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Bishop-Laboratory / RLPipes

RLPipes: A standardized R-loop-mapping pipeline.
https://anaconda.org/bioconda/rlpipes
MIT License
3 stars 1 forks source link

No report output #88

Closed LeoColmet-Daage closed 2 years ago

LeoColmet-Daage commented 2 years ago

Hi, I've managed to run the pipeline successfully it seems looking at the log files from snakemake. But when I look at the output folder there is no report folder and no report files for each samples. I didn't use the noreport option also to be clear.

Here is the begining of the snakemake log file. 

Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 12
Rules claiming more threads will be scaled down.
Job counts:
        count   jobs
        26      bam_stats
        17      bwa_mem
        26      calculate_coverage
        26      index_bam
        26      macs_callpeak
        1       output
        122
Select jobs to execute...

Here is the end of the snakemake log file and it's look like everything was done successfully.

[Wed Mar  2 08:02:23 2022]
localrule output:
    input: /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/peaks/786-O_IP_KO_1_S3_R1_001_hg38.broadPeak, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/peaks/786-O_IP_KO_2_S4_R1_001_hg38.broadPeak, /mnt/beegfs/userdata/l_colmet-daage/DRIP/r
lpipes_out/peaks/786-O_IP_WT1_S1_R1_001_hg38.broadPeak, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/peaks/786-O_IP_WT2_S2_R1_001_hg38.broadPeak, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/peaks/G700015_786_OKO1Tala_S15_R1_001_hg38.b
roadPeak, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/peaks/G700016_786_OKO2Tala_S16_R1_001_hg38.broadPeak, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/peaks/G700013_786_OTalaWT1_S13_R1_001_hg38.broadPeak, /mnt/beegfs/userdata/l_colm
et-daage/DRIP/rlpipes_out/peaks/G700014_786_OTalaWT2_S14_R1_001_hg38.broadPeak, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/peaks/G700005_H1299KO1_S5_R1_001_hg38.broadPeak, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/peaks/G700006_H1
299KO2_S6_R1_001_hg38.broadPeak, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/peaks/G700001_H1299WT1_S1_R1_001_hg38.broadPeak, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/peaks/G700002_H1299WT2_S2_R1_001_hg38.broadPeak, /mnt/beegfs/us
erdata/l_colmet-daage/DRIP/rlpipes_out/peaks/G700007_H1299KO1Tala_S7_R1_001_hg38.broadPeak, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/peaks/G700008_H1299KO2Tala_S8_R1_001_hg38.broadPeak, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/
peaks/G700003_H1299WT1Tala_S3_R1_001_hg38.broadPeak, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/peaks/G700004_H1299WT2Tala_S4_R1_001_hg38.broadPeak, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/peaks/U2OS_IP_KO_1_S7_R1_001_hg38.broad
Peak, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/peaks/U2OS_IP_KO_2_S17_R1_001_hg38.broadPeak, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/peaks/U2OS_IP_WT1_S5_R1_001_hg38.broadPeak, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_
out/peaks/U2OS_IP_WT2_S6_R1_001_hg38.broadPeak, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/peaks/Input_786-O_KO_S22_R1_001_hg38.broadPeak, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/peaks/Input_786-O_WT_S21_R1_001_hg38.broadPeak, /
mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/peaks/Input_786-O_KO_S22_R1_001_hg38.broadPeak, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/peaks/Input_786-O_WT_S21_R1_001_hg38.broadPeak, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_o
ut/peaks/G700020_InputH1299KO_S20_R1_001_hg38.broadPeak, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/peaks/G700019_InputH1299WT_S19_R1_001_hg38.broadPeak, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/peaks/G700020_InputH1299KO_S20_R1_
001_hg38.broadPeak, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/peaks/G700019_InputH1299WT_S19_R1_001_hg38.broadPeak, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/peaks/Input_U2OS_KO_S24_R1_001_hg38.broadPeak, /mnt/beegfs/userdata/l_c
olmet-daage/DRIP/rlpipes_out/peaks/Input_U2OS_WT_S23_R1_001_hg38.broadPeak, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/coverage/786-O_IP_KO_1_S3_R1_001_hg38.bw, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/coverage/786-O_IP_KO_2_S4_R
1_001_hg38.bw, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/coverage/786-O_IP_WT1_S1_R1_001_hg38.bw, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/coverage/786-O_IP_WT2_S2_R1_001_hg38.bw, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes
_out/coverage/G700015_786_OKO1Tala_S15_R1_001_hg38.bw, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/coverage/G700016_786_OKO2Tala_S16_R1_001_hg38.bw, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/coverage/G700013_786_OTalaWT1_S13_R1_001
_hg38.bw, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/coverage/G700014_786_OTalaWT2_S14_R1_001_hg38.bw, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/coverage/G700005_H1299KO1_S5_R1_001_hg38.bw, /mnt/beegfs/userdata/l_colmet-daage/DRIP
/rlpipes_out/coverage/G700006_H1299KO2_S6_R1_001_hg38.bw, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/coverage/G700001_H1299WT1_S1_R1_001_hg38.bw, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/coverage/G700002_H1299WT2_S2_R1_001_hg38.b
w, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/coverage/G700007_H1299KO1Tala_S7_R1_001_hg38.bw, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/coverage/G700008_H1299KO2Tala_S8_R1_001_hg38.bw, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlp
ipes_out/coverage/G700003_H1299WT1Tala_S3_R1_001_hg38.bw, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/coverage/G700004_H1299WT2Tala_S4_R1_001_hg38.bw, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/coverage/U2OS_IP_KO_1_S7_R1_001_hg38.b
w, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/coverage/U2OS_IP_KO_2_S17_R1_001_hg38.bw, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/coverage/U2OS_IP_WT1_S5_R1_001_hg38.bw, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/coverag
e/U2OS_IP_WT2_S6_R1_001_hg38.bw, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/coverage/Input_786-O_KO_S22_R1_001_hg38.bw, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/coverage/Input_786-O_WT_S21_R1_001_hg38.bw, /mnt/beegfs/userdata/l_c
olmet-daage/DRIP/rlpipes_out/coverage/Input_786-O_KO_S22_R1_001_hg38.bw, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/coverage/Input_786-O_WT_S21_R1_001_hg38.bw, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/coverage/G700020_InputH1299K
O_S20_R1_001_hg38.bw, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/coverage/G700019_InputH1299WT_S19_R1_001_hg38.bw, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/coverage/G700020_InputH1299KO_S20_R1_001_hg38.bw, /mnt/beegfs/userdata/l_
colmet-daage/DRIP/rlpipes_out/coverage/G700019_InputH1299WT_S19_R1_001_hg38.bw, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/coverage/Input_U2OS_KO_S24_R1_001_hg38.bw, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/coverage/Input_U2OS_WT
_S23_R1_001_hg38.bw, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/bam_stats/786-O_IP_KO_1_S3_R1_001_hg38__bam_stats.txt, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/bam_stats/786-O_IP_KO_2_S4_R1_001_hg38__bam_stats.txt, /mnt/beegfs/us
erdata/l_colmet-daage/DRIP/rlpipes_out/bam_stats/786-O_IP_WT1_S1_R1_001_hg38__bam_stats.txt, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/bam_stats/786-O_IP_WT2_S2_R1_001_hg38__bam_stats.txt, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_ou
t/bam_stats/G700015_786_OKO1Tala_S15_R1_001_hg38__bam_stats.txt, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/bam_stats/G700016_786_OKO2Tala_S16_R1_001_hg38__bam_stats.txt, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/bam_stats/G700013
_786_OTalaWT1_S13_R1_001_hg38__bam_stats.txt, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/bam_stats/G700014_786_OTalaWT2_S14_R1_001_hg38__bam_stats.txt, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/bam_stats/G700005_H1299KO1_S5_R1_001
_hg38__bam_stats.txt, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/bam_stats/G700006_H1299KO2_S6_R1_001_hg38__bam_stats.txt, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/bam_stats/G700001_H1299WT1_S1_R1_001_hg38__bam_stats.txt, /mnt/be
egfs/userdata/l_colmet-daage/DRIP/rlpipes_out/bam_stats/G700002_H1299WT2_S2_R1_001_hg38__bam_stats.txt, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/bam_stats/G700007_H1299KO1Tala_S7_R1_001_hg38__bam_stats.txt, /mnt/beegfs/userdata/l_colmet-da
age/DRIP/rlpipes_out/bam_stats/G700008_H1299KO2Tala_S8_R1_001_hg38__bam_stats.txt, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/bam_stats/G700003_H1299WT1Tala_S3_R1_001_hg38__bam_stats.txt, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/
bam_stats/G700004_H1299WT2Tala_S4_R1_001_hg38__bam_stats.txt, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/bam_stats/U2OS_IP_KO_1_S7_R1_001_hg38__bam_stats.txt, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/bam_stats/U2OS_IP_KO_2_S17_R1
_001_hg38__bam_stats.txt, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/bam_stats/U2OS_IP_WT1_S5_R1_001_hg38__bam_stats.txt, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/bam_stats/U2OS_IP_WT2_S6_R1_001_hg38__bam_stats.txt, /mnt/beegfs/u
serdata/l_colmet-daage/DRIP/rlpipes_out/bam_stats/Input_786-O_KO_S22_R1_001_hg38__bam_stats.txt, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/bam_stats/Input_786-O_WT_S21_R1_001_hg38__bam_stats.txt, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlp
ipes_out/bam_stats/Input_786-O_KO_S22_R1_001_hg38__bam_stats.txt, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/bam_stats/Input_786-O_WT_S21_R1_001_hg38__bam_stats.txt, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/bam_stats/G700020_Inpu
tH1299KO_S20_R1_001_hg38__bam_stats.txt, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/bam_stats/G700019_InputH1299WT_S19_R1_001_hg38__bam_stats.txt, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/bam_stats/G700020_InputH1299KO_S20_R1_001
_hg38__bam_stats.txt, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/bam_stats/G700019_InputH1299WT_S19_R1_001_hg38__bam_stats.txt, /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/bam_stats/Input_U2OS_KO_S24_R1_001_hg38__bam_stats.txt, /mnt
/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/bam_stats/Input_U2OS_WT_S23_R1_001_hg38__bam_stats.txt
    jobid: 0

[Wed Mar  2 08:02:23 2022]
Finished job 0.
122 of 122 steps (100%) done
Complete log: /mnt/beegfs/userdata/l_colmet-daage/DRIP/rlpipes_out/.snakemake/log/2022-03-01T163446.858664.snakemake.log

Should the jobid 0 "localrule output" be the report job ?

As all the bam, bamstat, peaks files seems to be there. Is there any easy way to generate those report from there ?

Many thanks for your help

EDIT : I've attached here config files, log and dag rlpipes.zip

millerh1 commented 2 years ago

Hi @LeoColmet-Daage -- thank you for your interest in RLPipes! I regret to inform you that this feature is not yet implemented in the current version of the tool -- so this is currently an error in the documentation, but not in the code.

For now, reports can be generated by using the {{ RLSeq }} R/Bioconductor package or the RLBase web service (though it has fewer analysis capabilities).

I plan to integrate this feature in a future release of RLPipes, along with other features that will improve the utility of RLPipes for R-loop data processing... so please stay tuned for that. I will leave this issue open until that gets merged.

LeoColmet-Daage commented 2 years ago

Hi ! ok I thought for a second that could be the explanation. Thx for the pipeline anyway. I will then use the packages and looking for further improvement !

Thx for the clarification !

millerh1 commented 2 years ago

Closed with https://github.com/Bishop-Laboratory/RLPipes/commit/bf38965909be507a7c5bc5b4869218ce457591cc