Job ID = 11245219 sra ファイルのダウンロード中... Completed: 412310K bytes transferred in 8 seconds (397750K bits/sec), in 1 file. Completed: 413028K bytes transferred in 7 seconds (434624K bits/sec), in 1 file. Completed: 415413K bytes transferred in 7 seconds (473790K bits/sec), in 1 file. Completed: 9035K bytes transferred in 2 seconds (26026K 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 82679 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669668/SRR7818318.sra Written 82679 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669668/SRR7818318.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669668/SRR7818317.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669668/SRR7818317.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669668/SRR7818316.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669668/SRR7818316.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669668/SRR7818315.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669668/SRR7818315.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: 00:10:57 12082679 reads; of these: 12082679 (100.00%) were paired; of these: 1608836 (13.32%) aligned concordantly 0 times 9133044 (75.59%) aligned concordantly exactly 1 time 1340799 (11.10%) aligned concordantly >1 times ---- 1608836 pairs aligned concordantly 0 times; of these: 145902 (9.07%) aligned discordantly 1 time ---- 1462934 pairs aligned 0 times concordantly or discordantly; of these: 2925868 mates make up the pairs; of these: 2450673 (83.76%) aligned 0 times 341179 (11.66%) aligned exactly 1 time 134016 (4.58%) aligned >1 times 89.86% overall alignment rate Time searching: 00:10:57 Overall time: 00:10:57 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 12 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] 194665 / 10587481 = 0.0184 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 @ Wed, 10 Oct 2018 00:11:05: # Command line: callpeak -t SRX4669668.bam -f BAM -g 12100000 -n SRX4669668.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669668.10 # format = BAM # ChIP-seq file = ['SRX4669668.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 @ Wed, 10 Oct 2018 00:11:05: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:11:05: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:11:05: # Command line: callpeak -t SRX4669668.bam -f BAM -g 12100000 -n SRX4669668.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669668.20 # format = BAM # ChIP-seq file = ['SRX4669668.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 @ Wed, 10 Oct 2018 00:11:05: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:11:05: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:11:05: # Command line: callpeak -t SRX4669668.bam -f BAM -g 12100000 -n SRX4669668.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669668.05 # format = BAM # ChIP-seq file = ['SRX4669668.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 @ Wed, 10 Oct 2018 00:11:05: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:11:05: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:11:12: 1000000 INFO @ Wed, 10 Oct 2018 00:11:13: 1000000 INFO @ Wed, 10 Oct 2018 00:11:13: 1000000 INFO @ Wed, 10 Oct 2018 00:11:20: 2000000 INFO @ Wed, 10 Oct 2018 00:11:20: 2000000 INFO @ Wed, 10 Oct 2018 00:11:20: 2000000 INFO @ Wed, 10 Oct 2018 00:11:28: 3000000 INFO @ Wed, 10 Oct 2018 00:11:28: 3000000 INFO @ Wed, 10 Oct 2018 00:11:28: 3000000 INFO @ Wed, 10 Oct 2018 00:11:36: 4000000 INFO @ Wed, 10 Oct 2018 00:11:36: 4000000 INFO @ Wed, 10 Oct 2018 00:11:36: 4000000 INFO @ Wed, 10 Oct 2018 00:11:43: 5000000 INFO @ Wed, 10 Oct 2018 00:11:43: 5000000 INFO @ Wed, 10 Oct 2018 00:11:44: 5000000 INFO @ Wed, 10 Oct 2018 00:11:50: 6000000 INFO @ Wed, 10 Oct 2018 00:11:51: 6000000 INFO @ Wed, 10 Oct 2018 00:11:52: 6000000 INFO @ Wed, 10 Oct 2018 00:11:57: 7000000 INFO @ Wed, 10 Oct 2018 00:11:59: 7000000 INFO @ Wed, 10 Oct 2018 00:12:00: 7000000 INFO @ Wed, 10 Oct 2018 00:12:05: 8000000 INFO @ Wed, 10 Oct 2018 00:12:07: 8000000 INFO @ Wed, 10 Oct 2018 00:12:08: 8000000 INFO @ Wed, 10 Oct 2018 00:12:12: 9000000 INFO @ Wed, 10 Oct 2018 00:12:14: 9000000 INFO @ Wed, 10 Oct 2018 00:12:16: 9000000 INFO @ Wed, 10 Oct 2018 00:12:19: 10000000 INFO @ Wed, 10 Oct 2018 00:12:22: 10000000 INFO @ Wed, 10 Oct 2018 00:12:25: 10000000 INFO @ Wed, 10 Oct 2018 00:12:26: 11000000 INFO @ Wed, 10 Oct 2018 00:12:30: 11000000 INFO @ Wed, 10 Oct 2018 00:12:33: 11000000 INFO @ Wed, 10 Oct 2018 00:12:34: 12000000 INFO @ Wed, 10 Oct 2018 00:12:37: 12000000 INFO @ Wed, 10 Oct 2018 00:12:41: 12000000 INFO @ Wed, 10 Oct 2018 00:12:42: 13000000 INFO @ Wed, 10 Oct 2018 00:12:44: 13000000 INFO @ Wed, 10 Oct 2018 00:12:49: 13000000 INFO @ Wed, 10 Oct 2018 00:12:50: 14000000 INFO @ Wed, 10 Oct 2018 00:12:51: 14000000 INFO @ Wed, 10 Oct 2018 00:12:58: 14000000 INFO @ Wed, 10 Oct 2018 00:12:58: 15000000 INFO @ Wed, 10 Oct 2018 00:12:59: 15000000 INFO @ Wed, 10 Oct 2018 00:13:06: 16000000 INFO @ Wed, 10 Oct 2018 00:13:06: 15000000 INFO @ Wed, 10 Oct 2018 00:13:06: 16000000 INFO @ Wed, 10 Oct 2018 00:13:13: 17000000 INFO @ Wed, 10 Oct 2018 00:13:13: 17000000 INFO @ Wed, 10 Oct 2018 00:13:14: 16000000 INFO @ Wed, 10 Oct 2018 00:13:20: 18000000 INFO @ Wed, 10 Oct 2018 00:13:21: 18000000 INFO @ Wed, 10 Oct 2018 00:13:22: 17000000 INFO @ Wed, 10 Oct 2018 00:13:28: 19000000 INFO @ Wed, 10 Oct 2018 00:13:29: 19000000 INFO @ Wed, 10 Oct 2018 00:13:30: 18000000 INFO @ Wed, 10 Oct 2018 00:13:35: 20000000 INFO @ Wed, 10 Oct 2018 00:13:37: 20000000 INFO @ Wed, 10 Oct 2018 00:13:38: 19000000 INFO @ Wed, 10 Oct 2018 00:13:42: 21000000 INFO @ Wed, 10 Oct 2018 00:13:44: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:13:44: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:13:44: #1 total tags in treatment: 10280159 INFO @ Wed, 10 Oct 2018 00:13:44: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:13:44: #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 00:13:45: #1 tags after filtering in treatment: 7716553 INFO @ Wed, 10 Oct 2018 00:13:45: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 10 Oct 2018 00:13:45: #1 finished! INFO @ Wed, 10 Oct 2018 00:13:45: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:13:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:13:45: 21000000 INFO @ Wed, 10 Oct 2018 00:13:45: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:13:45: Too few paired peaks (0) 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 00:13:45: Process for pairing-model is terminated! cat: SRX4669668.05_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 `SRX4669668.05_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 `SRX4669668.05_*.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 `SRX4669668.05_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 00:13:46: 20000000 INFO @ Wed, 10 Oct 2018 00:13:47: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:13:47: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:13:47: #1 total tags in treatment: 10280159 INFO @ Wed, 10 Oct 2018 00:13:47: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:13:47: #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 00:13:47: #1 tags after filtering in treatment: 7716553 INFO @ Wed, 10 Oct 2018 00:13:47: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 10 Oct 2018 00:13:47: #1 finished! INFO @ Wed, 10 Oct 2018 00:13:47: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:13:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:13:48: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:13:48: Too few paired peaks (0) 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 00:13:48: Process for pairing-model is terminated! cat: SRX4669668.20_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): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669668.20_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 `SRX4669668.20_*.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 `SRX4669668.20_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 INFO @ Wed, 10 Oct 2018 00:13:54: 21000000 INFO @ Wed, 10 Oct 2018 00:13:56: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:13:56: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:13:56: #1 total tags in treatment: 10280159 INFO @ Wed, 10 Oct 2018 00:13:56: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:13:56: #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 00:13:56: #1 tags after filtering in treatment: 7716553 INFO @ Wed, 10 Oct 2018 00:13:56: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 10 Oct 2018 00:13:56: #1 finished! INFO @ Wed, 10 Oct 2018 00:13:56: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:13:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:13:57: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:13:57: Too few paired peaks (0) 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 00:13:57: Process for pairing-model is terminated! cat: SRX4669668.10_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 `SRX4669668.10_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 `SRX4669668.10_*.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 `SRX4669668.10_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。