin/EviAnn-1.0.7/bin/gffread
Checking for blastp on the PATH... /home/foo/bin/EviAnn-1.0.7/bin/blastp
Checking for tblastn on the PATH... /home/foo/bin/EviAnn-1.0.7/bin/tblastn
Checking for makeblastdb on the PATH... /home/foo/bin/EviAnn-1.0.7/bin/makeblastdb
Checking for gffcompare on the PATH... /home/foo/bin/EviAnn-1.0.7/bin/gffcompare
Checking for TransDecoder.Predict on the PATH... /home/foo/bin/EviAnn-1.0.7/bin/TransDecoder.Predict
Checking for TransDecoder.LongOrfs on the PATH... /home/foo/bin/EviAnn-1.0.7/bin/TransDecoder.LongOrfs
[Mon Dec 18 12:48:15 PM UTC 2023] Unpacking Uniprot database
[Mon Dec 18 12:48:21 PM UTC 2023] Building HISAT2 index
[Mon Dec 18 01:38:39 PM UTC 2023] Aligning RNAseq reads
[Mon Dec 18 01:40:15 PM UTC 2023] Aligning proteins
[Mon Dec 18 01:40:16 PM UTC 2023] Aligning proteins to the genome
[Mon Dec 18 01:40:16 PM UTC 2023] Filtering protein alignment file
[Mon Dec 18 01:40:34 PM UTC 2023] Running exonerate on the filtered sequences
[Mon Dec 18 01:40:34 PM UTC 2023] Sorting alignment files
[Mon Dec 18 01:41:02 PM UTC 2023] Assembling transcripts from related species with Stringtie
[Mon Dec 18 01:41:08 PM UTC 2023] Deriving gene models from protein and transcript alignments

Here are all produced files:

-rw-r--r--  1 foo users  848 Dec 18 13:41 eviann.2430077.node374.err
-rw-r--r--  1 foo users   46 Dec 18 13:41 genome.fasta.masked.k.gff.tmp
-rw-r--r--  1 foo users    0 Dec 18 13:41 genome.fasta.masked.u.gff.tmp
-rw-r--r--  1 foo users    0 Dec 18 13:41 genome.fasta.masked.unused_proteins.gff.tmp
-rw-r--r--  1 foo users    0 Dec 18 13:41 combine.out
-rw-r--r--  1 hoffk83 users    0 Dec 18 13:41 genome.fasta.masked.palign.all.gff
-rw-r--r--  1 hoffk83 users    0 Dec 18 13:41 genome.fasta.masked.transcripts_to_keep.txt
-rw-r--r--  1 hoffk83 users  66M Dec 18 13:41 genome.fasta.masked.protref.combined.gtf
-rw-r--r--  1 hoffk83 users    0 Dec 18 13:41 genome.fasta.masked.palign.fixed.gff
-rw-r--r--  1 hoffk83 users 1.6K Dec 18 13:41 eviann.2430077.node374.out
-rw-r--r--  1 hoffk83 users    0 Dec 18 13:41 stringtie.success
-rw-r--r--  1 hoffk83 users  84M Dec 18 13:41 genome.fasta.masked.gtf
-rw-r--r--  1 hoffk83 users  76M Dec 18 13:41 tissue0.bam.sorted.bam.gtf
-rw-r--r--  1 hoffk83 users    0 Dec 18 13:41 sort.success
-rw-r--r--  1 hoffk83 users  96M Dec 18 13:41 tissue0.bam.sorted.bam
-rw-r--r--  1 hoffk83 users 185M Dec 18 13:40 tissue0.filter
-rw-r--r--  1 hoffk83 users  694 Dec 18 13:40 tissue0.header
-rw-r--r--  1 hoffk83 users    0 Dec 18 13:40 genome.fasta.masked.mus_caroli_prot.faa.palign.gff.tmp
-rw-r--r--  1 hoffk83 users    0 Dec 18 13:40 protein2genome.protein_align.success
-rw-r--r--  1 hoffk83 users  27M Dec 18 13:40 mus_caroli_prot.faa.uniq.faa
-rw-r--r--  1 hoffk83 users    0 Dec 18 13:40 align.success
-rw-r--r--  1 hoffk83 users  40M Dec 18 13:40 tissue0.bam
-rw-r--r--  1 hoffk83 users  767 Dec 18 13:40 tissue0.err
-rw-r--r--  1 hoffk83 users  329 Dec 18 13:38 hisat2.sh
-rw-r--r--  1 hoffk83 users    0 Dec 18 13:38 align-build.success
-rw-r--r--  1 hoffk83 users 6.3K Dec 18 13:38 hisat2-build.out
-rw-r--r--  1 hoffk83 users 1.1G Dec 18 13:38 genome.fasta.masked.hst.5.ht2
-rw-r--r--  1 hoffk83 users 644M Dec 18 13:38 genome.fasta.masked.hst.6.ht2
-rw-r--r--  1 hoffk83 users 847M Dec 18 13:34 genome.fasta.masked.hst.1.ht2
-rw-r--r--  1 hoffk83 users 632M Dec 18 13:34 genome.fasta.masked.hst.2.ht2
-rw-r--r--  1 hoffk83 users   12 Dec 18 12:48 genome.fasta.masked.hst.7.ht2
-rw-r--r--  1 hoffk83 users    8 Dec 18 12:48 genome.fasta.masked.hst.8.ht2
-rw-r--r--  1 hoffk83 users 2.4K Dec 18 12:48 genome.fasta.masked.hst.3.ht2
-rw-r--r--  1 hoffk83 users 632M Dec 18 12:48 genome.fasta.masked.hst.4.ht2
-rw-r--r--  1 hoffk83 users  536 Dec 18 12:48 uniprot.pjs
-rw-r--r--  1 hoffk83 users  375 Dec 18 12:48 makeblastdb.out
-rw-r--r--  1 hoffk83 users  16K Dec 18 12:48 uniprot.ptf
-rw-r--r--  1 hoffk83 users 1.2M Dec 18 12:48 uniprot.pto
-rw-r--r--  1 hoffk83 users 3.4M Dec 18 12:48 uniprot.pot
-rw-r--r--  1 hoffk83 users  20K Dec 18 12:48 uniprot.pdb
-rw-r--r--  1 hoffk83 users  54M Dec 18 12:48 uniprot.phr
-rw-r--r--  1 hoffk83 users 2.3M Dec 18 12:48 uniprot.pin
-rw-r--r--  1 hoffk83 users 108M Dec 18 12:48 uniprot.psq
-rw-r--r--  1 hoffk83 users 146M Dec 18 12:48 uniprot_sprot.nonred.85.fasta
-rw-r--r--  1 hoffk83 users  40M Dec 18 12:43 mus_caroli_prot.faa
-rw-r--r--  1 hoffk83 users 190M Dec 18 12:43 mus_caroli_transc.fa

Please let me know if you need further details.
@KatharinaHoff KatharinaHoff changed the title Failed run Failed run: Error: cannot open input file genome.fasta.masked.u.cds.gff! Dec 18, 2023
@alekseyzimin
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alekseyzimin commented Dec 18, 2023 via email

@KatharinaHoff
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Giving 1.0.8 a try :-)

@KatharinaHoff
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The run finished (with relative path, v 1.0.8). Thanks for your quick help!

@alekseyzimin
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alekseyzimin commented Dec 19, 2023 via email

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