source activate fail - Githubissues

yinshiyi commented 4 years ago

Specified adapter for rep1:00 (PE) : None /mnt/NFS/homeGene/HarrisLab/sxx128/atac.bds.20190717_200226_884_parallel_38/task.align_etc.read_length_rep1.line_17.id_10.sh: line 7: activate: No such file or directory /mnt/NFS/homeGene/HarrisLab/sxx128/atac.bds.20190717_200226_884_parallel_38/task.align_bowtie2.bowtie2_PE_rep1.line_142.id_11.sh: line 7: activate: No such file or directory Task failed: Program & line : '/mnt/NFS/homeGene/HarrisLab/sxx128/atac/atac_dnase_pipelines/modules/align_bowtie2.bds', line 142 Task Name : 'bowtie2_PE rep1' Task ID : 'atac.bds.20190717_200226_884_parallel_38/task.align_bowtie2.bowtie2_PE_rep1.line_142.id_11' Task PID : '13684' Task hint : 'bowtie2 -X2000 --mm --local --threads 8 -x /mnt/NFS/homeGene/HarrisLab/sxx128/atac/bds_pipeline_genome_data/hg19/hg19/bowtie2_index/male.hg19.fa; -1 /mnt/NFS/genetics01/HarrisLab/raw/2019_june_4_atacseq/FastQ/AH-JK-AH779-PE_S6_L006_R1_001.fastq.gz -2 /mnt/NFS/genetics01/HarrisLab/raw/2019_june4' Task resources : 'cpus: 8 mem: -1.0 B wall-timeout: 8640000' State : 'ERROR' Dependency state : 'ERROR' Retries available : '1' Input files : '[/mnt/NFS/genetics01/HarrisLab/raw/2019_june_4_atacseq/FastQ/AH-JK-AH779-PE_S6_L006_R1_001.fastq.gz, /mnt/NFS/genetics01/HarrisLab/raw/2019_june_4_atacseq/FastQ/AH-JK-AH779-PE_S6_L006_R2_001.fastq.gz]' Output files : '[/mnt/NFS/genetics01/HarrisLab/analysis_case/sxx128/bdavis_2019/testing/align/rep1/AH-JK-AH779-PE_S6_L006_R1_001.PE2SE.bam, /mnt/NFS/genetics01/HarrisLab/analysis_case/sxx128/bdavis_2019/testing/qc/rep1/AH-JK-AH779-PE_S6_L006_R1_001.PE2SE.align.log]' Script file : '/mnt/NFS/homeGene/HarrisLab/sxx128/atac.bds.20190717_200226_884_parallel_38/task.align_bowtie2.bowtie2_PE_rep1.line_142.id_11.sh' Exit status : '1' Program :

            # SYS command. line 144

             if [[ -f $(which conda) && $(conda env list | grep bds_atac | wc -l) != "0" ]]; then source activate bds_atac; sleep 5; fi;  export PATH=/mnt/NFS/homeGene/HarrisLab/sxx128/atac/atac_dnase_pipelines/.:/mnt/NFS/homeGene/HarrisLab/sxx128/atac/atac_dnase_pipelines/modules:/mnt/NFS/homeGene/HarrisLab/sxx128/atac/atac_dnase_pipelines/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

            # SYS command. line 149

             bowtie2    -X2000 --mm --local --threads 8 -x /mnt/NFS/homeGene/HarrisLab/sxx128/atac/bds_pipeline_genome_data/hg19/hg19/bowtie2_index/male.hg19.fa \
                                    -1 /mnt/NFS/genetics01/HarrisLab/raw/2019_june_4_atacseq/FastQ/AH-JK-AH779-PE_S6_L006_R1_001.fastq.gz -2 /mnt/NFS/genetics01/HarrisLab/raw/2019_june_4_atacseq/FastQ/AH-JK-AH779-PE_S6_L006_R2_001.fastq.gz 2>/mnt/NFS/genetics01/HarrisLab/analysis_case/sxx128/bdavis_2019/testing/qc/rep1/AH-JK-AH779-PE_S6_L006_R1_001.PE2SE.align.log | \
                                    samtools view -Su /dev/stdin | samtools sort - /mnt/NFS/genetics01/HarrisLab/analysis_case/sxx128/bdavis_2019/testing/align/rep1/AH-JK-AH779-PE_S6_L006_R1_001.PE2SE

            # SYS command. line 152

             samtools index /mnt/NFS/genetics01/HarrisLab/analysis_case/sxx128/bdavis_2019/testing/align/rep1/AH-JK-AH779-PE_S6_L006_R1_001.PE2SE.bam

            # SYS command. line 154

             TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0
    StdErr (100000000 lines)  :
            /mnt/NFS/homeGene/HarrisLab/sxx128/atac.bds.20190717_200226_884_parallel_38/task.align_bowtie2.bowtie2_PE_rep1.line_142.id_11.sh: line 7: activate: No such file or directory

Task failed: Program & line : '/mnt/NFS/homeGene/HarrisLab/sxx128/atac/atac_dnase_pipelines/modules/align_etc.bds', line 17 Task Name : 'read_length rep1' Task ID : 'atac.bds.20190717_200226_884_parallel_38/task.align_etc.read_length_rep1.line_17.id_10' Task PID : '13652' Task hint : 'python $(which get_read_length_from_fastq.py) /mnt/NFS/genetics01/HarrisLab/raw/2019_june_4_atacseq/FastQ/AH-JK-AH779-PE_S6_L006_R1_001.fastq.gz > /mnt/NFS/genetics01/HarrisLab/analysis_case/sxx128/bdavis_2019/testing/qc/rep1/AH-JK-AH779-PE_S6_L006_R1_001.read_length.txt; TASKTIME=$[$(date +%s)-${ST' Task resources : 'cpus: -1 mem: -1.0 B wall-timeout: 8640000' State : 'ERROR' Dependency state : 'ERROR' Retries available : '1' Input files : '[/mnt/NFS/genetics01/HarrisLab/raw/2019_june_4_atacseq/FastQ/AH-JK-AH779-PE_S6_L006_R1_001.fastq.gz]' Output files : '[/mnt/NFS/genetics01/HarrisLab/analysis_case/sxx128/bdavis_2019/testing/qc/rep1/AH-JK-AH779-PE_S6_L006_R1_001.read_length.txt]' Script file : '/mnt/NFS/homeGene/HarrisLab/sxx128/atac.bds.20190717_200226_884_parallel_38/task.align_etc.read_length_rep1.line_17.id_10.sh' Exit status : '1' Program :

            # SYS command. line 19

             if [[ -f $(which conda) && $(conda env list | grep bds_atac | wc -l) != "0" ]]; then source activate bds_atac; sleep 5; fi;  export PATH=/mnt/NFS/homeGene/HarrisLab/sxx128/atac/atac_dnase_pipelines/.:/mnt/NFS/homeGene/HarrisLab/sxx128/atac/atac_dnase_pipelines/modules:/mnt/NFS/homeGene/HarrisLab/sxx128/atac/atac_dnase_pipelines/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

            # SYS command. line 21

             python $(which get_read_length_from_fastq.py) /mnt/NFS/genetics01/HarrisLab/raw/2019_june_4_atacseq/FastQ/AH-JK-AH779-PE_S6_L006_R1_001.fastq.gz > /mnt/NFS/genetics01/HarrisLab/analysis_case/sxx128/bdavis_2019/testing/qc/rep1/AH-JK-AH779-PE_S6_L006_R1_001.read_length.txt

            # SYS command. line 23

             TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0
    StdErr (100000000 lines)  :
            /mnt/NFS/homeGene/HarrisLab/sxx128/atac.bds.20190717_200226_884_parallel_38/task.align_etc.read_length_rep1.line_17.id_10.sh: line 7: activate: No such file or directory

Fatal error: /mnt/NFS/homeGene/HarrisLab/sxx128/atac/atac_dnase_pipelines/atac.bds, line 780, pos 3. Task/s failed.

Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done. Fatal error: /mnt/NFS/homeGene/HarrisLab/sxx128/atac/atac_dnase_pipelines/atac.bds, line 417, pos 2. Task/s failed. atac.bds, line 78 : main() atac.bds, line 81 : void main() { // atac pipeline starts here atac.bds, line 91 : do_align() atac.bds, line 385 : void do_align() { atac.bds, line 417 : wait

Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done.

yinshiyi commented 4 years ago

activate: No such file or directory i tested i can use conda activate bds_atac but source activate bds_atac failed

leepc12 commented 4 years ago

We no longer maintain this pipeline. Please try with a new one at https://github.com/ENCODE-DCC/atac-seq-pipeline

yinshiyi commented 4 years ago

i think i solved it, i replace the if ( conda_env != "" ) conda_py2 = \ "if [[ -f $(which $conda_bin_dir"+"conda) && $($conda_bin_dir"+"conda env list | grep $conda_env | wc -l) != \"0\" ]];"+\ " then source $conda_bin_dir"+"activate $conda_env; sleep $delay_conda_env; fi; " if ( conda_env_py3 != "" ) conda_py3 = \ "if [[ -f $(which $conda_bin_dir"+"conda) && $($conda_bin_dir"+"conda env list | grep $conda_env_py3 | wc -l) != \"0\" ]];"+\ " then source $conda_bin_dir"+"activate $conda_env_py3; sleep $delay_conda_env; fi; "

with

"conda activate bds_atac"

in env.bds

which fixed it.

yes i will be transition to the new one soon

kundajelab / atac_dnase_pipelines

source activate fail #147