Job ID = 6626451 SRX = ERX402113 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 9474305 READS because READLEN < 1 Read 9474305 spots for ERR435842/ERR435842.sra Written 9474305 spots for ERR435842/ERR435842.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626567 ("srTdm6") has been submitted Warning: Could not open read file "ERX402113_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: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted BAM に変換しました。 Bed ファイルを作成中... [33mWARNING:[0m Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:03:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX402113/ERX402113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX402113/ERX402113.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX402113/ERX402113.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX402113/ERX402113.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 14 Jul 2020 07:03:58: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:03:58: #1 read treatment tags... Exception struct.error: 'unpack requires a string argument of length 4' in 'MACS2.IO.Parser.BAMParser.tsize' ignored INFO @ Tue, 14 Jul 2020 07:03:58: #1 tag size is determined as 0 bps INFO @ Tue, 14 Jul 2020 07:03:58: #1 tag size = 0 INFO @ Tue, 14 Jul 2020 07:03:58: #1 total tags in treatment: 0 INFO @ Tue, 14 Jul 2020 07:03:58: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:03:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:03:58: #1 tags after filtering in treatment: 0 Traceback (most recent call last): File "/usr/local/bin/macs2", line 4, in __import__('pkg_resources').run_script('MACS2==2.1.1.20160309', 'macs2') File "/usr/local/lib/python2.7/site-packages/setuptools-20.7.0-py2.7.egg/pkg_resources/__init__.py", line 719, in run_script File "/usr/local/lib/python2.7/site-packages/setuptools-20.7.0-py2.7.egg/pkg_resources/__init__.py", line 1511, 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 "/usr/local/lib/python2.7/site-packages/MACS2-2.1.1.20160309-py2.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 112, in run ZeroDivisionError: float division by zero cut: /home/okishinya/chipatlas/results/dm3/ERX402113/ERX402113.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/ERX402113/ERX402113.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/ERX402113/ERX402113.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/ERX402113/ERX402113.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling [33mWARNING:[0m Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:04:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX402113/ERX402113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX402113/ERX402113.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX402113/ERX402113.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX402113/ERX402113.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 14 Jul 2020 07:04:28: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:04:28: #1 read treatment tags... Exception struct.error: 'unpack requires a string argument of length 4' in 'MACS2.IO.Parser.BAMParser.tsize' ignored INFO @ Tue, 14 Jul 2020 07:04:28: #1 tag size is determined as 0 bps INFO @ Tue, 14 Jul 2020 07:04:28: #1 tag size = 0 INFO @ Tue, 14 Jul 2020 07:04:28: #1 total tags in treatment: 0 INFO @ Tue, 14 Jul 2020 07:04:28: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:04:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:04:28: #1 tags after filtering in treatment: 0 Traceback (most recent call last): File "/usr/local/bin/macs2", line 4, in __import__('pkg_resources').run_script('MACS2==2.1.1.20160309', 'macs2') File "/usr/local/lib/python2.7/site-packages/setuptools-20.7.0-py2.7.egg/pkg_resources/__init__.py", line 719, in run_script File "/usr/local/lib/python2.7/site-packages/setuptools-20.7.0-py2.7.egg/pkg_resources/__init__.py", line 1511, 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 "/usr/local/lib/python2.7/site-packages/MACS2-2.1.1.20160309-py2.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 112, in run ZeroDivisionError: float division by zero cut: /home/okishinya/chipatlas/results/dm3/ERX402113/ERX402113.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/ERX402113/ERX402113.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/ERX402113/ERX402113.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/ERX402113/ERX402113.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換中... *****ERROR: Unrecognized parameter: ERX402113.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。 [33mWARNING:[0m Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:04:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX402113/ERX402113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX402113/ERX402113.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX402113/ERX402113.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX402113/ERX402113.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 14 Jul 2020 07:04:58: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:04:58: #1 read treatment tags... Exception struct.error: 'unpack requires a string argument of length 4' in 'MACS2.IO.Parser.BAMParser.tsize' ignored INFO @ Tue, 14 Jul 2020 07:04:58: #1 tag size is determined as 0 bps INFO @ Tue, 14 Jul 2020 07:04:58: #1 tag size = 0 INFO @ Tue, 14 Jul 2020 07:04:58: #1 total tags in treatment: 0 INFO @ Tue, 14 Jul 2020 07:04:58: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:04:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:04:58: #1 tags after filtering in treatment: 0 Traceback (most recent call last): File "/usr/local/bin/macs2", line 4, in __import__('pkg_resources').run_script('MACS2==2.1.1.20160309', 'macs2') File "/usr/local/lib/python2.7/site-packages/setuptools-20.7.0-py2.7.egg/pkg_resources/__init__.py", line 719, in run_script File "/usr/local/lib/python2.7/site-packages/setuptools-20.7.0-py2.7.egg/pkg_resources/__init__.py", line 1511, 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 "/usr/local/lib/python2.7/site-packages/MACS2-2.1.1.20160309-py2.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 112, in run ZeroDivisionError: float division by zero cut: /home/okishinya/chipatlas/results/dm3/ERX402113/ERX402113.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/ERX402113/ERX402113.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/ERX402113/ERX402113.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/ERX402113/ERX402113.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling