Hi there! I'm trying to run eager to remove host contaminants, and I'm not sure if the program ran to completion or not? Here is my command:

nextflow run nf-core/eager \
-profile fsu_draco \
--input '00_raw/*_{1,2}.fastq' \
--fasta '/home/user/fastq/references/GRCh38.14/GCF_000001405.40_GRCh38.p14_genomic.fna' \
--hostremoval_input_fastq

And here is the error output I got:

ERROR: Failed to open file: ../data/subsampled/ERR5766177_PE.mapped.hostremoved.fwd.fq_subsample_1000000.fastq.gz

But in the output, it says the pipeline ran to completion:

-[nf-core/eager] Pipeline completed successfully-
-[nf-core/eager] MultiQC run report can be found in ./results/multiqc -
-[nf-core/eager] Further output documentation can be seen at <https://nf-core/eager/output> -
WARN: Graphviz is required to render the execution DAG in the given format -- See <http://www.graphviz.org> for more info.
Completed at: 05-Jul-2026 06:18:10
Duration    : 14h 8m 30s
CPU hours   : 73.1 (21.9% failed)
Succeeded   : 18
Failed      : 1

From the tutorial I'm following (spaam-community.org/intro-to-ancient-metagenomics-book/taxonomic-profiling.html), there should be a "data" folder in the output, but I don't have one. Can I trust the fastq files in

results/hostremoved_fastq/

to be what I need?

Hi! I'm not an expert, but eager does not produce a "data" folder in the output, it is more likely that the author simply moved the resulting files in that folder. Did you check the pipeline_info/ folder to see what are the failed steps? In the execution_trace{...}.txt file there should be more information about whether or not the step you are interested in was completed successfully.

Hi, thanks for your answer! In execution trace, I get only one failed task, but I get that got restarted and successfully completed?

task_id	hash	native_id	name	status	exit	submit	duration	realtime	%cpu	peak_rss	peak_vmem	rchar	wchar
3	35/d07f62	8401040	makeSeqDict (GCF_000001405.40_GRCh38.p14_genomic.fna)	COMPLETED	0	2026-07-04 16:09:47.422	39.6s	21s	104.9%	3.6 GB	10.3 GB	3.1 GB	749.9 KB
2	1d/1baa29	8401041	makeFastaIndex (GCF_000001405.40_GRCh38.p14_genomic.fna)	COMPLETED	0	2026-07-04 16:09:47.471	39.6s	10.2s	99.5%	6.3 MB	11.9 MB3.1 GB	25.8 KB
10	a8/09436f	8401044	get_software_versions	COMPLETED	0	2026-07-04 16:09:47.596	39.5s	13s	123.4%	380.5 MB	6.7 GB	156.5 MB	26.4 KB
9	75/e593a5	8401045	output_documentation	COMPLETED	0	2026-07-04 16:09:47.756	39.4s	776ms	84.7%	11 MB	16.7 MB	8.1 MB	7.4 MB
6	f2/56e4d6	8401042	lanemerge_hostremoval_fastq (ERR8202906)	COMPLETED	0	2026-07-04 16:09:47.524	1m 14s	59.2s	66.2%	5.8 MB	10.3 MB	18.3 GB	18.3 GB
4	19/448164	8401038	fastqc (ERR8202906_L0)	COMPLETED	0	2026-07-04 16:09:47.330	3m 25s	3m 15s	189.6%	360.8 MB	2.7 GB	18.3 GB	1.9 MB
5	74/3f2f79	8401043	adapter_removal (ERR8202906_L0)	COMPLETED	0	2026-07-04 16:09:47.563	20m 25s	19m 45s	148.6%	573.2 MB	6.2 GB	24.8 GB	7.4 GB
11	42/232e96	8401057	fastqc_after_clipping (ERR8202906_L0)	COMPLETED	0	2026-07-04 16:30:12.429	1m 55s	1m 52s	102.4%	406.3 MB	2.6 GB	896.9 MB	922.8 KB
1	1d/d5d80f	8401039	makeBWAIndex (GCF_000001405.40_GRCh38.p14_genomic.fna)	COMPLETED	0	2026-07-04 16:09:47.375	1h 7m 10s	1h 6m 57s	99.2%	4.6 GB	4.6 GB	12.4 GB	8.4 GB
13	2c/2ad8b6	8401240	bwa (ERR8202906)	FAILED	140	2026-07-04 17:16:57.447	4h 1m	4h 31s	-	-	-	-	-
15	c9/c6880f	8401377	bwa (ERR8202906)	COMPLETED	0	2026-07-04 21:17:57.801	6h 50m 51s	6h 50m 27s	779.6%	10.3 GB	11.1 GB	452 GB	6.4 GB
17	71/ee31f2	8402399	samtools_flagstat (ERR8202906)	COMPLETED	0	2026-07-05 04:08:48.614	2h 5m 10s	6.5s	102.3%	6.2 MB	11.9 MB	774.1 MB	616 B
20	91/6bed00	8402402	preseq (ERR8202906)	COMPLETED	0	2026-07-05 04:08:48.799	2h 6m 55s	34.6s	103.4%	7.9 MB	13.5 MB	774.1 MB	5.6 KB
23	07/377ec2	8402625	endorSpy (ERR8202906)	COMPLETED	0	2026-07-05 06:13:58.800	1m 55s	221ms	69.2%	10.7 MB	16 MB	721.4 KB	530 B
19	c7/38d1ca	8402400	markduplicates (ERR8202906)	COMPLETED	0	2026-07-05 04:08:48.679	2h 7m 20s	2m 2s	103.9%	2.4 GB	6.2 GB	1.6 GB	795.4 MB
25	47/e6cad9	8402630	damageprofiler (ERR8202906)	COMPLETED	0	2026-07-05 06:16:10.067	1m 4s	34s	113.7%	1.4 GB	6.2 GB	822.8 MB	302.4 KB
35	91/cf1c76	8402629	qualimap (ERR8202906)	COMPLETED	0	2026-07-05 06:16:08.841	1m 20s	51.4s	134.9%	2.8 GB	6.3 GB	821.8 MB	1 MB
16	bb/e3e6d7	8402401	hostremoval_input_fastq (ERR8202906)	COMPLETED	0	2026-07-05 04:08:48.735	2h 9m 5s	2m 53s	148.9%	85.7 MB	99.5 MB	34.2 GB	18.4 GB
38	0a/954503	8402631	multiqc (1)	COMPLETED	0	2026-07-05 06:17:29.360	39.3s	27.1s	91.9%	163.8 MB	667.1 MB	235.1 MB	9.3 MB

A bit odd for the data repository... The error above does come from the pipeline I believe. I'm gonna continue with the results then, thanks 🙂

Glad you found a solution! ^_^ eager