Closed Shirleyyyyyy closed 1 year ago
hyunhwan-jeong
commented
2 years ago Hi @Shirleyyyyyy,
Did the command generate any output? I don't think the bottom messages are error messages. I wonder what will happen if you run without --num_threads parameter.
Thank you,
Hyun-Hwan Jeong
Shirleyyyyyy
commented
2 years ago Hi,@hyunhwan-jeong. Thanks for your reply.
1.This is the output I got. Is this the final result supposed to be?
2.I tried without --num_threads parameter, and the same error is shown as below. SalmonTE.py quant --reference=hs ~/SalmonTE/example/CTRL_1_R1.fastq ~/SalmonTE/example/CTRL_1_R2.fastq 2021-07-30 10:20:33,651 Starting quantification mode 2021-07-30 10:20:33,652 Collecting FASTQ files... 2021-07-30 10:20:33,790 The input dataset is considered as a paired-ends dataset. 2021-07-30 10:20:33,790 Collected 1 FASTQ files. 2021-07-30 10:20:33,790 Quantification has been finished. 2021-07-30 10:20:33,791 Running Salmon using Snakemake 2021-07-30 10:20:57,955 Lock 140286377502864 acquired on /tmp/tmpx2tdreumsnakemake-runtime-source-cache/a25b8035675db9f47eac5986a70af6136e78a16e4a8d2d9ca00c61e28658f4c1.lock 2021-07-30 10:20:57,963 Lock 140286377502864 released on /tmp/tmpx2tdreumsnakemake-runtime-source-cache/a25b8035675db9f47eac5986a70af6136e78a16e4a8d2d9ca00c61e28658f4c1.lock Job stats: job count min threads max threads all 1 1 1 collect_abundance 1 1 1 collect_mappability 1 1 1 run_salmon_fq 1 1 1 total 4 1 1
2021-07-30 10:21:01,895 Job stats: job count min threads max threads all 1 1 1 collect_abundance 1 1 1 collect_mappability 1 1 1 run_salmon_fq 1 1 1 total 4 1 1
Failed to solve scheduling problem with ILP solver. Falling back to greedy solver. Run Snakemake with --verbose to see the full solver output for debugging the problem. Failed to solve scheduling problem with ILP solver. Falling back to greedy solver. Run Snakemake with --verbose to see the full solver output for debugging the problem.
3.BUT if I use my own fastq data to run, more errors are shown as follows. Do you have any idea about what appened here? SalmonTE.py quant --reference=mm ../O4C2-Ctr-1.R1.fastq ../O4C2-Ctr-1.R2.fastq 2021-07-30 10:27:23,831 Starting quantification mode 2021-07-30 10:27:23,831 Collecting FASTQ files... 2021-07-30 10:27:23,926 The input dataset is considered as a paired-ends dataset. 2021-07-30 10:27:23,926 Collected 1 FASTQ files. 2021-07-30 10:27:23,926 Quantification has been finished. 2021-07-30 10:27:23,926 Running Salmon using Snakemake 2021-07-30 10:27:24,603 Lock 140153770384720 acquired on /tmp/tmppcxacfx0snakemake-runtime-source-cache/a25b8035675db9f47eac5986a7 0af6136e78a16e4a8d2d9ca00c61e28658f4c1.lock 2021-07-30 10:27:24,604 Lock 140153770384720 released on /tmp/tmppcxacfx0snakemake-runtime-source-cache/a25b8035675db9f47eac5986a7 0af6136e78a16e4a8d2d9ca00c61e28658f4c1.lock Job stats: job count min threads max threads all 1 1 1 collect_abundance 1 1 1 collect_mappability 1 1 1 total 3 1 1
2021-07-30 10:27:24,843 Job stats: job count min threads max threads all 1 1 1 collect_abundance 1 1 1 collect_mappability 1 1 1 total 3 1 1
Failed to solve scheduling problem with ILP solver. Falling back to greedy solver. Run Snakemake with --verbose to see the full so lver output for debugging the problem. [Fri Jul 30 10:27:27 2021] Error in rule collect_mappability: jobid: 0 output: /Share/home/zhangqf3/haojing/chz/RNA-seq/cat/SalmonTE/SalmonTE_output/MAPPING_INFO.csv
RuleException:
KeyError in line 98 of /Share2/home/zhangqf3/SalmonTE/snakemake/Snakefile.paired:
"None of ['SampleID'] are in the columns"
File "/Share2/home/zhangqf3/SalmonTE/snakemake/Snakefile.paired", line 98, in __rule_collect_mappability
File "/Share/home/zhangqf3/apps/anaconda2/lib/python3.7/site-packages/pandas/core/frame.py", line 4555, in set_index
File "/Share/home/zhangqf3/apps/anaconda2/lib/python3.7/concurrent/futures/thread.py", line 57, in run
Exiting because a job execution failed. Look above for error message
Exiting because a job execution failed. Look above for error message
2021-07-30 10:27:28,105 Exiting because a job execution failed. Look above for error message
Traceback (most recent call last):
File "/Share2/home/zhangqf3/SalmonTE/SalmonTE.py", line 292, in
hyunhwan-jeong
commented
2 years ago @Shirleyyyyyy
O4C2-Ctr-1-R1_fastqO4C2-Ctr-1_R2.fastq`?Thank you,
Hyun-Hwan Jeong
Hello,I got an error as follow. I update snakemake (6.6.1), but it did not work either.
SalmonTE.py quant --num_threads 10 --reference=hs ~/SalmonTE/example/CTRL_1_R1.fastq ~/SalmonTE/example/CTRL_1_R2.fastq
2021-07-29 19:56:25,823 Starting quantification mode 2021-07-29 19:56:25,823 Collecting FASTQ files... 2021-07-29 19:56:25,830 The input dataset is considered as a paired-ends dataset. 2021-07-29 19:56:25,830 Collected 1 FASTQ files. 2021-07-29 19:56:25,830 Quantification has been finished. 2021-07-29 19:56:25,830 Running Salmon using Snakemake 2021-07-29 19:56:26,513 Lock 140044027502800 acquired on /tmp/tmpk47j2fprsnakemake-runtime-source-cache/a25b8035675db9f47eac5986a70af6136e78a16e4a8d2d9ca00c61e28658f4c1.lock 2021-07-29 19:56:26,514 Lock 140044027502800 released on /tmp/tmpk47j2fprsnakemake-runtime-source-cache/a25b8035675db9f47eac5986a70af6136e78a16e4a8d2d9ca00c61e28658f4c1.lock Job stats: job count min threads max threads all 1 1 1 collect_abundance 1 1 1 collect_mappability 1 1 1 run_salmon_fq 1 1 1 total 4 1 1
2021-07-29 19:56:26,756 Job stats: job count min threads max threads all 1 1 1 collect_abundance 1 1 1 collect_mappability 1 1 1 run_salmon_fq 1 1 1 total 4 1 1
Failed to solve scheduling problem with ILP solver. Falling back to greedy solver. Run Snakemake with --verbose to see the full solver output for debugging the problem. Failed to solve scheduling problem with ILP solver. Falling back to greedy solver. Run Snakemake with --verbose to see the full solver output for debugging the problem.