search

kundajelab / atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline
BSD 3-Clause "New" or "Revised" License
161 stars 81 forks source link

about tss footprint #86

Closed tanpuekai closed 6 years ago

tanpuekai commented 6 years ago

hi, lee

i am running your pipelines. just came across a few questions.

i have finished the pipeline, i have got the peaks. bed, bam etc. but i am not getting report.html under "out/". all report html are missing.

I clone your codes on Dec 5. Do u know what might be the problem?

Thanks.

Chan

============== out # root dir. of outputs │ ├ report.html # HTML report ├ tracks.json # Tracks datahub (JSON) for WashU browser ├ ENCODE_summary.json # Metadata of all datafiles and QC results

tanpuekai commented 6 years ago

on one of the reports, it says this:

Script file ../atac_dnase_pipelines/atac.bds

atac.bds.20171221_211950_985 2017-12-21 21:19:51 09:30:52.794 51 2 ataqc rep1 ataqc rep2 [-species, mm10, -nth, 10, -fastq1_1, ../inputs_fastq/CheahK_ATACSeqSO_SS-171107-02a/primary_seq/DP_E155_Gpos1_1.fastq.gz, -fastq1_2, ../inputs_fastq/CheahK_ATACSeqSO_SS-171107-02a/primary_seq/DP_E155_Gpos1_2.fastq.gz, -fastq2_1, ../inputs_fastq/CheahK_ATACSeqSO_SS-171107-02a/primary_seq/DP_E155_Gpos2_1.fastq.gz, -fastq2_2, ../inputs_fastq/CheahK_ATACSeqSO_SS-171107-02a/primary_seq/DP_E155_Gpos2_2.fastq.gz, -out_dir, out_DP_E155] local -1 1

tanpuekai commented 6 years ago

my samtool was version 1.3, would that be the problem?

leepc12 commented 6 years ago

Yes. Did you install Conda and run install_dependencies.sh? Please post a full error log here.

Jin

On Thu, Dec 21, 2017 at 11:49 PM, CHEN Peikai notifications@github.com wrote:

my samtool was version 1.3, would that be the problem?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/kundajelab/atac_dnase_pipelines/issues/86#issuecomment-353542498, or mute the thread https://github.com/notifications/unsubscribe-auth/AIOd_B2O4a68xtk4WVud1i6K3kiL4Sctks5tC17-gaJpZM4RKkmu .

tanpuekai commented 6 years ago

Hi Jin, Thanks for your prompt reply.

I did install Conda and run install_dependencies.sh before i ran the pipeline, and nothing unusual in the installation process.

Yesterday, I re-installed a newer version of samtools (v=1.6), and re-run the whole pipeline (cloned on dec 5), and still cannot get atacqc. other steps are ok, though.

Attached is the stderr messages for the part that fails (i.e. ataqc).

best chan

================attachment begins====================

    Task has finished (76 seconds).
    Task has finished (72 seconds).

    == Done naive_overlap()
    Task has finished (0 seconds).
    species_ataqc: mm10
    species_ataqc: mm10
    Traceback (most recent call last):
      File "/ourserver/E155_Gpos/../../atac_dnase_pipelines/ataqc/run_ataqc.py", line 14, in <module>
        import metaseq
      File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/metaseq/__init__.py", line 7, in <module>
        import plotutils
      File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/metaseq/plotutils.py", line 6, in <module>
        from matplotlib import pyplot as plt
      File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/pyplot.py", line 36, in <module>
    Traceback (most recent call last):
      File "/ourserver/E155_Gpos/../../atac_dnase_pipelines/ataqc/run_ataqc.py", line 14, in <module>
        import metaseq
      File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/metaseq/__init__.py", line 7, in <module>
        import plotutils
      File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/metaseq/plotutils.py", line 6, in <module>
        from matplotlib import pyplot as plt
      File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/pyplot.py", line 36, in <module>
        from matplotlib.figure import Figure, figaspect
      File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/figure.py", line 40, in <module>
        from matplotlib.axes import Axes, SubplotBase, subplot_class_factory
      File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/axes/__init__.py", line 4, in <module>
        from ._subplots import *
      File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/axes/_subplots.py", line 10, in <module>
        from matplotlib.figure import Figure, figaspect
      File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/figure.py", line 40, in <module>
        from matplotlib.axes import Axes, SubplotBase, subplot_class_factory
      File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/axes/__init__.py", line 4, in <module>
        from ._subplots import *
      File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/axes/_subplots.py", line 10, in <module>
        from matplotlib.axes._axes import Axes
      File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/axes/_axes.py", line 22, in <module>
        import matplotlib.dates as _  # <-registers a date unit converter
      File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/dates.py", line 126, in <module>
        from dateutil.rrule import (rrule, MO, TU, WE, TH, FR, SA, SU, YEARLY,
      File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/dateutil/rrule.py", line 19, in <module>
        from six.moves import _thread, range
    ImportError: cannot import name _thread
        from matplotlib.axes._axes import Axes
      File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/axes/_axes.py", line 22, in <module>
        import matplotlib.dates as _  # <-registers a date unit converter
      File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/dates.py", line 126, in <module>
        from dateutil.rrule import (rrule, MO, TU, WE, TH, FR, SA, SU, YEARLY,
      File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/dateutil/rrule.py", line 19, in <module>
        from six.moves import _thread, range
    ImportError: cannot import name _thread
    Task failed:
        Program & line     : '../../atac_dnase_pipelines/modules/ataqc.bds', line 109
        Task Name          : 'ataqc rep2'
        Task ID            : 'atac.bds.20171222_140505_349_parallel_181/task.ataqc.ataqc_rep2.line_109.id_98'
        Task PID           : '30729'
        Task hint          : 'if [ "${TMPDIR}" != "" ] && [ -d "${TMPDIR}" ]; then; fi; cd /ourserver/E155_Gpos/E155/qc/rep2; /ourserver/E155_Gpos/../../atac_dnase_pipelines/ataqc/run_ataqc.py; -'
        Task resources     : 'cpus: -1  mem: -1.0 B wall-timeout: 8640000'
        State              : 'ERROR'
        Dependency state   : 'ERROR'
        Retries available  : '1'
        Input files        : '[/ourserver/E155_Gpos/../../inputs_fastq/CheahK_ATACSeqSO_SS-171107-02a/primary_seq/DP_E155_Gpos2_1.fastq.gz, /ourserver/E155_Gpos/../../inputs_fastq/CheahK_ATACSeqSO_SS-171107-02a/primary_seq/DP_E155_Gpos2_2.fastq.gz, /ourserver/E155_Gpos/E155/align/rep2/DP_E155_Gpos2_1.PE2SE.bam, /ourserver/E155_Gpos/E155/qc/rep2/DP_E155_Gpos2_1.PE2SE.align.log, /ourserver/E155_Gpos/E155/qc/rep2/DP_E155_Gpos2_1.PE2SE.nodup.pbc.qc, /ourserver/E155_Gpos/E155/qc/rep2/DP_E155_Gpos2_1.PE2SE.dup.qc, /ourserver/E155_Gpos/E155/align/rep2/DP_E155_Gpos2_1.PE2SE.nodup.bam, /ourserver/E155_Gpos/E155/align/rep2/DP_E155_Gpos2_1.PE2SE.nodup.tn5.tagAlign.gz, /ourserver/E155_Gpos/E155/signal/macs2/rep2/DP_E155_Gpos2_1.PE2SE.nodup.tn5.pf.pval.signal.bigwig, /ourserver/E155_Gpos/E155/peak/macs2/overlap/optimal_set/E155_rep1-rep2.naive_overlap.filt.narrowPeak.gz]'
        Output files       : '[/ourserver/E155_Gpos/E155/qc/rep2/DP_E155_Gpos2_1.PE2SE_qc.html, /ourserver/E155_Gpos/E155/qc/rep2/DP_E155_Gpos2_1.PE2SE_qc.txt]'
        Script file        : '/ourserver/E155_Gpos/atac.bds.20171222_140505_349_parallel_181/task.ataqc.ataqc_rep2.line_109.id_98.sh'
        Exit status        : '1'
        Program            : 

            # SYS command. line 111

             if [[ -f $(which conda) && $(conda env list | grep bds_atac | wc -l) != "0" ]]; then source activate bds_atac; sleep 5; fi;  export PATH=/ourserver/E155_Gpos/../../atac_dnase_pipelines/.:/ourserver/E155_Gpos/../../atac_dnase_pipelines/modules:/ourserver/E155_Gpos/../../atac_dnase_pipelines/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

            # SYS command. line 114

             export _JAVA_OPTIONS="-Xms256M -Xmx20G -XX:ParallelGCThreads=1"

            # SYS command. line 116

             if [ "${TMPDIR}" != "" ] && [ -d "${TMPDIR}" ]; then \
                        export _JAVA_OPTIONS="${_JAVA_OPTIONS} -Djava.io.tmpdir=${TMPDIR}"; \
                    fi

            # SYS command. line 119

             cd /ourserver/E155_Gpos/E155/qc/rep2

            # SYS command. line 122

             if [ -f "$(which picard)" ]; then export PICARDROOT="$(dirname $(which picard))/../share/picard"*; fi

            # SYS command. line 124

             /ourserver/E155_Gpos/../../atac_dnase_pipelines/ataqc/run_ataqc.py \
                        --workdir /ourserver/E155_Gpos/E155/qc/rep2 \
                        --outdir /ourserver/E155_Gpos/E155/qc/rep2 \
                        --outprefix DP_E155_Gpos2_1.PE2SE \
                        --genome mm10 \
                        --chromsizes /nfs/home2/USER/genomedata/mm10/mm10.chrom.sizes \
                        --ref /nfs/home2/USER/genomedata/mm10/mm10_no_alt_analysis_set_ENCODE.fasta \
                        --tss /nfs/home2/USER/genomedata/mm10/ataqc/mm10_gencode_tss_unique.bed.gz \
                        --dnase /nfs/home2/USER/genomedata/mm10/ataqc/mm10_univ_dhs_ucsc.bed.gz \
                        --blacklist /nfs/home2/USER/genomedata/mm10/mm10.blacklist.bed.gz \
                        --prom /nfs/home2/USER/genomedata/mm10/ataqc/tss_mm10_master.bed.gz \
                        --enh /nfs/home2/USER/genomedata/mm10/ataqc/mm10_enh_dhs_ucsc.bed.gz \
                        --pbc /ourserver/E155_Gpos/E155/qc/rep2/DP_E155_Gpos2_1.PE2SE.nodup.pbc.qc\
                         --fastq1 /ourserver/E155_Gpos/../../inputs_fastq/CheahK_ATACSeqSO_SS-171107-02a/primary_seq/DP_E155_Gpos2_1.fastq.gz --fastq2 /ourserver/E155_Gpos/../../inputs_fastq/CheahK_ATACSeqSO_SS-171107-02a/primary_seq/DP_E155_Gpos2_2.fastq.gz \
                        --alignedbam /ourserver/E155_Gpos/E155/align/rep2/DP_E155_Gpos2_1.PE2SE.bam \
                        --alignmentlog /ourserver/E155_Gpos/E155/qc/rep2/DP_E155_Gpos2_1.PE2SE.align.log \
                        --coordsortbam /ourserver/E155_Gpos/E155/align/rep2/DP_E155_Gpos2_1.PE2SE.bam \
                        --duplog /ourserver/E155_Gpos/E155/qc/rep2/DP_E155_Gpos2_1.PE2SE.dup.qc \
                        --finalbam /ourserver/E155_Gpos/E155/align/rep2/DP_E155_Gpos2_1.PE2SE.nodup.bam \
                        --finalbed /ourserver/E155_Gpos/E155/align/rep2/DP_E155_Gpos2_1.PE2SE.nodup.tn5.tagAlign.gz \
                        --bigwig /ourserver/E155_Gpos/E155/signal/macs2/rep2/DP_E155_Gpos2_1.PE2SE.nodup.tn5.pf.pval.signal.bigwig \
                        --peaks /ourserver/E155_Gpos/E155/peak/macs2/overlap/optimal_set/E155_rep1-rep2.naive_overlap.filt.narrowPeak.gz  --naive_overlap_peaks /ourserver/E155_Gpos/E155/peak/macs2/overlap/optimal_set/E155_rep1-rep2.naive_overlap.filt.narrowPeak.gz   \
                         --reg2map /nfs/home2/USER/genomedata/mm10/ataqc/mm10_dnase_avg_fseq_signal_formatted.txt.gz  --reg2map_bed /nfs/home2/USER/genomedata/mm10/ataqc/mm10_celltype_compare_subsample.bed.gz  --meta /nfs/home2/USER/genomedata/mm10/ataqc/mm10_dnase_avg_fseq_signal_metadata.txt

            # SYS command. line 147

             rm -f test.log test.png

            # SYS command. line 149

             TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0
        StdErr (100000000 lines)  :
            Traceback (most recent call last):
              File "/ourserver/E155_Gpos/../../atac_dnase_pipelines/ataqc/run_ataqc.py", line 14, in <module>
                import metaseq
              File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/metaseq/__init__.py", line 7, in <module>
                import plotutils
              File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/metaseq/plotutils.py", line 6, in <module>
                from matplotlib import pyplot as plt
              File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/pyplot.py", line 36, in <module>
                from matplotlib.figure import Figure, figaspect
              File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/figure.py", line 40, in <module>
                from matplotlib.axes import Axes, SubplotBase, subplot_class_factory
              File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/axes/__init__.py", line 4, in <module>
                from ._subplots import *
              File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/axes/_subplots.py", line 10, in <module>
                from matplotlib.axes._axes import Axes
              File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/axes/_axes.py", line 22, in <module>
                import matplotlib.dates as _  # <-registers a date unit converter
              File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/dates.py", line 126, in <module>
                from dateutil.rrule import (rrule, MO, TU, WE, TH, FR, SA, SU, YEARLY,
              File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/dateutil/rrule.py", line 19, in <module>
                from six.moves import _thread, range
            ImportError: cannot import name _thread

    Task failed:
        Program & line     : '../../atac_dnase_pipelines/modules/ataqc.bds', line 109
        Task Name          : 'ataqc rep1'
        Task ID            : 'atac.bds.20171222_140505_349_parallel_180/task.ataqc.ataqc_rep1.line_109.id_97'
        Task PID           : '30727'
        Task hint          : 'if [ "${TMPDIR}" != "" ] && [ -d "${TMPDIR}" ]; then; fi; cd /ourserver/E155_Gpos/E155/qc/rep1; /ourserver/E155_Gpos/../../atac_dnase_pipelines/ataqc/run_ataqc.py; -'
        Task resources     : 'cpus: -1  mem: -1.0 B wall-timeout: 8640000'
        State              : 'ERROR'
        Dependency state   : 'ERROR'
        Retries available  : '1'
        Input files        : '[/ourserver/E155_Gpos/../../inputs_fastq/CheahK_ATACSeqSO_SS-171107-02a/primary_seq/DP_E155_Gpos1_1.fastq.gz, /ourserver/E155_Gpos/../../inputs_fastq/CheahK_ATACSeqSO_SS-171107-02a/primary_seq/DP_E155_Gpos1_2.fastq.gz, /ourserver/E155_Gpos/E155/align/rep1/DP_E155_Gpos1_1.PE2SE.bam, /ourserver/E155_Gpos/E155/qc/rep1/DP_E155_Gpos1_1.PE2SE.align.log, /ourserver/E155_Gpos/E155/qc/rep1/DP_E155_Gpos1_1.PE2SE.nodup.pbc.qc, /ourserver/E155_Gpos/E155/qc/rep1/DP_E155_Gpos1_1.PE2SE.dup.qc, /ourserver/E155_Gpos/E155/align/rep1/DP_E155_Gpos1_1.PE2SE.nodup.bam, /ourserver/E155_Gpos/E155/align/rep1/DP_E155_Gpos1_1.PE2SE.nodup.tn5.tagAlign.gz, /ourserver/E155_Gpos/E155/signal/macs2/rep1/DP_E155_Gpos1_1.PE2SE.nodup.tn5.pf.pval.signal.bigwig, /ourserver/E155_Gpos/E155/peak/macs2/overlap/optimal_set/E155_rep1-rep2.naive_overlap.filt.narrowPeak.gz]'
        Output files       : '[/ourserver/E155_Gpos/E155/qc/rep1/DP_E155_Gpos1_1.PE2SE_qc.html, /ourserver/E155_Gpos/E155/qc/rep1/DP_E155_Gpos1_1.PE2SE_qc.txt]'
        Script file        : '/ourserver/E155_Gpos/atac.bds.20171222_140505_349_parallel_180/task.ataqc.ataqc_rep1.line_109.id_97.sh'
        Exit status        : '1'
        Program            : 

            # SYS command. line 111

             if [[ -f $(which conda) && $(conda env list | grep bds_atac | wc -l) != "0" ]]; then source activate bds_atac; sleep 5; fi;  export PATH=/ourserver/E155_Gpos/../../atac_dnase_pipelines/.:/ourserver/E155_Gpos/../../atac_dnase_pipelines/modules:/ourserver/E155_Gpos/../../atac_dnase_pipelines/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

            # SYS command. line 114

             export _JAVA_OPTIONS="-Xms256M -Xmx20G -XX:ParallelGCThreads=1"

            # SYS command. line 116

             if [ "${TMPDIR}" != "" ] && [ -d "${TMPDIR}" ]; then \
                        export _JAVA_OPTIONS="${_JAVA_OPTIONS} -Djava.io.tmpdir=${TMPDIR}"; \
                    fi

            # SYS command. line 119

             cd /ourserver/E155_Gpos/E155/qc/rep1

            # SYS command. line 122

             if [ -f "$(which picard)" ]; then export PICARDROOT="$(dirname $(which picard))/../share/picard"*; fi

            # SYS command. line 124

             /ourserver/E155_Gpos/../../atac_dnase_pipelines/ataqc/run_ataqc.py \
                        --workdir /ourserver/E155_Gpos/E155/qc/rep1 \
                        --outdir /ourserver/E155_Gpos/E155/qc/rep1 \
                        --outprefix DP_E155_Gpos1_1.PE2SE \
                        --genome mm10 \
                        --chromsizes /nfs/home2/USER/genomedata/mm10/mm10.chrom.sizes \
                        --ref /nfs/home2/USER/genomedata/mm10/mm10_no_alt_analysis_set_ENCODE.fasta \
                        --tss /nfs/home2/USER/genomedata/mm10/ataqc/mm10_gencode_tss_unique.bed.gz \
                        --dnase /nfs/home2/USER/genomedata/mm10/ataqc/mm10_univ_dhs_ucsc.bed.gz \
                        --blacklist /nfs/home2/USER/genomedata/mm10/mm10.blacklist.bed.gz \
                        --prom /nfs/home2/USER/genomedata/mm10/ataqc/tss_mm10_master.bed.gz \
                        --enh /nfs/home2/USER/genomedata/mm10/ataqc/mm10_enh_dhs_ucsc.bed.gz \
                        --pbc /ourserver/E155_Gpos/E155/qc/rep1/DP_E155_Gpos1_1.PE2SE.nodup.pbc.qc\
                         --fastq1 /ourserver/E155_Gpos/../../inputs_fastq/CheahK_ATACSeqSO_SS-171107-02a/primary_seq/DP_E155_Gpos1_1.fastq.gz --fastq2 /ourserver/E155_Gpos/../../inputs_fastq/CheahK_ATACSeqSO_SS-171107-02a/primary_seq/DP_E155_Gpos1_2.fastq.gz \
                        --alignedbam /ourserver/E155_Gpos/E155/align/rep1/DP_E155_Gpos1_1.PE2SE.bam \
                        --alignmentlog /ourserver/E155_Gpos/E155/qc/rep1/DP_E155_Gpos1_1.PE2SE.align.log \
                        --coordsortbam /ourserver/E155_Gpos/E155/align/rep1/DP_E155_Gpos1_1.PE2SE.bam \
                        --duplog /ourserver/E155_Gpos/E155/qc/rep1/DP_E155_Gpos1_1.PE2SE.dup.qc \
                        --finalbam /ourserver/E155_Gpos/E155/align/rep1/DP_E155_Gpos1_1.PE2SE.nodup.bam \
                        --finalbed /ourserver/E155_Gpos/E155/align/rep1/DP_E155_Gpos1_1.PE2SE.nodup.tn5.tagAlign.gz \
                        --bigwig /ourserver/E155_Gpos/E155/signal/macs2/rep1/DP_E155_Gpos1_1.PE2SE.nodup.tn5.pf.pval.signal.bigwig \
                        --peaks /ourserver/E155_Gpos/E155/peak/macs2/overlap/optimal_set/E155_rep1-rep2.naive_overlap.filt.narrowPeak.gz  --naive_overlap_peaks /ourserver/E155_Gpos/E155/peak/macs2/overlap/optimal_set/E155_rep1-rep2.naive_overlap.filt.narrowPeak.gz   \
                         --reg2map /nfs/home2/USER/genomedata/mm10/ataqc/mm10_dnase_avg_fseq_signal_formatted.txt.gz  --reg2map_bed /nfs/home2/USER/genomedata/mm10/ataqc/mm10_celltype_compare_subsample.bed.gz  --meta /nfs/home2/USER/genomedata/mm10/ataqc/mm10_dnase_avg_fseq_signal_metadata.txt

            # SYS command. line 147

             rm -f test.log test.png

            # SYS command. line 149

             TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0
        StdErr (100000000 lines)  :
            Traceback (most recent call last):
              File "/ourserver/E155_Gpos/../../atac_dnase_pipelines/ataqc/run_ataqc.py", line 14, in <module>
                import metaseq
              File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/metaseq/__init__.py", line 7, in <module>
                import plotutils
              File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/metaseq/plotutils.py", line 6, in <module>
                from matplotlib import pyplot as plt
              File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/pyplot.py", line 36, in <module>
                from matplotlib.figure import Figure, figaspect
              File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/figure.py", line 40, in <module>
                from matplotlib.axes import Axes, SubplotBase, subplot_class_factory
              File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/axes/__init__.py", line 4, in <module>
                from ._subplots import *
              File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/axes/_subplots.py", line 10, in <module>
                from matplotlib.axes._axes import Axes
              File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/axes/_axes.py", line 22, in <module>
                import matplotlib.dates as _  # <-registers a date unit converter
              File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/dates.py", line 126, in <module>
                from dateutil.rrule import (rrule, MO, TU, WE, TH, FR, SA, SU, YEARLY,
              File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/dateutil/rrule.py", line 19, in <module>
                from six.moves import _thread, range
            ImportError: cannot import name _thread

    Fatal error: ../../atac_dnase_pipelines/atac.bds, line 1612, pos 2. Task/s failed.

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

    finished

================attachment ends====================

leepc12 commented 6 years ago

Please run the following for more debugging info.

$ uname -a # type of OS $ conda env list $ source activate bds_atac $ which conda $ conda list $ source deactivate

Thanks,

Jin

On Fri, Dec 22, 2017 at 7:04 PM, CHEN Peikai notifications@github.com wrote:

Hi Jin, Thanks for your prompt reply. I re-installed a newer version of samtools (v=1.6), and re-run the whole pipeline (cloned on dec 5), and still cannot get atacqc. other steps are ok, though.

Attached is the stderr messages for the part that fails (i.e. ataqc).

best chan

================attachment begins====================

Task has finished (76 seconds). Task has finished (72 seconds).

== Done naive_overlap() Task has finished (0 seconds). species_ataqc: mm10 species_ataqc: mm10 Traceback (most recent call last): File "/ourserver/E155_Gpos/../../atac_dnase_pipelines/ataqc/run_ataqc.py", line 14, in import metaseq File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/metaseq/init.py", line 7, in import plotutils File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/metaseq/plotutils.py", line 6, in from matplotlib import pyplot as plt File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/pyplot.py", line 36, in Traceback (most recent call last): File "/ourserver/E155_Gpos/../../atac_dnase_pipelines/ataqc/run_ataqc.py", line 14, in import metaseq File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/metaseq/init.py", line 7, in import plotutils File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/metaseq/plotutils.py", line 6, in from matplotlib import pyplot as plt File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/pyplot.py", line 36, in from matplotlib.figure import Figure, figaspect File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/figure.py", line 40, in from matplotlib.axes import Axes, SubplotBase, subplot_class_factory File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/axes/init.py", line 4, in from ._subplots import File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/axes/_subplots.py", line 10, in from matplotlib.figure import Figure, figaspect File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/figure.py", line 40, in from matplotlib.axes import Axes, SubplotBase, subplot_class_factory File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/axes/init.py", line 4, in from ._subplots import File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/axes/_subplots.py", line 10, in from matplotlib.axes._axes import Axes File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/axes/axes.py", line 22, in import matplotlib.dates as # <-registers a date unit converter File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/dates.py", line 126, in from dateutil.rrule import (rrule, MO, TU, WE, TH, FR, SA, SU, YEARLY, File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/dateutil/rrule.py", line 19, in from six.moves import _thread, range ImportError: cannot import name _thread from matplotlib.axes._axes import Axes File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/axes/axes.py", line 22, in import matplotlib.dates as # <-registers a date unit converter File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/dates.py", line 126, in from dateutil.rrule import (rrule, MO, TU, WE, TH, FR, SA, SU, YEARLY, File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/dateutil/rrule.py", line 19, in from six.moves import _thread, range ImportError: cannot import name _thread Task failed: Program & line : '../../atac_dnase_pipelines/modules/ataqc.bds', line 109 Task Name : 'ataqc rep2' Task ID : 'atac.bds.20171222_140505_349_parallel_181/task.ataqc.ataqc_rep2.line_109.id_98' Task PID : '30729' Task hint : 'if [ "${TMPDIR}" != "" ] && [ -d "${TMPDIR}" ]; then; fi; cd /ourserver/E155_Gpos/E155/qc/rep2; /ourserver/E155_Gpos/../../atac_dnase_pipelines/ataqc/run_ataqc.py; -' Task resources : 'cpus: -1 mem: -1.0 B wall-timeout: 8640000' State : 'ERROR' Dependency state : 'ERROR' Retries available : '1' Input files : '[/ourserver/E155_Gpos/../../inputs_fastq/CheahK_ATACSeqSO_SS-171107-02a/primary_seq/DP_E155_Gpos2_1.fastq.gz, /ourserver/E155_Gpos/../../inputs_fastq/CheahK_ATACSeqSO_SS-171107-02a/primary_seq/DP_E155_Gpos2_2.fastq.gz, /ourserver/E155_Gpos/E155/align/rep2/DP_E155_Gpos2_1.PE2SE.bam, /ourserver/E155_Gpos/E155/qc/rep2/DP_E155_Gpos2_1.PE2SE.align.log, /ourserver/E155_Gpos/E155/qc/rep2/DP_E155_Gpos2_1.PE2SE.nodup.pbc.qc, /ourserver/E155_Gpos/E155/qc/rep2/DP_E155_Gpos2_1.PE2SE.dup.qc, /ourserver/E155_Gpos/E155/align/rep2/DP_E155_Gpos2_1.PE2SE.nodup.bam, /ourserver/E155_Gpos/E155/align/rep2/DP_E155_Gpos2_1.PE2SE.nodup.tn5.tagAlign.gz, /ourserver/E155_Gpos/E155/signal/macs2/rep2/DP_E155_Gpos2_1.PE2SE.nodup.tn5.pf.pval.signal.bigwig, /ourserver/E155_Gpos/E155/peak/macs2/overlap/optimal_set/E155_rep1-rep2.naive_overlap.filt.narrowPeak.gz]' Output files : '[/ourserver/E155_Gpos/E155/qc/rep2/DP_E155_Gpos2_1.PE2SE_qc.html, /ourserver/E155_Gpos/E155/qc/rep2/DP_E155_Gpos2_1.PE2SE_qc.txt]' Script file : '/ourserver/E155_Gpos/atac.bds.20171222_140505_349_parallel_181/task.ataqc.ataqc_rep2.line_109.id_98.sh' Exit status : '1' Program :

      # SYS command. line 111

       if [[ -f $(which conda) && $(conda env list | grep bds_atac | wc -l) != "0" ]]; then source activate bds_atac; sleep 5; fi;  export PATH=/ourserver/E155_Gpos/../../atac_dnase_pipelines/.:/ourserver/E155_Gpos/../../atac_dnase_pipelines/modules:/ourserver/E155_Gpos/../../atac_dnase_pipelines/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

      # SYS command. line 114

       export _JAVA_OPTIONS="-Xms256M -Xmx20G -XX:ParallelGCThreads=1"

      # SYS command. line 116

       if [ "${TMPDIR}" != "" ] && [ -d "${TMPDIR}" ]; then \
                  export _JAVA_OPTIONS="${_JAVA_OPTIONS} -Djava.io.tmpdir=${TMPDIR}"; \
              fi

      # SYS command. line 119

       cd /ourserver/E155_Gpos/E155/qc/rep2

      # SYS command. line 122

       if [ -f "$(which picard)" ]; then export PICARDROOT="$(dirname $(which picard))/../share/picard"*; fi

      # SYS command. line 124

       /ourserver/E155_Gpos/../../atac_dnase_pipelines/ataqc/run_ataqc.py \
                  --workdir /ourserver/E155_Gpos/E155/qc/rep2 \
                  --outdir /ourserver/E155_Gpos/E155/qc/rep2 \
                  --outprefix DP_E155_Gpos2_1.PE2SE \
                  --genome mm10 \
                  --chromsizes /nfs/home2/USER/genomedata/mm10/mm10.chrom.sizes \
                  --ref /nfs/home2/USER/genomedata/mm10/mm10_no_alt_analysis_set_ENCODE.fasta \
                  --tss /nfs/home2/USER/genomedata/mm10/ataqc/mm10_gencode_tss_unique.bed.gz \
                  --dnase /nfs/home2/USER/genomedata/mm10/ataqc/mm10_univ_dhs_ucsc.bed.gz \
                  --blacklist /nfs/home2/USER/genomedata/mm10/mm10.blacklist.bed.gz \
                  --prom /nfs/home2/USER/genomedata/mm10/ataqc/tss_mm10_master.bed.gz \
                  --enh /nfs/home2/USER/genomedata/mm10/ataqc/mm10_enh_dhs_ucsc.bed.gz \
                  --pbc /ourserver/E155_Gpos/E155/qc/rep2/DP_E155_Gpos2_1.PE2SE.nodup.pbc.qc\
                   --fastq1 /ourserver/E155_Gpos/../../inputs_fastq/CheahK_ATACSeqSO_SS-171107-02a/primary_seq/DP_E155_Gpos2_1.fastq.gz --fastq2 /ourserver/E155_Gpos/../../inputs_fastq/CheahK_ATACSeqSO_SS-171107-02a/primary_seq/DP_E155_Gpos2_2.fastq.gz \
                  --alignedbam /ourserver/E155_Gpos/E155/align/rep2/DP_E155_Gpos2_1.PE2SE.bam \
                  --alignmentlog /ourserver/E155_Gpos/E155/qc/rep2/DP_E155_Gpos2_1.PE2SE.align.log \
                  --coordsortbam /ourserver/E155_Gpos/E155/align/rep2/DP_E155_Gpos2_1.PE2SE.bam \
                  --duplog /ourserver/E155_Gpos/E155/qc/rep2/DP_E155_Gpos2_1.PE2SE.dup.qc \
                  --finalbam /ourserver/E155_Gpos/E155/align/rep2/DP_E155_Gpos2_1.PE2SE.nodup.bam \
                  --finalbed /ourserver/E155_Gpos/E155/align/rep2/DP_E155_Gpos2_1.PE2SE.nodup.tn5.tagAlign.gz \
                  --bigwig /ourserver/E155_Gpos/E155/signal/macs2/rep2/DP_E155_Gpos2_1.PE2SE.nodup.tn5.pf.pval.signal.bigwig \
                  --peaks /ourserver/E155_Gpos/E155/peak/macs2/overlap/optimal_set/E155_rep1-rep2.naive_overlap.filt.narrowPeak.gz  --naive_overlap_peaks /ourserver/E155_Gpos/E155/peak/macs2/overlap/optimal_set/E155_rep1-rep2.naive_overlap.filt.narrowPeak.gz   \
                   --reg2map /nfs/home2/USER/genomedata/mm10/ataqc/mm10_dnase_avg_fseq_signal_formatted.txt.gz  --reg2map_bed /nfs/home2/USER/genomedata/mm10/ataqc/mm10_celltype_compare_subsample.bed.gz  --meta /nfs/home2/USER/genomedata/mm10/ataqc/mm10_dnase_avg_fseq_signal_metadata.txt

      # SYS command. line 147

       rm -f test.log test.png

      # SYS command. line 149

       TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0
  StdErr (100000000 lines)  :
      Traceback (most recent call last):
        File "/ourserver/E155_Gpos/../../atac_dnase_pipelines/ataqc/run_ataqc.py", line 14, in <module>
          import metaseq
        File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/metaseq/__init__.py", line 7, in <module>
          import plotutils
        File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/metaseq/plotutils.py", line 6, in <module>
          from matplotlib import pyplot as plt
        File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/pyplot.py", line 36, in <module>
          from matplotlib.figure import Figure, figaspect
        File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/figure.py", line 40, in <module>
          from matplotlib.axes import Axes, SubplotBase, subplot_class_factory
        File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/axes/__init__.py", line 4, in <module>
          from ._subplots import *
        File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/axes/_subplots.py", line 10, in <module>
          from matplotlib.axes._axes import Axes
        File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/axes/_axes.py", line 22, in <module>
          import matplotlib.dates as _  # <-registers a date unit converter
        File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/dates.py", line 126, in <module>
          from dateutil.rrule import (rrule, MO, TU, WE, TH, FR, SA, SU, YEARLY,
        File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/dateutil/rrule.py", line 19, in <module>
          from six.moves import _thread, range
      ImportError: cannot import name _thread

Task failed: Program & line : '../../atac_dnase_pipelines/modules/ataqc.bds', line 109 Task Name : 'ataqc rep1' Task ID : 'atac.bds.20171222_140505_349_parallel_180/task.ataqc.ataqc_rep1.line_109.id_97' Task PID : '30727' Task hint : 'if [ "${TMPDIR}" != "" ] && [ -d "${TMPDIR}" ]; then; fi; cd /ourserver/E155_Gpos/E155/qc/rep1; /ourserver/E155_Gpos/../../atac_dnase_pipelines/ataqc/run_ataqc.py; -' Task resources : 'cpus: -1 mem: -1.0 B wall-timeout: 8640000' State : 'ERROR' Dependency state : 'ERROR' Retries available : '1' Input files : '[/ourserver/E155_Gpos/../../inputs_fastq/CheahK_ATACSeqSO_SS-171107-02a/primary_seq/DP_E155_Gpos1_1.fastq.gz, /ourserver/E155_Gpos/../../inputs_fastq/CheahK_ATACSeqSO_SS-171107-02a/primary_seq/DP_E155_Gpos1_2.fastq.gz, /ourserver/E155_Gpos/E155/align/rep1/DP_E155_Gpos1_1.PE2SE.bam, /ourserver/E155_Gpos/E155/qc/rep1/DP_E155_Gpos1_1.PE2SE.align.log, /ourserver/E155_Gpos/E155/qc/rep1/DP_E155_Gpos1_1.PE2SE.nodup.pbc.qc, /ourserver/E155_Gpos/E155/qc/rep1/DP_E155_Gpos1_1.PE2SE.dup.qc, /ourserver/E155_Gpos/E155/align/rep1/DP_E155_Gpos1_1.PE2SE.nodup.bam, /ourserver/E155_Gpos/E155/align/rep1/DP_E155_Gpos1_1.PE2SE.nodup.tn5.tagAlign.gz, /ourserver/E155_Gpos/E155/signal/macs2/rep1/DP_E155_Gpos1_1.PE2SE.nodup.tn5.pf.pval.signal.bigwig, /ourserver/E155_Gpos/E155/peak/macs2/overlap/optimal_set/E155_rep1-rep2.naive_overlap.filt.narrowPeak.gz]' Output files : '[/ourserver/E155_Gpos/E155/qc/rep1/DP_E155_Gpos1_1.PE2SE_qc.html, /ourserver/E155_Gpos/E155/qc/rep1/DP_E155_Gpos1_1.PE2SE_qc.txt]' Script file : '/ourserver/E155_Gpos/atac.bds.20171222_140505_349_parallel_180/task.ataqc.ataqc_rep1.line_109.id_97.sh' Exit status : '1' Program :

      # SYS command. line 111

       if [[ -f $(which conda) && $(conda env list | grep bds_atac | wc -l) != "0" ]]; then source activate bds_atac; sleep 5; fi;  export PATH=/ourserver/E155_Gpos/../../atac_dnase_pipelines/.:/ourserver/E155_Gpos/../../atac_dnase_pipelines/modules:/ourserver/E155_Gpos/../../atac_dnase_pipelines/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

      # SYS command. line 114

       export _JAVA_OPTIONS="-Xms256M -Xmx20G -XX:ParallelGCThreads=1"

      # SYS command. line 116

       if [ "${TMPDIR}" != "" ] && [ -d "${TMPDIR}" ]; then \
                  export _JAVA_OPTIONS="${_JAVA_OPTIONS} -Djava.io.tmpdir=${TMPDIR}"; \
              fi

      # SYS command. line 119

       cd /ourserver/E155_Gpos/E155/qc/rep1

      # SYS command. line 122

       if [ -f "$(which picard)" ]; then export PICARDROOT="$(dirname $(which picard))/../share/picard"*; fi

      # SYS command. line 124

       /ourserver/E155_Gpos/../../atac_dnase_pipelines/ataqc/run_ataqc.py \
                  --workdir /ourserver/E155_Gpos/E155/qc/rep1 \
                  --outdir /ourserver/E155_Gpos/E155/qc/rep1 \
                  --outprefix DP_E155_Gpos1_1.PE2SE \
                  --genome mm10 \
                  --chromsizes /nfs/home2/USER/genomedata/mm10/mm10.chrom.sizes \
                  --ref /nfs/home2/USER/genomedata/mm10/mm10_no_alt_analysis_set_ENCODE.fasta \
                  --tss /nfs/home2/USER/genomedata/mm10/ataqc/mm10_gencode_tss_unique.bed.gz \
                  --dnase /nfs/home2/USER/genomedata/mm10/ataqc/mm10_univ_dhs_ucsc.bed.gz \
                  --blacklist /nfs/home2/USER/genomedata/mm10/mm10.blacklist.bed.gz \
                  --prom /nfs/home2/USER/genomedata/mm10/ataqc/tss_mm10_master.bed.gz \
                  --enh /nfs/home2/USER/genomedata/mm10/ataqc/mm10_enh_dhs_ucsc.bed.gz \
                  --pbc /ourserver/E155_Gpos/E155/qc/rep1/DP_E155_Gpos1_1.PE2SE.nodup.pbc.qc\
                   --fastq1 /ourserver/E155_Gpos/../../inputs_fastq/CheahK_ATACSeqSO_SS-171107-02a/primary_seq/DP_E155_Gpos1_1.fastq.gz --fastq2 /ourserver/E155_Gpos/../../inputs_fastq/CheahK_ATACSeqSO_SS-171107-02a/primary_seq/DP_E155_Gpos1_2.fastq.gz \
                  --alignedbam /ourserver/E155_Gpos/E155/align/rep1/DP_E155_Gpos1_1.PE2SE.bam \
                  --alignmentlog /ourserver/E155_Gpos/E155/qc/rep1/DP_E155_Gpos1_1.PE2SE.align.log \
                  --coordsortbam /ourserver/E155_Gpos/E155/align/rep1/DP_E155_Gpos1_1.PE2SE.bam \
                  --duplog /ourserver/E155_Gpos/E155/qc/rep1/DP_E155_Gpos1_1.PE2SE.dup.qc \
                  --finalbam /ourserver/E155_Gpos/E155/align/rep1/DP_E155_Gpos1_1.PE2SE.nodup.bam \
                  --finalbed /ourserver/E155_Gpos/E155/align/rep1/DP_E155_Gpos1_1.PE2SE.nodup.tn5.tagAlign.gz \
                  --bigwig /ourserver/E155_Gpos/E155/signal/macs2/rep1/DP_E155_Gpos1_1.PE2SE.nodup.tn5.pf.pval.signal.bigwig \
                  --peaks /ourserver/E155_Gpos/E155/peak/macs2/overlap/optimal_set/E155_rep1-rep2.naive_overlap.filt.narrowPeak.gz  --naive_overlap_peaks /ourserver/E155_Gpos/E155/peak/macs2/overlap/optimal_set/E155_rep1-rep2.naive_overlap.filt.narrowPeak.gz   \
                   --reg2map /nfs/home2/USER/genomedata/mm10/ataqc/mm10_dnase_avg_fseq_signal_formatted.txt.gz  --reg2map_bed /nfs/home2/USER/genomedata/mm10/ataqc/mm10_celltype_compare_subsample.bed.gz  --meta /nfs/home2/USER/genomedata/mm10/ataqc/mm10_dnase_avg_fseq_signal_metadata.txt

      # SYS command. line 147

       rm -f test.log test.png

      # SYS command. line 149

       TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0
  StdErr (100000000 lines)  :
      Traceback (most recent call last):
        File "/ourserver/E155_Gpos/../../atac_dnase_pipelines/ataqc/run_ataqc.py", line 14, in <module>
          import metaseq
        File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/metaseq/__init__.py", line 7, in <module>
          import plotutils
        File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/metaseq/plotutils.py", line 6, in <module>
          from matplotlib import pyplot as plt
        File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/pyplot.py", line 36, in <module>
          from matplotlib.figure import Figure, figaspect
        File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/figure.py", line 40, in <module>
          from matplotlib.axes import Axes, SubplotBase, subplot_class_factory
        File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/axes/__init__.py", line 4, in <module>
          from ._subplots import *
        File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/axes/_subplots.py", line 10, in <module>
          from matplotlib.axes._axes import Axes
        File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/axes/_axes.py", line 22, in <module>
          import matplotlib.dates as _  # <-registers a date unit converter
        File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/matplotlib/dates.py", line 126, in <module>
          from dateutil.rrule import (rrule, MO, TU, WE, TH, FR, SA, SU, YEARLY,
        File "/userChan/utilities/conda/pwd/envs/bds_atac/lib/python2.7/site-packages/dateutil/rrule.py", line 19, in <module>
          from six.moves import _thread, range
      ImportError: cannot import name _thread

Fatal error: ../../atac_dnase_pipelines/atac.bds, line 1612, pos 2. Task/s failed.

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

finished

================attachment ends====================

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/kundajelab/atac_dnase_pipelines/issues/86#issuecomment-353703298, or mute the thread https://github.com/notifications/unsubscribe-auth/AIOd_LLEb7eXA6KDgZrOyV8sAa8YSWX0ks5tDG3YgaJpZM4RKkmu .

tanpuekai commented 6 years ago

Hi Jin,

Thanks a lot. Below are the messages of running your debugging scripts.

Merry X'mas and happy new year!

Best Chan

    $ uname -a # type of OS
    Linux OURSERVER 3.2.0-124-generic #167-Ubuntu SMP Fri Mar 3 15:25:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
    $ conda env list
    # conda environments:
    #
    bds_atac                 /home/USER1/utilities/conda/pwd/envs/bds_atac
    bds_atac_py3             /home/USER1/utilities/conda/pwd/envs/bds_atac_py3
    root                  *  /home/USER1/utilities/conda/pwd
    $source activate bds_atac
    (bds_atac) 
    $which conda
    /home/USER1/utilities/conda/pwd/envs/bds_atac/bin/conda
    (bds_atac) 
    $conda list
    # packages in environment at /home/USER1/utilities/conda/pwd/envs/bds_atac:
    #
    argcomplete               1.0.0                    py27_1
    argh                      0.26.1                   py27_0    bioconda
    bcftools                  1.6                           0    bioconda
    bedtools                  2.26.0                        0    bioconda
    bioconductor-biocgenerics 0.18.0                 r3.2.2_0    bioconda
    bioconductor-biocparallel 1.4.3                  r3.2.2_0    bioconda
    bioconductor-biostrings   2.38.4                        0    bioconda
    bioconductor-genomeinfodb 1.6.3                         0    bioconda
    bioconductor-genomicranges 1.22.4                        0    bioconda
    bioconductor-iranges      2.4.8                         0    bioconda
    bioconductor-rsamtools    1.22.0                 r3.2.2_1    bioconda
    bioconductor-s4vectors    0.8.11                        0    bioconda
    bioconductor-xvector      0.10.0                        1    bioconda
    bioconductor-zlibbioc     1.16.0                 r3.2.2_1    bioconda
    biopython                 1.67                np110py27_0
    boost                     1.57.0                        4
    bowtie                    1.1.2                    py27_2    bioconda
    bowtie2                   2.2.6                    py27_0    bioconda
    bx-python                 0.7.3               np110py27_1    bioconda
    bzip2                     1.0.6                h6d464ef_2
    ca-certificates           2017.08.26           h1d4fec5_0
    cairo                     1.14.8                        0
    certifi                   2017.11.5        py27h71e7faf_0
    curl                      7.55.1               h78862de_4
    cutadapt                  1.9.1                    py27_0    bioconda
    cycler                    0.10.0           py27hc7354d3_0
    cython                    0.27.3           py27hc56b35e_0
    expat                     2.2.5                he0dffb1_0
    fastqc                    0.11.5                        1    bioconda
    fisher                    0.1.4                    py27_0    bioconda
    fontconfig                2.12.1                        3
    freetype                  2.5.5                         2
    gffutils                  0.9                      py27_0    bioconda
    ghostscript               9.18                          1    bioconda
    glib                      2.53.6               h5d9569c_2
    gnuplot                   4.6.0                         1    bioconda
    graphviz                  2.38.0                        5    anaconda
    gsl                       1.16                          1    asmeurer
    harfbuzz                  0.9.39                        2
    htslib                    1.4                           0    bioconda
    icu                       58.2                 h9c2bf20_1
    intel-openmp              2018.0.0             hc7b2577_8
    java-jdk                  8.0.92                        1    bioconda
    jinja2                    2.10             py27h4114e70_0
    jpeg                      9b                   h024ee3a_2
    libedit                   3.1                  heed3624_0
    libffi                    3.2.1                hd88cf55_4
    libgcc                    7.2.0                h69d50b8_2
    libgcc-ng                 7.2.0                h7cc24e2_2
    libgfortran               3.0.0                         1
    libgfortran-ng            7.2.0                h9f7466a_2
    libiconv                  1.14                          0
    libpng                    1.6.32               hbd3595f_4
    libssh2                   1.8.0                h2d05a93_3
    libstdcxx-ng              7.2.0                h7a57d05_2
    libtiff                   4.0.9                h28f6b97_0
    libtool                   2.4.6                h544aabb_3
    libuuid                   1.0.3                h5bb35a6_1
    libxml2                   2.9.4                h2e8b1d7_6
    macs2                     2.1.0                         0    bioconda
    markupsafe                1.0              py27h97b2822_1
    matplotlib                1.5.1               np110py27_0
    metaseq                   0.5.6                    py27_0    bioconda
    mkl                       2018.0.1             h19d6760_4
    mysql-connector-c         6.1.6                         2    bioconda
    ncurses                   6.0                  h9df7e31_2
    nose                      1.3.7            py27heec2199_2
    numpy                     1.10.2                   py27_0
    openblas                  0.2.14                        4
    openssl                   1.0.2n               hb7f436b_0
    pandas                    0.18.0              np110py27_0
    pango                     1.36.8                        3    asmeurer
    pcre                      8.41                 hc27e229_1
    perl-threaded             5.22.0                       10    bioconda
    picard                    1.126                         4    bioconda
    pigz                      2.3                           0
    pip                       9.0.1            py27ha730c48_4
    pixman                    0.34.0               hceecf20_3
    preseq                    2.0.2                 gsl1.16_0    bioconda
    pybedtools                0.6.9                    py27_0    bcbio
    pycairo                   1.13.3           py27hea6d626_0
    pyfaidx                   0.4.7.1                  py27_0    bioconda
    pyparsing                 2.2.0            py27hf1513f8_1
    pyqt                      4.10.4                   py27_0    asmeurer
    pysam                     0.8.2.1                  py27_0    bcbio
    python                    2.7.14              h1571d57_29
    python-dateutil           2.6.1            py27h4ca5741_1
    python-levenshtein        0.12.0                   py27_1    bioconda
    pytz                      2017.3           py27h001bace_0
    pyyaml                    3.12             py27h2d70dd7_1
    qt                        4.8.7                         4
    r                         3.2.2                         0
    r-base                    3.2.2                         0
    r-bitops                  1.0_6                 r3.2.2_1a
    r-boot                    1.3_17                r3.2.2_0a
    r-catools                 1.17.1                r3.2.2_2a
    r-class                   7.3_14                r3.2.2_0a
    r-cluster                 2.0.3                 r3.2.2_0a
    r-codetools               0.2_14                r3.2.2_0a
    r-foreign                 0.8_66                r3.2.2_0a
    r-futile.logger           1.4.1                  r3.2.2_0    bioconda
    r-futile.options          1.0.0                  r3.2.2_0    bioconda
    r-kernsmooth              2.23_15               r3.2.2_0a
    r-lambda.r                1.1.7                  r3.2.2_0    bioconda
    r-lattice                 0.20_33               r3.2.2_0a
    r-mass                    7.3_45                r3.2.2_0a
    r-matrix                  1.2_2                 r3.2.2_0a
    r-mgcv                    1.8_9                 r3.2.2_0a
    r-nlme                    3.1_122               r3.2.2_0a
    r-nnet                    7.3_11                r3.2.2_0a
    r-recommended             3.2.2                  r3.2.2_0
    r-rpart                   4.1_10                r3.2.2_0a
    r-snow                    0.4_1                  r3.2.2_0    bioconda
    r-snowfall                1.84_6.1               r3.2.2_0    bioconda
    r-spatial                 7.3_11                r3.2.2_0a
    r-spp                     1.13                   r3.2.2_0    bioconda
    r-survival                2.38_3                r3.2.2_0a
    readline                  7.0                  ha6073c6_4
    sambamba                  0.6.5                         0    bioconda
    samtools                  1.2                           2    bioconda
    scikit-learn              0.19.1           py27h445a80a_0
    scipy                     1.0.0            py27hf5f0f52_0
    setuptools                36.5.0           py27h68b189e_0
    simplejson                3.12.0           py27h264bab0_0
    sip                       4.18.1           py27he9ba0ab_2
    six                       1.4.1                    py27_0
    sqlite                    3.20.1               hb898158_2
    system                    5.8                           2
    tk                        8.6.7                hc745277_3
    trim-galore               0.4.1                         0    bioconda
    ucsc-bedclip              357                           0    bioconda
    ucsc-bedgraphtobigwig     357                           0    bioconda
    ucsc-bedtobigbed          357                           0    bioconda
    ucsc-bigwigaverageoverbed 357                           0    bioconda
    ucsc-bigwiginfo           357                           0    bioconda
    ucsc-fetchchromsizes      357                           0    bioconda
    ucsc-twobittofa           357                           0    bioconda
    ucsc-wigtobigwig          357                           0    bioconda
    wheel                     0.30.0           py27h2bc6bb2_1
    xz                        5.2.3                h55aa19d_2
    yaml                      0.1.7                had09818_2
    zlib                      1.2.11               ha838bed_2
    $  source deactivate
leepc12 commented 6 years ago

It's weird that your six version is 1.4.1. Please try the following:

$ source activate bds_atac $ conda install six==1.10.0 $ source deactivate

Thanks,

Jin

On Sun, Dec 24, 2017 at 6:24 PM, CHEN Peikai notifications@github.com wrote:

Hi Jin,

Thanks a lot. Below are the messages of running the debugging info.

Best Chan

$ uname -a # type of OS Linux OURSERVER 3.2.0-124-generic #167-Ubuntu SMP Fri Mar 3 15:25:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux $ conda env list

conda environments:

# bds_atac /home/USER1/utilities/conda/pwd/envs/bds_atac bds_atac_py3 /home/USER1/utilities/conda/pwd/envs/bds_atac_py3 root * /home/USER1/utilities/conda/pwd $source activate bds_atac (bds_atac) $which conda /home/USER1/utilities/conda/pwd/envs/bds_atac/bin/conda (bds_atac) $conda list

packages in environment at /home/USER1/utilities/conda/pwd/envs/bds_atac:

# argcomplete 1.0.0 py27_1 argh 0.26.1 py27_0 bioconda bcftools 1.6 0 bioconda bedtools 2.26.0 0 bioconda bioconductor-biocgenerics 0.18.0 r3.2.2_0 bioconda bioconductor-biocparallel 1.4.3 r3.2.2_0 bioconda bioconductor-biostrings 2.38.4 0 bioconda bioconductor-genomeinfodb 1.6.3 0 bioconda bioconductor-genomicranges 1.22.4 0 bioconda bioconductor-iranges 2.4.8 0 bioconda bioconductor-rsamtools 1.22.0 r3.2.2_1 bioconda bioconductor-s4vectors 0.8.11 0 bioconda bioconductor-xvector 0.10.0 1 bioconda bioconductor-zlibbioc 1.16.0 r3.2.2_1 bioconda biopython 1.67 np110py27_0 boost 1.57.0 4 bowtie 1.1.2 py27_2 bioconda bowtie2 2.2.6 py27_0 bioconda bx-python 0.7.3 np110py27_1 bioconda bzip2 1.0.6 h6d464ef_2 ca-certificates 2017.08.26 h1d4fec5_0 cairo 1.14.8 0 certifi 2017.11.5 py27h71e7faf_0 curl 7.55.1 h78862de_4 cutadapt 1.9.1 py27_0 bioconda cycler 0.10.0 py27hc7354d3_0 cython 0.27.3 py27hc56b35e_0 expat 2.2.5 he0dffb1_0 fastqc 0.11.5 1 bioconda fisher 0.1.4 py27_0 bioconda fontconfig 2.12.1 3 freetype 2.5.5 2 gffutils 0.9 py27_0 bioconda ghostscript 9.18 1 bioconda glib 2.53.6 h5d9569c_2 gnuplot 4.6.0 1 bioconda graphviz 2.38.0 5 anaconda gsl 1.16 1 asmeurer harfbuzz 0.9.39 2 htslib 1.4 0 bioconda icu 58.2 h9c2bf20_1 intel-openmp 2018.0.0 hc7b2577_8 java-jdk 8.0.92 1 bioconda jinja2 2.10 py27h4114e70_0 jpeg 9b h024ee3a_2 libedit 3.1 heed3624_0 libffi 3.2.1 hd88cf55_4 libgcc 7.2.0 h69d50b8_2 libgcc-ng 7.2.0 h7cc24e2_2 libgfortran 3.0.0 1 libgfortran-ng 7.2.0 h9f7466a_2 libiconv 1.14 0 libpng 1.6.32 hbd3595f_4 libssh2 1.8.0 h2d05a93_3 libstdcxx-ng 7.2.0 h7a57d05_2 libtiff 4.0.9 h28f6b97_0 libtool 2.4.6 h544aabb_3 libuuid 1.0.3 h5bb35a6_1 libxml2 2.9.4 h2e8b1d7_6 macs2 2.1.0 0 bioconda markupsafe 1.0 py27h97b2822_1 matplotlib 1.5.1 np110py27_0 metaseq 0.5.6 py27_0 bioconda mkl 2018.0.1 h19d6760_4 mysql-connector-c 6.1.6 2 bioconda ncurses 6.0 h9df7e31_2 nose 1.3.7 py27heec2199_2 numpy 1.10.2 py27_0 openblas 0.2.14 4 openssl 1.0.2n hb7f436b_0 pandas 0.18.0 np110py27_0 pango 1.36.8 3 asmeurer pcre 8.41 hc27e229_1 perl-threaded 5.22.0 10 bioconda picard 1.126 4 bioconda pigz 2.3 0 pip 9.0.1 py27ha730c48_4 pixman 0.34.0 hceecf20_3 preseq 2.0.2 gsl1.16_0 bioconda pybedtools 0.6.9 py27_0 bcbio pycairo 1.13.3 py27hea6d626_0 pyfaidx 0.4.7.1 py27_0 bioconda pyparsing 2.2.0 py27hf1513f8_1 pyqt 4.10.4 py27_0 asmeurer pysam 0.8.2.1 py27_0 bcbio python 2.7.14 h1571d57_29 python-dateutil 2.6.1 py27h4ca5741_1 python-levenshtein 0.12.0 py27_1 bioconda pytz 2017.3 py27h001bace_0 pyyaml 3.12 py27h2d70dd7_1 qt 4.8.7 4 r 3.2.2 0 r-base 3.2.2 0 r-bitops 1.0_6 r3.2.2_1a r-boot 1.3_17 r3.2.2_0a r-catools 1.17.1 r3.2.2_2a r-class 7.3_14 r3.2.2_0a r-cluster 2.0.3 r3.2.2_0a r-codetools 0.2_14 r3.2.2_0a r-foreign 0.8_66 r3.2.2_0a r-futile.logger 1.4.1 r3.2.2_0 bioconda r-futile.options 1.0.0 r3.2.2_0 bioconda r-kernsmooth 2.23_15 r3.2.2_0a r-lambda.r 1.1.7 r3.2.2_0 bioconda r-lattice 0.20_33 r3.2.2_0a r-mass 7.3_45 r3.2.2_0a r-matrix 1.2_2 r3.2.2_0a r-mgcv 1.8_9 r3.2.2_0a r-nlme 3.1_122 r3.2.2_0a r-nnet 7.3_11 r3.2.2_0a r-recommended 3.2.2 r3.2.2_0 r-rpart 4.1_10 r3.2.2_0a r-snow 0.4_1 r3.2.2_0 bioconda r-snowfall 1.84_6.1 r3.2.2_0 bioconda r-spatial 7.3_11 r3.2.2_0a r-spp 1.13 r3.2.2_0 bioconda r-survival 2.38_3 r3.2.2_0a readline 7.0 ha6073c6_4 sambamba 0.6.5 0 bioconda samtools 1.2 2 bioconda scikit-learn 0.19.1 py27h445a80a_0 scipy 1.0.0 py27hf5f0f52_0 setuptools 36.5.0 py27h68b189e_0 simplejson 3.12.0 py27h264bab0_0 sip 4.18.1 py27he9ba0ab_2 six 1.4.1 py27_0 sqlite 3.20.1 hb898158_2 system 5.8 2 tk 8.6.7 hc745277_3 trim-galore 0.4.1 0 bioconda ucsc-bedclip 357 0 bioconda ucsc-bedgraphtobigwig 357 0 bioconda ucsc-bedtobigbed 357 0 bioconda ucsc-bigwigaverageoverbed 357 0 bioconda ucsc-bigwiginfo 357 0 bioconda ucsc-fetchchromsizes 357 0 bioconda ucsc-twobittofa 357 0 bioconda ucsc-wigtobigwig 357 0 bioconda wheel 0.30.0 py27h2bc6bb2_1 xz 5.2.3 h55aa19d_2 yaml 0.1.7 had09818_2 zlib 1.2.11 ha838bed_2 $ source deactivate

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/kundajelab/atac_dnase_pipelines/issues/86#issuecomment-353816549, or mute the thread https://github.com/notifications/unsubscribe-auth/AIOd_MP44OeBWAQCoyGyXNVwbffngFIYks5tDwdKgaJpZM4RKkmu .

tanpuekai commented 6 years ago

Hi Jin,

Thanks a lot. Do I need to update Samtools (appears to be 1.2 under this environment) as well?

Best Chan

leepc12 commented 6 years ago

No, you don't. Our pipeline is designed to use softwares installed in the Conda environment bds_atac and bds_atac_py3.

Jin

On Mon, Dec 25, 2017 at 12:19 AM, CHEN Peikai notifications@github.com wrote:

Hi Jin,

Thanks a lot. Do I need to update Samtools (appears to be 1.2 under this environment) as well?

Best Chan

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/kundajelab/atac_dnase_pipelines/issues/86#issuecomment-353847225, or mute the thread https://github.com/notifications/unsubscribe-auth/AIOd_PtgS4rIX9fNqUI2Qvire2nKQlngks5tD1p7gaJpZM4RKkmu .

tanpuekai commented 6 years ago

Hi Jin，

Thanks a lot. I have changed version of "six" to 1.10.0, and re-run the pipeline. See what happens in 10 hours (that is the time for my two samples).

BTW, is there a way I can directly just run the last two steps (i.e. atacqc) that failed in my earlier run of the pipeline? Rather than re-running whole pipeline and wait for 10 hours to get ATAQC?

Best Chan

leepc12 commented 6 years ago

If you use the same command line on the same working directory then you can resume pipelines from where it left off.

Jin

On Mon, Dec 25, 2017 at 12:28 AM, CHEN Peikai notifications@github.com wrote:

Hi Jin，

Thanks a lot. I have changed version of "six" to 1.10.0, and re-run the pipeline. See what happens in 10 hours (that is the time for my two samples).

BTW, is there a way I can directly just run the last two steps (i.e. atacqc) that failed in my earlier run of the pipeline? Rather than re-running whole pipeline and wait for 10 hours to get ATAQC?

Best Chan

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/kundajelab/atac_dnase_pipelines/issues/86#issuecomment-353848183, or mute the thread https://github.com/notifications/unsubscribe-auth/AIOd_JZt6sBANd5t_b_BjUwgF5ISxdUJks5tD1ywgaJpZM4RKkmu .

tanpuekai commented 6 years ago

Hi Jin,

Thanks so much.

It did re-run from where it last left off (which is a great feature), ie, the ATAQC step. And it seemed to move one step further, but unfortunately it then still produced errors, as below. The program is still running though.

Best Chan

    == Done naive_overlap()
    species_ataqc: mm10
    species_ataqc: mm10
    00:01:43.781    ExecutionerLocal 'Local[94]': Tasks [Local[94]]         Pending: 0      Running: 2      Done: 0 Failed: 0
                    | PID   | Task state        | Task name  | Dependencies | Task definition
                    | ----- | ----------------- | ---------- | ------------ | -------------------------------------------------------------------------------------------------------------------------------------------------------------------
                    | 11847 | running (RUNNING) | ataqc rep2 |              | if [ "${TMPDIR}" != "" ] && [ -d "${TMPDIR}" ]; then; fi; cd /PROJECT_DIR/out__Gpos/out_/qc/re
                    | 11853 | running (RUNNING) | ataqc rep1 |              | if [ "${TMPDIR}" != "" ] && [ -d "${TMPDIR}" ]; then; fi; cd /PROJECT_DIR/out__Gpos/out_/qc/re

    Picked up _JAVA_OPTIONS: -Xms256M -Xmx20G -XX:ParallelGCThreads=1
    Picked up _JAVA_OPTIONS: -Xms256M -Xmx20G -XX:ParallelGCThreads=1
    00:02:44.797    ExecutionerLocal 'Local[94]': Tasks [Local[94]]         Pending: 0      Running: 2      Done: 0 Failed: 0
                    | PID   | Task state        | Task name  | Dependencies | Task definition
                    | ----- | ----------------- | ---------- | ------------ | -------------------------------------------------------------------------------------------------------------------------------------------------------------------
                    | 11847 | running (RUNNING) | ataqc rep2 |              | if [ "${TMPDIR}" != "" ] && [ -d "${TMPDIR}" ]; then; fi; cd /PROJECT_DIR/out__Gpos/out_/qc/re
                    | 11853 | running (RUNNING) | ataqc rep1 |              | if [ "${TMPDIR}" != "" ] && [ -d "${TMPDIR}" ]; then; fi; cd /PROJECT_DIR/out__Gpos/out_/qc/re

    00:03:45.812    ExecutionerLocal 'Local[94]': Tasks [Local[94]]         Pending: 0      Running: 2      Done: 0 Failed: 0
                    | PID   | Task state        | Task name  | Dependencies | Task definition
                    | ----- | ----------------- | ---------- | ------------ | -------------------------------------------------------------------------------------------------------------------------------------------------------------------
                    | 11847 | running (RUNNING) | ataqc rep2 |              | if [ "${TMPDIR}" != "" ] && [ -d "${TMPDIR}" ]; then; fi; cd /PROJECT_DIR/out__Gpos/out_/qc/re
                    | 11853 | running (RUNNING) | ataqc rep1 |              | if [ "${TMPDIR}" != "" ] && [ -d "${TMPDIR}" ]; then; fi; cd /PROJECT_DIR/out__Gpos/out_/qc/re

    00:04:46.828    ExecutionerLocal 'Local[94]': Tasks [Local[94]]         Pending: 0      Running: 2      Done: 0 Failed: 0
                    | PID   | Task state        | Task name  | Dependencies | Task definition
                    | ----- | ----------------- | ---------- | ------------ | -------------------------------------------------------------------------------------------------------------------------------------------------------------------
                    | 11847 | running (RUNNING) | ataqc rep2 |              | if [ "${TMPDIR}" != "" ] && [ -d "${TMPDIR}" ]; then; fi; cd /PROJECT_DIR/out__Gpos/out_/qc/re
                    | 11853 | running (RUNNING) | ataqc rep1 |              | if [ "${TMPDIR}" != "" ] && [ -d "${TMPDIR}" ]; then; fi; cd /PROJECT_DIR/out__Gpos/out_/qc/re

    ERROR   2017-12-25 16:44:39     ProcessExecutor Warning messages:
    ERROR   2017-12-25 16:44:39     ProcessExecutor 1: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
    ERROR   2017-12-25 16:44:39     ProcessExecutor   zero-length arrow is of indeterminate angle and so skipped
    ERROR   2017-12-25 16:44:39     ProcessExecutor 2: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
    ERROR   2017-12-25 16:44:39     ProcessExecutor   zero-length arrow is of indeterminate angle and so skipped
    ERROR   2017-12-25 16:44:39     ProcessExecutor 3: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
    ERROR   2017-12-25 16:44:39     ProcessExecutor   zero-length arrow is of indeterminate angle and so skipped
    ERROR   2017-12-25 16:44:39     ProcessExecutor 4: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
    ERROR   2017-12-25 16:44:39     ProcessExecutor   zero-length arrow is of indeterminate angle and so skipped
    ERROR   2017-12-25 16:44:39     ProcessExecutor 5: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
    ERROR   2017-12-25 16:44:39     ProcessExecutor   zero-length arrow is of indeterminate angle and so skipped
    ERROR   2017-12-25 16:44:39     ProcessExecutor 6: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
    ERROR   2017-12-25 16:44:39     ProcessExecutor   zero-length arrow is of indeterminate angle and so skipped
    ERROR   2017-12-25 16:44:39     ProcessExecutor 7: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
    ERROR   2017-12-25 16:44:39     ProcessExecutor   zero-length arrow is of indeterminate angle and so skipped
    ERROR   2017-12-25 16:44:39     ProcessExecutor 8: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
    ERROR   2017-12-25 16:44:39     ProcessExecutor   zero-length arrow is of indeterminate angle and so skipped
    ERROR   2017-12-25 16:44:39     ProcessExecutor 9: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
    ERROR   2017-12-25 16:44:39     ProcessExecutor   zero-length arrow is of indeterminate angle and so skipped
    ERROR   2017-12-25 16:44:39     ProcessExecutor There were 11 warnings (use warnings() to see them)
    Picked up _JAVA_OPTIONS: -Xms256M -Xmx20G -XX:ParallelGCThreads=1
    Picked up _JAVA_OPTIONS: -Xms256M -Xmx20G -XX:ParallelGCThreads=1
    00:05:47.843    ExecutionerLocal 'Local[94]': Tasks [Local[94]]         Pending: 0      Running: 2      Done: 0 Failed: 0
                    | PID   | Task state        | Task name  | Dependencies | Task definition
                    | ----- | ----------------- | ---------- | ------------ | -------------------------------------------------------------------------------------------------------------------------------------------------------------------
                    | 11847 | running (RUNNING) | ataqc rep2 |              | if [ "${TMPDIR}" != "" ] && [ -d "${TMPDIR}" ]; then; fi; cd /PROJECT_DIR/out__Gpos/out_/qc/re
                    | 11853 | running (RUNNING) | ataqc rep1 |              | if [ "${TMPDIR}" != "" ] && [ -d "${TMPDIR}" ]; then; fi; cd /PROJECT_DIR/out__Gpos/out_/qc/re
leepc12 commented 6 years ago

They are not errors but warnings, you can simply ignore them.

tanpuekai commented 6 years ago

successfully resolved. thanks a lot. case closed.