Job ID = 11245202 sra ファイルのダウンロード中... Completed: 414774K bytes transferred in 8 seconds (381369K bits/sec), in 1 file. Completed: 233011K bytes transferred in 6 seconds (312895K 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... Read 2221877 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669655/SRR7818278.sra Written 2221877 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669655/SRR7818278.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669655/SRR7818277.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669655/SRR7818277.sra 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 fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:53 6221877 reads; of these: 6221877 (100.00%) were paired; of these: 700185 (11.25%) aligned concordantly 0 times 5057012 (81.28%) aligned concordantly exactly 1 time 464680 (7.47%) aligned concordantly >1 times ---- 700185 pairs aligned concordantly 0 times; of these: 78869 (11.26%) aligned discordantly 1 time ---- 621316 pairs aligned 0 times concordantly or discordantly; of these: 1242632 mates make up the pairs; of these: 1029971 (82.89%) aligned 0 times 157442 (12.67%) aligned exactly 1 time 55219 (4.44%) aligned >1 times 91.72% overall alignment rate Time searching: 00:05:53 Overall time: 00:05:53 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 44703 / 5575583 = 0.0080 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Tue, 09 Oct 2018 23:59:48: # Command line: callpeak -t SRX4669655.bam -f BAM -g 12100000 -n SRX4669655.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669655.10 # format = BAM # ChIP-seq file = ['SRX4669655.bam'] # control file = None # effective genome size = 1.21e+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 @ Tue, 09 Oct 2018 23:59:48: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:59:48: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:59:48: # Command line: callpeak -t SRX4669655.bam -f BAM -g 12100000 -n SRX4669655.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669655.05 # format = BAM # ChIP-seq file = ['SRX4669655.bam'] # control file = None # effective genome size = 1.21e+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, 09 Oct 2018 23:59:48: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:59:48: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:59:48: # Command line: callpeak -t SRX4669655.bam -f BAM -g 12100000 -n SRX4669655.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669655.20 # format = BAM # ChIP-seq file = ['SRX4669655.bam'] # control file = None # effective genome size = 1.21e+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, 09 Oct 2018 23:59:48: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:59:48: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:59:55: 1000000 INFO @ Tue, 09 Oct 2018 23:59:55: 1000000 INFO @ Tue, 09 Oct 2018 23:59:55: 1000000 INFO @ Wed, 10 Oct 2018 00:00:01: 2000000 INFO @ Wed, 10 Oct 2018 00:00:01: 2000000 INFO @ Wed, 10 Oct 2018 00:00:02: 2000000 INFO @ Wed, 10 Oct 2018 00:00:08: 3000000 INFO @ Wed, 10 Oct 2018 00:00:08: 3000000 INFO @ Wed, 10 Oct 2018 00:00:08: 3000000 INFO @ Wed, 10 Oct 2018 00:00:15: 4000000 INFO @ Wed, 10 Oct 2018 00:00:15: 4000000 INFO @ Wed, 10 Oct 2018 00:00:16: 4000000 INFO @ Wed, 10 Oct 2018 00:00:23: 5000000 INFO @ Wed, 10 Oct 2018 00:00:23: 5000000 INFO @ Wed, 10 Oct 2018 00:00:25: 5000000 INFO @ Wed, 10 Oct 2018 00:00:30: 6000000 INFO @ Wed, 10 Oct 2018 00:00:30: 6000000 INFO @ Wed, 10 Oct 2018 00:00:33: 6000000 INFO @ Wed, 10 Oct 2018 00:00:38: 7000000 INFO @ Wed, 10 Oct 2018 00:00:38: 7000000 INFO @ Wed, 10 Oct 2018 00:00:41: 7000000 INFO @ Wed, 10 Oct 2018 00:00:46: 8000000 INFO @ Wed, 10 Oct 2018 00:00:46: 8000000 INFO @ Wed, 10 Oct 2018 00:00:50: 8000000 INFO @ Wed, 10 Oct 2018 00:00:53: 9000000 INFO @ Wed, 10 Oct 2018 00:00:53: 9000000 INFO @ Wed, 10 Oct 2018 00:00:58: 9000000 INFO @ Wed, 10 Oct 2018 00:01:00: 10000000 INFO @ Wed, 10 Oct 2018 00:01:00: 10000000 INFO @ Wed, 10 Oct 2018 00:01:06: 10000000 INFO @ Wed, 10 Oct 2018 00:01:08: 11000000 INFO @ Wed, 10 Oct 2018 00:01:08: 11000000 INFO @ Wed, 10 Oct 2018 00:01:10: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:01:10: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:01:10: #1 total tags in treatment: 5477275 INFO @ Wed, 10 Oct 2018 00:01:10: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:01:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:01:10: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:01:10: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:01:10: #1 total tags in treatment: 5477275 INFO @ Wed, 10 Oct 2018 00:01:10: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:01:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:01:11: #1 tags after filtering in treatment: 4554673 INFO @ Wed, 10 Oct 2018 00:01:11: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 10 Oct 2018 00:01:11: #1 finished! INFO @ Wed, 10 Oct 2018 00:01:11: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:01:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:01:11: #1 tags after filtering in treatment: 4554673 INFO @ Wed, 10 Oct 2018 00:01:11: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 10 Oct 2018 00:01:11: #1 finished! INFO @ Wed, 10 Oct 2018 00:01:11: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:01:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:01:11: #2 number of paired peaks: 25 WARNING @ Wed, 10 Oct 2018 00:01:11: Too few paired peaks (25) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 10 Oct 2018 00:01:11: Process for pairing-model is terminated! cat: SRX4669655.05_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) rm: cannot remove `SRX4669655.05_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 `SRX4669655.05_*.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 `SRX4669655.05_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 INFO @ Wed, 10 Oct 2018 00:01:11: #2 number of paired peaks: 25 WARNING @ Wed, 10 Oct 2018 00:01:11: Too few paired peaks (25) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 10 Oct 2018 00:01:11: Process for pairing-model is terminated! cat: SRX4669655.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669655.10_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 `SRX4669655.10_*.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 `SRX4669655.10_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 INFO @ Wed, 10 Oct 2018 00:01:15: 11000000 INFO @ Wed, 10 Oct 2018 00:01:17: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:01:17: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:01:17: #1 total tags in treatment: 5477275 INFO @ Wed, 10 Oct 2018 00:01:17: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:01:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:01:18: #1 tags after filtering in treatment: 4554673 INFO @ Wed, 10 Oct 2018 00:01:18: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 10 Oct 2018 00:01:18: #1 finished! INFO @ Wed, 10 Oct 2018 00:01:18: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:01:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:01:18: #2 number of paired peaks: 25 WARNING @ Wed, 10 Oct 2018 00:01:18: Too few paired peaks (25) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 10 Oct 2018 00:01:18: Process for pairing-model is terminated! cat: SRX4669655.20_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669655.20_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 `SRX4669655.20_*.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 `SRX4669655.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。