Job ID = 9161784 sra ファイルのダウンロード中... Completed: 1124973K bytes transferred in 16 seconds (571320K 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 25676031 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1044173/SRR2045654.sra Written 25676031 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:20:05 25676031 reads; of these: 25676031 (100.00%) were paired; of these: 3207895 (12.49%) aligned concordantly 0 times 18829681 (73.34%) aligned concordantly exactly 1 time 3638455 (14.17%) aligned concordantly >1 times ---- 3207895 pairs aligned concordantly 0 times; of these: 1069372 (33.34%) aligned discordantly 1 time ---- 2138523 pairs aligned 0 times concordantly or discordantly; of these: 4277046 mates make up the pairs; of these: 3250286 (75.99%) aligned 0 times 424684 (9.93%) aligned exactly 1 time 602076 (14.08%) aligned >1 times 93.67% overall alignment rate Time searching: 00:20:06 Overall time: 00:20:06 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 20 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] 1064122 / 22951855 = 0.0464 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, 28 Jun 2017 05:07:41: # Command line: callpeak -t SRX1044173.bam -f BAM -g 12100000 -n SRX1044173.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1044173.20 # format = BAM # ChIP-seq file = ['SRX1044173.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, 28 Jun 2017 05:07:41: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:07:41: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:07:41: # Command line: callpeak -t SRX1044173.bam -f BAM -g 12100000 -n SRX1044173.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1044173.10 # format = BAM # ChIP-seq file = ['SRX1044173.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, 28 Jun 2017 05:07:41: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:07:41: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:07:41: # Command line: callpeak -t SRX1044173.bam -f BAM -g 12100000 -n SRX1044173.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1044173.05 # format = BAM # ChIP-seq file = ['SRX1044173.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, 28 Jun 2017 05:07:41: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:07:41: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:07:48: 1000000 INFO @ Wed, 28 Jun 2017 05:07:48: 1000000 INFO @ Wed, 28 Jun 2017 05:07:48: 1000000 INFO @ Wed, 28 Jun 2017 05:07:55: 2000000 INFO @ Wed, 28 Jun 2017 05:07:55: 2000000 INFO @ Wed, 28 Jun 2017 05:07:55: 2000000 INFO @ Wed, 28 Jun 2017 05:08:02: 3000000 INFO @ Wed, 28 Jun 2017 05:08:02: 3000000 INFO @ Wed, 28 Jun 2017 05:08:02: 3000000 INFO @ Wed, 28 Jun 2017 05:08:08: 4000000 INFO @ Wed, 28 Jun 2017 05:08:09: 4000000 INFO @ Wed, 28 Jun 2017 05:08:09: 4000000 INFO @ Wed, 28 Jun 2017 05:08:15: 5000000 INFO @ Wed, 28 Jun 2017 05:08:16: 5000000 INFO @ Wed, 28 Jun 2017 05:08:16: 5000000 INFO @ Wed, 28 Jun 2017 05:08:24: 6000000 INFO @ Wed, 28 Jun 2017 05:08:24: 6000000 INFO @ Wed, 28 Jun 2017 05:08:24: 6000000 INFO @ Wed, 28 Jun 2017 05:08:32: 7000000 INFO @ Wed, 28 Jun 2017 05:08:33: 7000000 INFO @ Wed, 28 Jun 2017 05:08:33: 7000000 INFO @ Wed, 28 Jun 2017 05:08:41: 8000000 INFO @ Wed, 28 Jun 2017 05:08:41: 8000000 INFO @ Wed, 28 Jun 2017 05:08:41: 8000000 INFO @ Wed, 28 Jun 2017 05:08:49: 9000000 INFO @ Wed, 28 Jun 2017 05:08:49: 9000000 INFO @ Wed, 28 Jun 2017 05:08:50: 9000000 INFO @ Wed, 28 Jun 2017 05:08:57: 10000000 INFO @ Wed, 28 Jun 2017 05:08:57: 10000000 INFO @ Wed, 28 Jun 2017 05:08:58: 10000000 INFO @ Wed, 28 Jun 2017 05:09:06: 11000000 INFO @ Wed, 28 Jun 2017 05:09:06: 11000000 INFO @ Wed, 28 Jun 2017 05:09:07: 11000000 INFO @ Wed, 28 Jun 2017 05:09:14: 12000000 INFO @ Wed, 28 Jun 2017 05:09:14: 12000000 INFO @ Wed, 28 Jun 2017 05:09:15: 12000000 INFO @ Wed, 28 Jun 2017 05:09:22: 13000000 INFO @ Wed, 28 Jun 2017 05:09:22: 13000000 INFO @ Wed, 28 Jun 2017 05:09:24: 13000000 INFO @ Wed, 28 Jun 2017 05:09:30: 14000000 INFO @ Wed, 28 Jun 2017 05:09:30: 14000000 INFO @ Wed, 28 Jun 2017 05:09:33: 14000000 INFO @ Wed, 28 Jun 2017 05:09:36: 15000000 INFO @ Wed, 28 Jun 2017 05:09:36: 15000000 INFO @ Wed, 28 Jun 2017 05:09:40: 15000000 INFO @ Wed, 28 Jun 2017 05:09:43: 16000000 INFO @ Wed, 28 Jun 2017 05:09:43: 16000000 INFO @ Wed, 28 Jun 2017 05:09:46: 16000000 INFO @ Wed, 28 Jun 2017 05:09:50: 17000000 INFO @ Wed, 28 Jun 2017 05:09:50: 17000000 INFO @ Wed, 28 Jun 2017 05:09:53: 17000000 INFO @ Wed, 28 Jun 2017 05:09:57: 18000000 INFO @ Wed, 28 Jun 2017 05:09:57: 18000000 INFO @ Wed, 28 Jun 2017 05:10:00: 18000000 INFO @ Wed, 28 Jun 2017 05:10:04: 19000000 INFO @ Wed, 28 Jun 2017 05:10:04: 19000000 INFO @ Wed, 28 Jun 2017 05:10:06: 19000000 INFO @ Wed, 28 Jun 2017 05:10:10: 20000000 INFO @ Wed, 28 Jun 2017 05:10:10: 20000000 INFO @ Wed, 28 Jun 2017 05:10:13: 20000000 INFO @ Wed, 28 Jun 2017 05:10:17: 21000000 INFO @ Wed, 28 Jun 2017 05:10:17: 21000000 INFO @ Wed, 28 Jun 2017 05:10:20: 21000000 INFO @ Wed, 28 Jun 2017 05:10:24: 22000000 INFO @ Wed, 28 Jun 2017 05:10:24: 22000000 INFO @ Wed, 28 Jun 2017 05:10:26: 22000000 INFO @ Wed, 28 Jun 2017 05:10:31: 23000000 INFO @ Wed, 28 Jun 2017 05:10:31: 23000000 INFO @ Wed, 28 Jun 2017 05:10:33: 23000000 INFO @ Wed, 28 Jun 2017 05:10:37: 24000000 INFO @ Wed, 28 Jun 2017 05:10:37: 24000000 INFO @ Wed, 28 Jun 2017 05:10:40: 24000000 INFO @ Wed, 28 Jun 2017 05:10:44: 25000000 INFO @ Wed, 28 Jun 2017 05:10:44: 25000000 INFO @ Wed, 28 Jun 2017 05:10:46: 25000000 INFO @ Wed, 28 Jun 2017 05:10:51: 26000000 INFO @ Wed, 28 Jun 2017 05:10:51: 26000000 INFO @ Wed, 28 Jun 2017 05:10:53: 26000000 INFO @ Wed, 28 Jun 2017 05:10:58: 27000000 INFO @ Wed, 28 Jun 2017 05:10:58: 27000000 INFO @ Wed, 28 Jun 2017 05:11:00: 27000000 INFO @ Wed, 28 Jun 2017 05:11:05: 28000000 INFO @ Wed, 28 Jun 2017 05:11:05: 28000000 INFO @ Wed, 28 Jun 2017 05:11:06: 28000000 INFO @ Wed, 28 Jun 2017 05:11:11: 29000000 INFO @ Wed, 28 Jun 2017 05:11:11: 29000000 INFO @ Wed, 28 Jun 2017 05:11:13: 29000000 INFO @ Wed, 28 Jun 2017 05:11:18: 30000000 INFO @ Wed, 28 Jun 2017 05:11:18: 30000000 INFO @ Wed, 28 Jun 2017 05:11:19: 30000000 INFO @ Wed, 28 Jun 2017 05:11:25: 31000000 INFO @ Wed, 28 Jun 2017 05:11:25: 31000000 INFO @ Wed, 28 Jun 2017 05:11:26: 31000000 INFO @ Wed, 28 Jun 2017 05:11:32: 32000000 INFO @ Wed, 28 Jun 2017 05:11:32: 32000000 INFO @ Wed, 28 Jun 2017 05:11:33: 32000000 INFO @ Wed, 28 Jun 2017 05:11:38: 33000000 INFO @ Wed, 28 Jun 2017 05:11:38: 33000000 INFO @ Wed, 28 Jun 2017 05:11:39: 33000000 INFO @ Wed, 28 Jun 2017 05:11:45: 34000000 INFO @ Wed, 28 Jun 2017 05:11:45: 34000000 INFO @ Wed, 28 Jun 2017 05:11:46: 34000000 INFO @ Wed, 28 Jun 2017 05:11:52: 35000000 INFO @ Wed, 28 Jun 2017 05:11:52: 35000000 INFO @ Wed, 28 Jun 2017 05:11:53: 35000000 INFO @ Wed, 28 Jun 2017 05:11:58: 36000000 INFO @ Wed, 28 Jun 2017 05:11:58: 36000000 INFO @ Wed, 28 Jun 2017 05:12:00: 36000000 INFO @ Wed, 28 Jun 2017 05:12:05: 37000000 INFO @ Wed, 28 Jun 2017 05:12:05: 37000000 INFO @ Wed, 28 Jun 2017 05:12:06: 37000000 INFO @ Wed, 28 Jun 2017 05:12:12: 38000000 INFO @ Wed, 28 Jun 2017 05:12:12: 38000000 INFO @ Wed, 28 Jun 2017 05:12:13: 38000000 INFO @ Wed, 28 Jun 2017 05:12:18: 39000000 INFO @ Wed, 28 Jun 2017 05:12:18: 39000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 28 Jun 2017 05:12:20: 39000000 INFO @ Wed, 28 Jun 2017 05:12:25: 40000000 INFO @ Wed, 28 Jun 2017 05:12:25: 40000000 INFO @ Wed, 28 Jun 2017 05:12:27: 40000000 INFO @ Wed, 28 Jun 2017 05:12:32: 41000000 INFO @ Wed, 28 Jun 2017 05:12:32: 41000000 INFO @ Wed, 28 Jun 2017 05:12:34: 41000000 INFO @ Wed, 28 Jun 2017 05:12:39: 42000000 INFO @ Wed, 28 Jun 2017 05:12:39: 42000000 INFO @ Wed, 28 Jun 2017 05:12:41: 42000000 BigWig に変換しました。 INFO @ Wed, 28 Jun 2017 05:12:46: 43000000 INFO @ Wed, 28 Jun 2017 05:12:46: 43000000 INFO @ Wed, 28 Jun 2017 05:12:48: 43000000 INFO @ Wed, 28 Jun 2017 05:12:53: 44000000 INFO @ Wed, 28 Jun 2017 05:12:53: 44000000 INFO @ Wed, 28 Jun 2017 05:12:55: 44000000 INFO @ Wed, 28 Jun 2017 05:13:00: 45000000 INFO @ Wed, 28 Jun 2017 05:13:00: 45000000 INFO @ Wed, 28 Jun 2017 05:13:01: 45000000 INFO @ Wed, 28 Jun 2017 05:13:07: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:13:07: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:13:07: #1 total tags in treatment: 21412594 INFO @ Wed, 28 Jun 2017 05:13:07: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:13:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:13:07: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:13:07: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:13:07: #1 total tags in treatment: 21412594 INFO @ Wed, 28 Jun 2017 05:13:07: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:13:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:13:07: #1 tags after filtering in treatment: 12686477 INFO @ Wed, 28 Jun 2017 05:13:07: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 28 Jun 2017 05:13:07: #1 finished! INFO @ Wed, 28 Jun 2017 05:13:07: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:13:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:13:07: #1 tags after filtering in treatment: 12686477 INFO @ Wed, 28 Jun 2017 05:13:07: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 28 Jun 2017 05:13:07: #1 finished! INFO @ Wed, 28 Jun 2017 05:13:07: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:13:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:13:08: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:13:08: 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, 28 Jun 2017 05:13:08: Process for pairing-model is terminated! cat: SRX1044173.05_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 `SRX1044173.05_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 `SRX1044173.05_*.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 `SRX1044173.05_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, 28 Jun 2017 05:13:08: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:13:08: 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, 28 Jun 2017 05:13:08: Process for pairing-model is terminated! cat: SRX1044173.10_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 `SRX1044173.10_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 `SRX1044173.10_*.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 `SRX1044173.10_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, 28 Jun 2017 05:13:08: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:13:08: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:13:08: #1 total tags in treatment: 21412594 INFO @ Wed, 28 Jun 2017 05:13:08: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:13:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:13:09: #1 tags after filtering in treatment: 12686477 INFO @ Wed, 28 Jun 2017 05:13:09: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 28 Jun 2017 05:13:09: #1 finished! INFO @ Wed, 28 Jun 2017 05:13:09: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:13:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:13:10: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:13:10: 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, 28 Jun 2017 05:13:10: Process for pairing-model is terminated! cat: SRX1044173.20_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 `SRX1044173.20_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 `SRX1044173.20_*.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 `SRX1044173.20_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