Job ID = 10196135 sra ファイルのダウンロード中... Completed: 1245134K bytes transferred in 22 seconds (448712K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Written 47790140 spots for /home/okishinya/chipatlas/results/ce10/SRX1010105/SRR1998061.sra Written 47790140 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません ls: cannot access SRX1010105_1.fq: そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Warning: Could not open read file "SRX1010105_1.fq" for reading; skipping... Error: No input read files were valid (ERR): bowtie2-align exited with value 1 マッピングが完了しました。 samtools でBAM に変換中... [samopen] no @SQ lines in the header. [sam_read1] missing header? Abort! [bam_header_read] EOF marker is absent. The input is probably truncated. awk: コマンドライン:1: (FILENAME=- FNR=1) 致命的: ゼロによる除算が試みられました awk: コマンドライン:1: (FILENAME=- FNR=1) 致命的: ゼロによる除算が試みられました awk: コマンドライン:1: (FILENAME=- FNR=1) 致命的: ゼロによる除算が試みられました BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... *****ERROR: Unrecognized parameter: SRX1010105.bam ***** Tool: bedtools genomecov (aka genomeCoverageBed) Version: v2.17.0 Summary: Compute the coverage of a feature file among a genome. Usage: bedtools genomecov [OPTIONS] -i -g Options: -ibam The input file is in BAM format. Note: BAM _must_ be sorted by position -d Report the depth at each genome position (with one-based coordinates). Default behavior is to report a histogram. -dz Report the depth at each genome position (with zero-based coordinates). Reports only non-zero positions. Default behavior is to report a histogram. -bg Report depth in BedGraph format. For details, see: genome.ucsc.edu/goldenPath/help/bedgraph.html -bga Report depth in BedGraph format, as above (-bg). However with this option, regions with zero coverage are also reported. This allows one to quickly extract all regions of a genome with 0 coverage by applying: "grep -w 0$" to the output. -split Treat "split" BAM or BED12 entries as distinct BED intervals. when computing coverage. For BAM files, this uses the CIGAR "N" and "D" operations to infer the blocks for computing coverage. For BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). -strand Calculate coverage of intervals from a specific strand. With BED files, requires at least 6 columns (strand is column 6). - (STRING): can be + or - -5 Calculate coverage of 5" positions (instead of entire interval). -3 Calculate coverage of 3" positions (instead of entire interval). -max Combine all positions with a depth >= max into a single bin in the histogram. Irrelevant for -d and -bedGraph - (INTEGER) -scale Scale the coverage by a constant factor. Each coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM). - Default is 1.0; i.e., unscaled. - (FLOAT) -trackline Adds a UCSC/Genome-Browser track line definition in the first line of the output. - See here for more details about track line definition: http://genome.ucsc.edu/goldenPath/help/bedgraph.html - NOTE: When adding a trackline definition, the output BedGraph can be easily uploaded to the Genome Browser as a custom track, BUT CAN NOT be converted into a BigWig file (w/o removing the first line). -trackopts Writes additional track line definition parameters in the first line. - Example: -trackopts 'name="My Track" visibility=2 color=255,30,30' Note the use of single-quotes if you have spaces in your parameters. - (TEXT) Notes: (1) The genome file should tab delimited and structured as follows: For example, Human (hg19): chr1 249250621 chr2 243199373 ... chr18_gl000207_random 4262 (2) The input BED (-i) file must be grouped by chromosome. A simple "sort -k 1,1 > .sorted" will suffice. (3) The input BAM (-ibam) file must be sorted by position. A "samtools sort " should suffice. Tips: One can use the UCSC Genome Browser's MySQL database to extract chromosome sizes. For example, H. sapiens: mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \ "select chrom, size from hg19.chromInfo" > hg19.genome BedGraph に変換しました。 BigWig に変換中... needLargeMem: trying to allocate 0 bytes (limit: 100000000000) BigWig に変換しました。 INFO @ Sat, 11 Nov 2017 14:03:10: # Command line: callpeak -t SRX1010105.bam -f BAM -g ce -n SRX1010105.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1010105.05 # format = BAM # ChIP-seq file = ['SRX1010105.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 11 Nov 2017 14:03:10: # Command line: callpeak -t SRX1010105.bam -f BAM -g ce -n SRX1010105.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1010105.10 # format = BAM # ChIP-seq file = ['SRX1010105.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 11 Nov 2017 14:03:10: # Command line: callpeak -t SRX1010105.bam -f BAM -g ce -n SRX1010105.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1010105.20 # format = BAM # ChIP-seq file = ['SRX1010105.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 11 Nov 2017 14:03:10: #1 read tag files... INFO @ Sat, 11 Nov 2017 14:03:10: #1 read tag files... INFO @ Sat, 11 Nov 2017 14:03:10: #1 read tag files... INFO @ Sat, 11 Nov 2017 14:03:10: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 14:03:10: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 14:03:10: #1 read treatment tags... Exception Exception structException .structerror.: error': u'nupnapcakc kr erqeuqiurierse sa as tsrtirnign gastructr.gerror: 'aurngpuamcekn tr eoqfu ilreensg tah s4t'r in i'nMgA CaSr2g.uImOe.nPta rosfe rl.eBnAgMtPha r4s'e in r'.MtAsCiSuzmee'n ignored t2 .oIf lOe.nPgatrhs e4r'. in B'AMMAPCaSr2s.eIrO..tPsairzes'e ignored r.BAMParser.tsize' ignored INFO @ Sat, 11 Nov 2017 14:03:10: #1 tag size is determined as 0 bps INFO @ Sat, 11 Nov 2017 14:03:10: #1 tag size is determined as 0 bps INFO @ Sat, 11 Nov 2017 14:03:10: #1 tag size = 0 INFO @ Sat, 11 Nov 2017 14:03:10: #1 tag size is determined as 0 bps INFO @ Sat, 11 Nov 2017 14:03:10: #1 tag size = 0 INFO @ Sat, 11 Nov 2017 14:03:10: #1 total tags in treatment: 0 INFO @ Sat, 11 Nov 2017 14:03:10: #1 tag size = 0 INFO @ Sat, 11 Nov 2017 14:03:10: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 14:03:10: #1 total tags in treatment: 0 INFO @ Sat, 11 Nov 2017 14:03:10: #1 total tags in treatment: 0 INFO @ Sat, 11 Nov 2017 14:03:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 14:03:10: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 14:03:10: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 14:03:10: #1 tags after filtering in treatment: 0 INFO @ Sat, 11 Nov 2017 14:03:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) Traceback (most recent call last): INFO @ Sat, 11 Nov 2017 14:03:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) File "/usr/local/bin/macs2", line 5, in INFO @ Sat, 11 Nov 2017 14:03:10: #1 tags after filtering in treatment: 0 INFO @ Sat, 11 Nov 2017 14:03:10: #1 tags after filtering in treatment: 0 pkg_resources.run_script('MACS2==2.1.1.20160309', 'macs2') Traceback (most recent call last): Traceback (most recent call last): File "/usr/local/bin/macs2", line 5, in File "/usr/local/bin/macs2", line 5, in File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 489, in run_script pkg_resources.run_script('MACS2==2.1.1.20160309', 'macs2') pkg_resources.run_script('MACS2==2.1.1.20160309', 'macs2') File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 489, in run_script File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 489, in run_script File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 1214, in run_script File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 1214, in run_script File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 1214, in run_script File "/usr/local/lib/python2.7/site-packages/MACS2-2.1.1.20160309-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 617, in File "/usr/local/lib/python2.7/site-packages/MACS2-2.1.1.20160309-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 617, in File "/usr/local/lib/python2.7/site-packages/MACS2-2.1.1.20160309-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 617, in File "/usr/local/lib/python2.7/site-packages/MACS2-2.1.1.20160309-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 57, in main File "build/bdist.linux-x86_64/egg/MACS2/callpeak_cmd.py", line 112, in run File "/usr/local/lib/python2.7/site-packages/MACS2-2.1.1.20160309-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 57, in main File "/usr/local/lib/python2.7/site-packages/MACS2-2.1.1.20160309-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 57, in main ZeroDivisionError: float division by zero File "build/bdist.linux-x86_64/egg/MACS2/callpeak_cmd.py", line 112, in run File "build/bdist.linux-x86_64/egg/MACS2/callpeak_cmd.py", line 112, in run ZeroDivisionErrorZeroDivisionError: : float division by zerofloat division by zero cat: SRX1010105.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX1010105.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX1010105.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1010105.20_model.r'pass1 - making usageList (0 chroms): 2 millis : そのようなファイルやディレクトリはありません rm: cannot remove `SRX1010105.20_*.xls': そのようなファイルやディレクトリはありません rm: cannot remove `SRX1010105.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 5 millis CompletedMACS2peakCalling needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1010105.10_model.r': そのようなファイルやディレクトリはありません rm: cannot remove `SRX1010105.10_*.xls': そのようなファイルやディレクトリはありません rm: cannot remove `SRX1010105.10_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling rm: cannot remove `SRX1010105.05_model.r': そのようなファイルやディレクトリはありません rm: cannot remove `SRX1010105.05_*.xls': そのようなファイルやディレクトリはありません rm: cannot remove `SRX1010105.05_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling