Error: File stdout.fasta, Line 1: First header in fasta file is missing

[aureliendejode]

Hi,
I am trying to run dentitst and got that error.

File stdout.fasta, Line 1: First header in fasta file is missing

I am thinking it might be because of the names on the contigs in the ref ? My seqeunce names only contains "_" letters and numbers.

Any idea ?
Thanks for your help

[aureliendejode]

Here is my full error message:

Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 8
Rules claiming more threads will be scaled down.
Conda environments: ignored
Singularity containers: ignored
Job stats:
job count min threads max threads

---

ALL 1 1 1
collect 1 8 8
make_merge_config 1 1 1
mark_assembly_preliminary_gap_closed 1 1 1
mark_assembly_reference 1 1 1
mask_dust 2 1 1
mask_reads 1 1 1
mask_self 2 1 1
mask_tandem 2 1 1
mask_tandem_block 2 1 1
merge_insertions 1 1 1
preliminary_closed_gaps_bed2mask 1 1 1
preliminary_gap_closed2dam 1 1 1
preliminary_gap_closed_vs_reads_alignment 1 1 1
preliminary_gap_closed_vs_reads_alignment_block 1 8 8
preliminary_output 1 1 1
process 1 8 8
propagate_mask_back_to_reference 3 1 1
propagate_mask_back_to_reference_block 3 1 1
propagate_mask_batch 3 1 1
propagate_mask_to_reads_block 3 1 1
reads2db 1 1 1
ref_vs_reads_alignment 1 1 1
ref_vs_reads_alignment_block 1 8 8
reference2dam 1 1 1
self_alignment 2 1 1
self_alignment_block 2 8 8
split_preliminary_gap_closed_vs_reads_alignment 1 1 1
tandem_alignment_block 2 8 8
unpurged_output 1 1 1
validate_regions 1 1 1
validate_regions_block 32 8 8
weak_coverage_mask 1 1 1
total 79 1 8

Select jobs to execute...

[Fri Mar 24 16:43:54 2023]
localrule mark_assembly_reference:
input: /proj/snic2020-6-155/gap_closing_nobackup/Lsax_genome_CLR_HiC_curated_freeze_1_2023_02_17.fasta
output: /proj/snic2020-6-155/gap_closing_nobackup/dentist/workdir/.assembly.Lsax_genome_CLR_HiC_curated_freeze_1_2023_02_17
jobid: 12
reason: Missing output files: /proj/snic2020-6-155/gap_closing_nobackup/dentist/workdir/.assembly.Lsax_genome_CLR_HiC_curated_freeze_1_2023_02_17
resources: tmpdir=/scratch/36024016

[Fri Mar 24 16:43:54 2023]
localcheckpoint reads2db:
input: /proj/snic2020-6-155/gap_closing_nobackup/littorina_pacbio_new_pacbio_all_third_lib.fastq
output: /proj/snic2020-6-155/gap_closing_nobackup/dentist/workdir/littorina_pacbio_new_pacbio_all_third_lib.db, /proj/snic2020-6-155/gap_closing_nobackup/dentist/workdir/.littorina_pacbio_new_pacbio_
all_third_lib.bps, /proj/snic2020-6-155/gap_closing_nobackup/dentist/workdir/.littorina_pacbio_new_pacbio_all_third_lib.idx
jobid: 3
reason: Missing output files: /proj/snic2020-6-155/gap_closing_nobackup/dentist/workdir/littorina_pacbio_new_pacbio_all_third_lib.db
resources: tmpdir=/scratch/36024016
Downstream jobs will be updated after completion.

[Fri Mar 24 16:43:54 2023]
localcheckpoint reference2dam:
input: /proj/snic2020-6-155/gap_closing_nobackup/Lsax_genome_CLR_HiC_curated_freeze_1_2023_02_17.fasta
output: /proj/snic2020-6-155/gap_closing_nobackup/dentist/workdir/Lsax_genome_CLR_HiC_curated_freeze_1_2023_02_17.dam, /proj/snic2020-6-155/gap_closing_nobackup/dentist/workdir/.Lsax_genome_CLR_HiC_c
urated_freeze_1_2023_02_17.bps, /proj/snic2020-6-155/gap_closing_nobackup/dentist/workdir/.Lsax_genome_CLR_HiC_curated_freeze_1_2023_02_17.hdr, /proj/snic2020-6-155/gap_closing_nobackup/dentist/workdir/.
Lsax_genome_CLR_HiC_curated_freeze_1_2023_02_17.idx
jobid: 2
reason: Missing output files: /proj/snic2020-6-155/gap_closing_nobackup/dentist/workdir/Lsax_genome_CLR_HiC_curated_freeze_1_2023_02_17.dam
resources: tmpdir=/scratch/36024016
Downstream jobs will be updated after completion.

Touching output file /proj/snic2020-6-155/gap_closing_nobackup/dentist/workdir/.assembly.Lsax_genome_CLR_HiC_curated_freeze_1_2023_02_17.
[Fri Mar 24 16:43:54 2023]
Finished job 12.
1 of 79 steps (1%) done
[Fri Mar 24 16:43:55 2023]
Error in rule reads2db:
jobid: 3
input: /proj/snic2020-6-155/gap_closing_nobackup/littorina_pacbio_new_pacbio_all_third_lib.fastq
output: /proj/snic2020-6-155/gap_closing_nobackup/dentist/workdir/littorina_pacbio_new_pacbio_all_third_lib.db, /proj/snic2020-6-155/gap_closing_nobackup/dentist/workdir/.littorina_pacbio_new_pacbio_
all_third_lib.bps, /proj/snic2020-6-155/gap_closing_nobackup/dentist/workdir/.littorina_pacbio_new_pacbio_all_third_lib.idx
conda-env: /crex/proj/snic2020-6-155/gap_closing_nobackup/dentist/dentist_root/.snakemake/conda/72711f497d278812653381ae144ea3d8_
shell:
fold -w9998 /proj/snic2020-6-155/gap_closing_nobackup/littorina_pacbio_new_pacbio_all_third_lib.fastq | fasta2DB -i /proj/snic2020-6-155/gap_closing_nobackup/dentist/workdir/littorina_pacbio_new_
pacbio_all_third_lib.db && DBsplit -x1000 -a -s200 /proj/snic2020-6-155/gap_closing_nobackup/dentist/workdir/littorina_pacbio_new_pacbio_all_third_lib.db
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Fri Mar 24 16:44:44 2023]
Finished job 2.
2 of 79 steps (3%) done
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2023-03-24T164351.424234.snakemake.log

[a-ludi]

Hi @aureliendejode, please split off the FASTA from /proj/snic2020-6-155/gap_closing_nobackup/littorina_pacbio_new_pacbio_all_third_lib.fastq sequence and use that instead. DENTIST does not support .fastq files.

Cheers!