Question: Snakemake - Missing MissingInputException in line 20: Missing input files for rule stringt:
0
gravatar for shivani.avera
8 weeks ago by
shivani.avera0 wrote:

I am unable to successfully run this small snakemake program for StringTie; the dry-run gives an error of MissingInputException for the "rule stringt", I am unable to understand the issue here since the same directory structures works fine for a different snakemake program.

I have already generated the bam files using "hisat2" and is located in the directory : "/alternate_splice/bam_out/" which is stored as " bamdir". The snakemake should be able to locate the input file since the names and location are appropriate, however it throws an error every time. I dont have anyone in my group who works with Snakemake or can help me.

If anyone can help me out here, it would be great!

There are 4 samples: for the wildcards, it takes the list from the directory which has the fastq files

-rw-r--r-- 1 shivani domain^users 1306438351 Jan 2 09:46 TL-19-DA4299_T_RSQ1_2.fastq.gz

-rw-r--r-- 1 shivani domain^users 1185743896 Jan 2 09:46 TL-19-DA4299_T_RSQ1_1.fastq.gz

-rw-r--r-- 1 shivani domain^users 1896352262 Jan 9 08:49 TL-20-24D57D_T_RSQ1_2.fastq.gz

-rw-r--r-- 1 shivani domain^users 1730191383 Jan 9 08:49 TL-20-24D57D_T_RSQ1_1.fastq.gz

-rwxr-xr-x 1 shivani domain^users 3215901253 Mar 25 10:28 BREAST_817_N1_RNA_REP1_1.fastq.gz

-rwxr-xr-x 1 shivani domain^users 3396212102 Mar 25 10:36 BREAST_817_N1_RNA_REP1_2.fastq.gz

-rwxr-xr-x 1 shivani domain^users 3633768287 Mar 25 10:45 BREAST_792_N1_RNA_REP1_1.fastq.gz

-rwxr-xr-x 1 shivani domain^users 3932340643 Mar 25 10:54 BREAST_792_N1_RNA_REP1_2.fastq.gz

(SAMPLE,)=glob_wildcards("/home/shivani/alternate_splice/expdata/{sample}_1.fastq.gz")
#(SAMPLE,)=glob_wildcards("/home/shivani/alternate_splice/bam_out/{sample}.bam")
 bamdir = "/home/shivani/alternate_splice/bam_out/"
 refere_genome = "/home/shivani/ccb1_shivani/hisat2_trans_bam/hisat2_index/"
  geneGTF = "/home/shivani/stringtie_run/Homo_sapiens.GRCh37.87.gtf"

rule all:
        input:
               expand(bamdir+"{sample}_transcript.gft",sample=SAMPLE),
               expand(bamdir+"{sample}_abundance.tsv",sample=SAMPLE),
               expand(bamdir+"{sample}_coverage.gtf",sample=SAMPLE)
             expand(bamdir+"{sample}_stringtie_merge.gtf",sample=SAMPLE)


rule stringt:
        input:
                bm=bamdir+"{sample}.bam",
                gtf=geneGTF,
                tname="{sample}"
        output:
                tscripts=bamdir+"{sample}_transcript.gft",
                abund=bamdir+"{sample}_abundance.tsv",
                cov=bamdir+"{sample}_coverage.gtf"
        shell:
                """stringtie -p 4 -e -c 3.5 -G {input.gtf} -o {output.tscripts} -A {output.abund} -C {output.cov} -l {sample}{input.bm}"""


rule merge:
       input:
               trnsgtf=bamdir+"{sample}_transcript.gft",
               ggtf=geneGTF
       output :bamdir+"{sample}_stringtie_merge.gtf"
       shell:"stringtie -p 4 --merge -G {input.ggtf} -o {output} {input.trnsgtf}"

Error message ::: (spladder_run) shivani@ccb2:~/alternate_splice$ snakemake -n -r -s stringtie_trans

Building DAG of jobs...

MissingInputException in line 20 of /home/shivani/alternate_splice/stringtie_trans: Missing input files for rule stringt: BREAST_792_N1_RNA_REP1

ADD COMMENTlink modified 8 weeks ago by Asaf7.6k • written 8 weeks ago by shivani.avera0
1
gravatar for Devon Ryan
8 weeks ago by
Devon Ryan95k
Freiburg, Germany
Devon Ryan95k wrote:

I think the tname line should just be removed (and then remove the comma on the line above).

ADD COMMENTlink written 8 weeks ago by Devon Ryan95k

Yes, I did that and it worked, thanks!

ADD REPLYlink written 8 weeks ago by shivani.avera0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 833 users visited in the last hour