Job ID = 9157357 sra ファイルのダウンロード中... Completed: 1234836K bytes transferred in 13 seconds (765888K bits/sec), in 1 file, 2 directories. 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/SRX1010104/SRR1998060.sra Written 47790140 spots total fastq に変換しました。 bowtie でマッピング中... Warning: Could not open read file "SRX1010104_2.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: SRX1010104.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 @ Tue, 27 Jun 2017 11:30:28: # Command line: callpeak -t SRX1010104.bam -f BAM -g ce -n SRX1010104.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1010104.20 # format = BAM # ChIP-seq file = ['SRX1010104.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 @ Tue, 27 Jun 2017 11:30:28: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:30:28: #1 read treatment tags... Exception struct.error: 'unpack reqINFO @ Tue, 27 Jun 2017 11:30:28: # Command line: callpeak -t SRX1010104.bam -f BAM -g ce -n SRX1010104.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1010104.10 # format = BAM # ChIP-seq file = ['SRX1010104.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 uires a INFO @ Tue, 27 Jun 2017 11:30:28: #1 read tag files... string INFO @ Tue, 27 Jun 2017 11:30:28: #1 read treatment tags... argument of length 4' in 'MACS2.IO.Parser.BAMParser.tsize' ignored INFO @ Tue, 27 Jun 2017 11:30:28: #1 tag size is determined as 0 bps INFO @ Tue, 27 Jun 2017 11:30:28: #1 tag size = 0 Exception struct.error: INFO @ Tue, 27 Jun 2017 11:30:28: #1 total tags in treatment: 0 'unpacINFO @ Tue, 27 Jun 2017 11:30:28: #1 user defined the maximum tags... k requINFO @ Tue, 27 Jun 2017 11:30:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) ires INFO @ Tue, 27 Jun 2017 11:30:28: # Command line: callpeak -t SRX1010104.bam -f BAM -g ce -n SRX1010104.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1010104.05 # format = BAM # ChIP-seq file = ['SRX1010104.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 @ Tue, 27 Jun 2017 11:30:28: #1 tags after filtering in treatment: 0 a stTraceback (most recent call last): r File "/usr/local/bin/macs2", line 5, in iINFO @ Tue, 27 Jun 2017 11:30:28: #1 read tag files... n gpkg_resources.run_script('MACS2==2.1.1.20160309', 'macs2') INFO @ Tue, 27 Jun 2017 11:30:28: #1 read treatment tags... a File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 489, in run_script rgument of le File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 1214, in run_script ngth 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 4' in 'MACS2.IO.Parser.BAMParse r . 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 tsiz e File "build/bdist.linux-x86_64/egg/MACS2/callpeak_cmd.py", line 112, in run ' ignored ZeroDivisionError: float division by zero INFO @ Tue, 27 Jun 2017 11:30:28: #1 tag size is determined as 0 bps INFO @ Tue, 27 Jun 2017 11:30:28: #1 tag size = 0 INFO @ Tue, 27 Jun 2017 11:30:28: #1 total tags in treatment: 0 INFO @ Tue, 27 Jun 2017 11:30:28: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:30:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) Exception struct.error: 'INFO @ Tue, 27 Jun 2017 11:30:28: #1 tags after filtering in treatment: 0 unpaTraceback (most recent call last): c File "/usr/local/bin/macs2", line 5, in k r epkg_resources.run_script('MACS2==2.1.1.20160309', 'macs2') qu File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 489, in run_script ires a File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 1214, in run_script stri 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 ng argument of length 4' in 'M A CS 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 2.IO. P a File "build/bdist.linux-x86_64/egg/MACS2/callpeak_cmd.py", line 112, in run rser.ZeroDivisionErrorB: Afloat division by zeroM Parser.tsize' ignored INFO @ Tue, 27 Jun 2017 11:30:28: #1 tag size is determined as 0 bps INFO @ Tue, 27 Jun 2017 11:30:28: #1 tag size = 0 INFO @ Tue, 27 Jun 2017 11:30:28: #1 total tags in treatment: 0 INFO @ Tue, 27 Jun 2017 11:30:28: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:30:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:30:28: #1 tags after filtering in treatment: 0 Traceback (most recent call last): File "/usr/local/bin/macs2", line 5, in 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 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 57, in main File "build/bdist.linux-x86_64/egg/MACS2/callpeak_cmd.py", line 112, in run ZeroDivisionError: float division by zero cat: SRX1010104.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX1010104.10_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: SRX1010104.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1010104.20_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 `SRX1010104.20_*.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 `SRX1010104.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません rm: cannot remove `SRX1010104.10_model.r'CompletedMACS2peakCalling : 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 `SRX1010104.10_*.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 `SRX1010104.10_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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1010104.05_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 `SRX1010104.05_*.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 `SRX1010104.05_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