Job ID = 9732063 sra ファイルのダウンロード中... Completed: 336121K bytes transferred in 8 seconds (310693K 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 15256564 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675863/SRR5380640.sra Written 15256564 spots total rm: cannot remove `[DSE]RR*.fastq': 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: 00:07:49 15256564 reads; of these: 15256564 (100.00%) were paired; of these: 3750627 (24.58%) aligned concordantly 0 times 10561163 (69.22%) aligned concordantly exactly 1 time 944774 (6.19%) aligned concordantly >1 times ---- 3750627 pairs aligned concordantly 0 times; of these: 1403143 (37.41%) aligned discordantly 1 time ---- 2347484 pairs aligned 0 times concordantly or discordantly; of these: 4694968 mates make up the pairs; of these: 3204461 (68.25%) aligned 0 times 1088297 (23.18%) aligned exactly 1 time 402210 (8.57%) aligned >1 times 89.50% overall alignment rate Time searching: 00:07:49 Overall time: 00:07:49 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] 1168266 / 12153405 = 0.0961 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 @ Sun, 03 Sep 2017 19:35:28: # Command line: callpeak -t SRX2675863.bam -f BAM -g 12100000 -n SRX2675863.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675863.05 # format = BAM # ChIP-seq file = ['SRX2675863.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 @ Sun, 03 Sep 2017 19:35:28: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:35:28: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:35:28: # Command line: callpeak -t SRX2675863.bam -f BAM -g 12100000 -n SRX2675863.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675863.10 # format = BAM # ChIP-seq file = ['SRX2675863.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 @ Sun, 03 Sep 2017 19:35:28: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:35:28: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:35:28: # Command line: callpeak -t SRX2675863.bam -f BAM -g 12100000 -n SRX2675863.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675863.20 # format = BAM # ChIP-seq file = ['SRX2675863.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 @ Sun, 03 Sep 2017 19:35:28: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:35:28: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:35:33: 1000000 INFO @ Sun, 03 Sep 2017 19:35:33: 1000000 INFO @ Sun, 03 Sep 2017 19:35:33: 1000000 INFO @ Sun, 03 Sep 2017 19:35:38: 2000000 INFO @ Sun, 03 Sep 2017 19:35:38: 2000000 INFO @ Sun, 03 Sep 2017 19:35:38: 2000000 INFO @ Sun, 03 Sep 2017 19:35:43: 3000000 INFO @ Sun, 03 Sep 2017 19:35:44: 3000000 INFO @ Sun, 03 Sep 2017 19:35:44: 3000000 INFO @ Sun, 03 Sep 2017 19:35:47: 4000000 INFO @ Sun, 03 Sep 2017 19:35:49: 4000000 INFO @ Sun, 03 Sep 2017 19:35:49: 4000000 INFO @ Sun, 03 Sep 2017 19:35:52: 5000000 INFO @ Sun, 03 Sep 2017 19:35:54: 5000000 INFO @ Sun, 03 Sep 2017 19:35:54: 5000000 INFO @ Sun, 03 Sep 2017 19:35:57: 6000000 INFO @ Sun, 03 Sep 2017 19:35:59: 6000000 INFO @ Sun, 03 Sep 2017 19:35:59: 6000000 INFO @ Sun, 03 Sep 2017 19:36:02: 7000000 INFO @ Sun, 03 Sep 2017 19:36:04: 7000000 INFO @ Sun, 03 Sep 2017 19:36:04: 7000000 INFO @ Sun, 03 Sep 2017 19:36:07: 8000000 INFO @ Sun, 03 Sep 2017 19:36:10: 8000000 INFO @ Sun, 03 Sep 2017 19:36:10: 8000000 INFO @ Sun, 03 Sep 2017 19:36:12: 9000000 INFO @ Sun, 03 Sep 2017 19:36:15: 9000000 INFO @ Sun, 03 Sep 2017 19:36:15: 9000000 INFO @ Sun, 03 Sep 2017 19:36:17: 10000000 INFO @ Sun, 03 Sep 2017 19:36:20: 10000000 INFO @ Sun, 03 Sep 2017 19:36:20: 10000000 INFO @ Sun, 03 Sep 2017 19:36:21: 11000000 INFO @ Sun, 03 Sep 2017 19:36:25: 11000000 INFO @ Sun, 03 Sep 2017 19:36:25: 11000000 INFO @ Sun, 03 Sep 2017 19:36:26: 12000000 INFO @ Sun, 03 Sep 2017 19:36:30: 12000000 INFO @ Sun, 03 Sep 2017 19:36:30: 12000000 INFO @ Sun, 03 Sep 2017 19:36:31: 13000000 INFO @ Sun, 03 Sep 2017 19:36:36: 13000000 INFO @ Sun, 03 Sep 2017 19:36:36: 13000000 INFO @ Sun, 03 Sep 2017 19:36:36: 14000000 INFO @ Sun, 03 Sep 2017 19:36:41: 15000000 INFO @ Sun, 03 Sep 2017 19:36:41: 14000000 INFO @ Sun, 03 Sep 2017 19:36:41: 14000000 INFO @ Sun, 03 Sep 2017 19:36:46: 16000000 INFO @ Sun, 03 Sep 2017 19:36:46: 15000000 INFO @ Sun, 03 Sep 2017 19:36:46: 15000000 INFO @ Sun, 03 Sep 2017 19:36:50: 17000000 INFO @ Sun, 03 Sep 2017 19:36:51: 16000000 INFO @ Sun, 03 Sep 2017 19:36:51: 16000000 INFO @ Sun, 03 Sep 2017 19:36:55: 18000000 INFO @ Sun, 03 Sep 2017 19:36:56: 17000000 INFO @ Sun, 03 Sep 2017 19:36:56: 17000000 INFO @ Sun, 03 Sep 2017 19:37:00: 19000000 INFO @ Sun, 03 Sep 2017 19:37:02: 18000000 INFO @ Sun, 03 Sep 2017 19:37:02: 18000000 INFO @ Sun, 03 Sep 2017 19:37:05: 20000000 INFO @ Sun, 03 Sep 2017 19:37:07: 19000000 INFO @ Sun, 03 Sep 2017 19:37:07: 19000000 INFO @ Sun, 03 Sep 2017 19:37:10: 21000000 INFO @ Sun, 03 Sep 2017 19:37:12: 20000000 INFO @ Sun, 03 Sep 2017 19:37:12: 20000000 INFO @ Sun, 03 Sep 2017 19:37:15: 22000000 INFO @ Sun, 03 Sep 2017 19:37:17: 21000000 INFO @ Sun, 03 Sep 2017 19:37:17: 21000000 INFO @ Sun, 03 Sep 2017 19:37:20: 23000000 INFO @ Sun, 03 Sep 2017 19:37:23: 22000000 INFO @ Sun, 03 Sep 2017 19:37:23: 22000000 INFO @ Sun, 03 Sep 2017 19:37:24: 24000000 INFO @ Sun, 03 Sep 2017 19:37:28: 23000000 INFO @ Sun, 03 Sep 2017 19:37:28: 23000000 INFO @ Sun, 03 Sep 2017 19:37:29: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:37:29: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:37:29: #1 total tags in treatment: 10344680 INFO @ Sun, 03 Sep 2017 19:37:29: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:37:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:37:29: #1 tags after filtering in treatment: 4615220 INFO @ Sun, 03 Sep 2017 19:37:29: #1 Redundant rate of treatment: 0.55 INFO @ Sun, 03 Sep 2017 19:37:29: #1 finished! INFO @ Sun, 03 Sep 2017 19:37:29: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:37:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:37:30: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:37:30: 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 @ Sun, 03 Sep 2017 19:37:30: Process for pairing-model is terminated! cat: SRX2675863.10_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): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675863.10_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 `SRX2675863.10_*.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 `SRX2675863.10_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 @ Sun, 03 Sep 2017 19:37:33: 24000000 INFO @ Sun, 03 Sep 2017 19:37:33: 24000000 INFO @ Sun, 03 Sep 2017 19:37:38: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:37:38: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:37:38: #1 total tags in treatment: 10344680 INFO @ Sun, 03 Sep 2017 19:37:38: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:37:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:37:38: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:37:38: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:37:38: #1 total tags in treatment: 10344680 INFO @ Sun, 03 Sep 2017 19:37:38: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:37:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:37:39: #1 tags after filtering in treatment: 4615220 INFO @ Sun, 03 Sep 2017 19:37:39: #1 Redundant rate of treatment: 0.55 INFO @ Sun, 03 Sep 2017 19:37:39: #1 finished! INFO @ Sun, 03 Sep 2017 19:37:39: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:37:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:37:39: #1 tags after filtering in treatment: 4615220 INFO @ Sun, 03 Sep 2017 19:37:39: #1 Redundant rate of treatment: 0.55 INFO @ Sun, 03 Sep 2017 19:37:39: #1 finished! INFO @ Sun, 03 Sep 2017 19:37:39: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:37:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:37:39: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:37:39: 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 @ Sun, 03 Sep 2017 19:37:39: Process for pairing-model is terminated! INFO @ Sun, 03 Sep 2017 19:37:39: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:37:39: 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 @ Sun, 03 Sep 2017 19:37:39: Process for pairing-model is terminated! cat: SRX2675863.20_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): 19 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) cat: SRX2675863.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません rm: cannot remove `SRX2675863.20_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 `SRX2675863.20_*.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 `SRX2675863.20_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 pass1 - making usageList (0 chroms): 24 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675863.05_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 `SRX2675863.05_*.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 `SRX2675863.05_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。