Job ID = 10714517 sra ファイルのダウンロード中... Completed: 2553037K bytes transferred in 33 seconds (627967K 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 37159439 spots for /home/okishinya/chipatlas/results/ce10/SRX4085431/SRR7167460.sra Written 37159439 spots for /home/okishinya/chipatlas/results/ce10/SRX4085431/SRR7167460.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 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: 00:36:53 37159439 reads; of these: 37159439 (100.00%) were paired; of these: 1928872 (5.19%) aligned concordantly 0 times 30833791 (82.98%) aligned concordantly exactly 1 time 4396776 (11.83%) aligned concordantly >1 times ---- 1928872 pairs aligned concordantly 0 times; of these: 380151 (19.71%) aligned discordantly 1 time ---- 1548721 pairs aligned 0 times concordantly or discordantly; of these: 3097442 mates make up the pairs; of these: 1870901 (60.40%) aligned 0 times 932911 (30.12%) aligned exactly 1 time 293630 (9.48%) aligned >1 times 97.48% overall alignment rate Time searching: 00:36:53 Overall time: 00:36:53 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 32 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 chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 3282129 / 35454788 = 0.0926 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 Jun 2018 14:05:54: # Command line: callpeak -t SRX4085431.bam -f BAM -g ce -n SRX4085431.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085431.20 # format = BAM # ChIP-seq file = ['SRX4085431.bam'] # control file = None # effective genome size = 9.00e+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 Jun 2018 14:05:54: # Command line: callpeak -t SRX4085431.bam -f BAM -g ce -n SRX4085431.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085431.10 # format = BAM # ChIP-seq file = ['SRX4085431.bam'] # control file = None # effective genome size = 9.00e+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 Jun 2018 14:05:54: # Command line: callpeak -t SRX4085431.bam -f BAM -g ce -n SRX4085431.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085431.05 # format = BAM # ChIP-seq file = ['SRX4085431.bam'] # control file = None # effective genome size = 9.00e+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 Jun 2018 14:05:54: #1 read tag files... INFO @ Sun, 03 Jun 2018 14:05:54: #1 read tag files... INFO @ Sun, 03 Jun 2018 14:05:54: #1 read tag files... INFO @ Sun, 03 Jun 2018 14:05:54: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 14:05:54: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 14:05:54: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 14:05:59: 1000000 INFO @ Sun, 03 Jun 2018 14:05:59: 1000000 INFO @ Sun, 03 Jun 2018 14:06:00: 1000000 INFO @ Sun, 03 Jun 2018 14:06:05: 2000000 INFO @ Sun, 03 Jun 2018 14:06:05: 2000000 INFO @ Sun, 03 Jun 2018 14:06:05: 2000000 INFO @ Sun, 03 Jun 2018 14:06:10: 3000000 INFO @ Sun, 03 Jun 2018 14:06:10: 3000000 INFO @ Sun, 03 Jun 2018 14:06:11: 3000000 INFO @ Sun, 03 Jun 2018 14:06:16: 4000000 INFO @ Sun, 03 Jun 2018 14:06:16: 4000000 INFO @ Sun, 03 Jun 2018 14:06:17: 4000000 INFO @ Sun, 03 Jun 2018 14:06:21: 5000000 INFO @ Sun, 03 Jun 2018 14:06:22: 5000000 INFO @ Sun, 03 Jun 2018 14:06:23: 5000000 INFO @ Sun, 03 Jun 2018 14:06:27: 6000000 INFO @ Sun, 03 Jun 2018 14:06:27: 6000000 INFO @ Sun, 03 Jun 2018 14:06:29: 6000000 INFO @ Sun, 03 Jun 2018 14:06:32: 7000000 INFO @ Sun, 03 Jun 2018 14:06:33: 7000000 INFO @ Sun, 03 Jun 2018 14:06:35: 7000000 INFO @ Sun, 03 Jun 2018 14:06:38: 8000000 INFO @ Sun, 03 Jun 2018 14:06:38: 8000000 INFO @ Sun, 03 Jun 2018 14:06:40: 8000000 INFO @ Sun, 03 Jun 2018 14:06:43: 9000000 INFO @ Sun, 03 Jun 2018 14:06:44: 9000000 INFO @ Sun, 03 Jun 2018 14:06:46: 9000000 INFO @ Sun, 03 Jun 2018 14:06:49: 10000000 INFO @ Sun, 03 Jun 2018 14:06:49: 10000000 INFO @ Sun, 03 Jun 2018 14:06:52: 10000000 INFO @ Sun, 03 Jun 2018 14:06:54: 11000000 INFO @ Sun, 03 Jun 2018 14:06:55: 11000000 INFO @ Sun, 03 Jun 2018 14:06:57: 11000000 INFO @ Sun, 03 Jun 2018 14:07:00: 12000000 INFO @ Sun, 03 Jun 2018 14:07:00: 12000000 INFO @ Sun, 03 Jun 2018 14:07:03: 12000000 INFO @ Sun, 03 Jun 2018 14:07:05: 13000000 INFO @ Sun, 03 Jun 2018 14:07:06: 13000000 INFO @ Sun, 03 Jun 2018 14:07:09: 13000000 INFO @ Sun, 03 Jun 2018 14:07:11: 14000000 INFO @ Sun, 03 Jun 2018 14:07:11: 14000000 INFO @ Sun, 03 Jun 2018 14:07:14: 14000000 INFO @ Sun, 03 Jun 2018 14:07:16: 15000000 INFO @ Sun, 03 Jun 2018 14:07:17: 15000000 INFO @ Sun, 03 Jun 2018 14:07:20: 15000000 INFO @ Sun, 03 Jun 2018 14:07:22: 16000000 INFO @ Sun, 03 Jun 2018 14:07:22: 16000000 INFO @ Sun, 03 Jun 2018 14:07:26: 16000000 INFO @ Sun, 03 Jun 2018 14:07:27: 17000000 INFO @ Sun, 03 Jun 2018 14:07:28: 17000000 INFO @ Sun, 03 Jun 2018 14:07:31: 17000000 INFO @ Sun, 03 Jun 2018 14:07:33: 18000000 INFO @ Sun, 03 Jun 2018 14:07:33: 18000000 INFO @ Sun, 03 Jun 2018 14:07:37: 18000000 INFO @ Sun, 03 Jun 2018 14:07:38: 19000000 INFO @ Sun, 03 Jun 2018 14:07:38: 19000000 INFO @ Sun, 03 Jun 2018 14:07:42: 19000000 INFO @ Sun, 03 Jun 2018 14:07:44: 20000000 INFO @ Sun, 03 Jun 2018 14:07:44: 20000000 INFO @ Sun, 03 Jun 2018 14:07:48: 20000000 INFO @ Sun, 03 Jun 2018 14:07:49: 21000000 INFO @ Sun, 03 Jun 2018 14:07:49: 21000000 INFO @ Sun, 03 Jun 2018 14:07:54: 21000000 INFO @ Sun, 03 Jun 2018 14:07:54: 22000000 INFO @ Sun, 03 Jun 2018 14:07:54: 22000000 INFO @ Sun, 03 Jun 2018 14:07:59: 22000000 INFO @ Sun, 03 Jun 2018 14:08:00: 23000000 INFO @ Sun, 03 Jun 2018 14:08:00: 23000000 INFO @ Sun, 03 Jun 2018 14:08:05: 23000000 INFO @ Sun, 03 Jun 2018 14:08:05: 24000000 INFO @ Sun, 03 Jun 2018 14:08:05: 24000000 INFO @ Sun, 03 Jun 2018 14:08:10: 25000000 INFO @ Sun, 03 Jun 2018 14:08:10: 25000000 INFO @ Sun, 03 Jun 2018 14:08:10: 24000000 INFO @ Sun, 03 Jun 2018 14:08:16: 26000000 INFO @ Sun, 03 Jun 2018 14:08:16: 26000000 INFO @ Sun, 03 Jun 2018 14:08:16: 25000000 INFO @ Sun, 03 Jun 2018 14:08:21: 27000000 INFO @ Sun, 03 Jun 2018 14:08:21: 27000000 INFO @ Sun, 03 Jun 2018 14:08:22: 26000000 INFO @ Sun, 03 Jun 2018 14:08:26: 28000000 INFO @ Sun, 03 Jun 2018 14:08:26: 28000000 INFO @ Sun, 03 Jun 2018 14:08:27: 27000000 INFO @ Sun, 03 Jun 2018 14:08:32: 29000000 INFO @ Sun, 03 Jun 2018 14:08:32: 29000000 INFO @ Sun, 03 Jun 2018 14:08:33: 28000000 INFO @ Sun, 03 Jun 2018 14:08:37: 30000000 INFO @ Sun, 03 Jun 2018 14:08:37: 30000000 INFO @ Sun, 03 Jun 2018 14:08:38: 29000000 INFO @ Sun, 03 Jun 2018 14:08:42: 31000000 INFO @ Sun, 03 Jun 2018 14:08:42: 31000000 INFO @ Sun, 03 Jun 2018 14:08:44: 30000000 INFO @ Sun, 03 Jun 2018 14:08:48: 32000000 INFO @ Sun, 03 Jun 2018 14:08:48: 32000000 INFO @ Sun, 03 Jun 2018 14:08:50: 31000000 INFO @ Sun, 03 Jun 2018 14:08:53: 33000000 INFO @ Sun, 03 Jun 2018 14:08:53: 33000000 INFO @ Sun, 03 Jun 2018 14:08:55: 32000000 INFO @ Sun, 03 Jun 2018 14:08:58: 34000000 INFO @ Sun, 03 Jun 2018 14:08:59: 34000000 INFO @ Sun, 03 Jun 2018 14:09:01: 33000000 INFO @ Sun, 03 Jun 2018 14:09:04: 35000000 INFO @ Sun, 03 Jun 2018 14:09:04: 35000000 INFO @ Sun, 03 Jun 2018 14:09:07: 34000000 INFO @ Sun, 03 Jun 2018 14:09:09: 36000000 INFO @ Sun, 03 Jun 2018 14:09:09: 36000000 INFO @ Sun, 03 Jun 2018 14:09:12: 35000000 INFO @ Sun, 03 Jun 2018 14:09:15: 37000000 INFO @ Sun, 03 Jun 2018 14:09:15: 37000000 INFO @ Sun, 03 Jun 2018 14:09:18: 36000000 INFO @ Sun, 03 Jun 2018 14:09:20: 38000000 INFO @ Sun, 03 Jun 2018 14:09:20: 38000000 INFO @ Sun, 03 Jun 2018 14:09:24: 37000000 INFO @ Sun, 03 Jun 2018 14:09:25: 39000000 INFO @ Sun, 03 Jun 2018 14:09:26: 39000000 INFO @ Sun, 03 Jun 2018 14:09:30: 38000000 INFO @ Sun, 03 Jun 2018 14:09:31: 40000000 INFO @ Sun, 03 Jun 2018 14:09:31: 40000000 INFO @ Sun, 03 Jun 2018 14:09:35: 39000000 INFO @ Sun, 03 Jun 2018 14:09:36: 41000000 INFO @ Sun, 03 Jun 2018 14:09:36: 41000000 INFO @ Sun, 03 Jun 2018 14:09:41: 40000000 INFO @ Sun, 03 Jun 2018 14:09:42: 42000000 INFO @ Sun, 03 Jun 2018 14:09:42: 42000000 INFO @ Sun, 03 Jun 2018 14:09:47: 41000000 INFO @ Sun, 03 Jun 2018 14:09:47: 43000000 INFO @ Sun, 03 Jun 2018 14:09:47: 43000000 INFO @ Sun, 03 Jun 2018 14:09:53: 44000000 INFO @ Sun, 03 Jun 2018 14:09:53: 42000000 INFO @ Sun, 03 Jun 2018 14:09:53: 44000000 INFO @ Sun, 03 Jun 2018 14:09:58: 45000000 INFO @ Sun, 03 Jun 2018 14:09:58: 45000000 INFO @ Sun, 03 Jun 2018 14:09:58: 43000000 INFO @ Sun, 03 Jun 2018 14:10:03: 46000000 INFO @ Sun, 03 Jun 2018 14:10:04: 46000000 INFO @ Sun, 03 Jun 2018 14:10:04: 44000000 INFO @ Sun, 03 Jun 2018 14:10:09: 47000000 INFO @ Sun, 03 Jun 2018 14:10:09: 47000000 INFO @ Sun, 03 Jun 2018 14:10:10: 45000000 INFO @ Sun, 03 Jun 2018 14:10:14: 48000000 INFO @ Sun, 03 Jun 2018 14:10:14: 48000000 INFO @ Sun, 03 Jun 2018 14:10:16: 46000000 INFO @ Sun, 03 Jun 2018 14:10:19: 49000000 INFO @ Sun, 03 Jun 2018 14:10:20: 49000000 INFO @ Sun, 03 Jun 2018 14:10:21: 47000000 INFO @ Sun, 03 Jun 2018 14:10:24: 50000000 INFO @ Sun, 03 Jun 2018 14:10:25: 50000000 INFO @ Sun, 03 Jun 2018 14:10:27: 48000000 INFO @ Sun, 03 Jun 2018 14:10:30: 51000000 INFO @ Sun, 03 Jun 2018 14:10:31: 51000000 INFO @ Sun, 03 Jun 2018 14:10:33: 49000000 INFO @ Sun, 03 Jun 2018 14:10:35: 52000000 INFO @ Sun, 03 Jun 2018 14:10:36: 52000000 INFO @ Sun, 03 Jun 2018 14:10:39: 50000000 INFO @ Sun, 03 Jun 2018 14:10:40: 53000000 INFO @ Sun, 03 Jun 2018 14:10:42: 53000000 INFO @ Sun, 03 Jun 2018 14:10:45: 51000000 INFO @ Sun, 03 Jun 2018 14:10:46: 54000000 INFO @ Sun, 03 Jun 2018 14:10:47: 54000000 INFO @ Sun, 03 Jun 2018 14:10:50: 52000000 INFO @ Sun, 03 Jun 2018 14:10:51: 55000000 INFO @ Sun, 03 Jun 2018 14:10:53: 55000000 INFO @ Sun, 03 Jun 2018 14:10:56: 53000000 INFO @ Sun, 03 Jun 2018 14:10:56: 56000000 INFO @ Sun, 03 Jun 2018 14:10:58: 56000000 INFO @ Sun, 03 Jun 2018 14:11:02: 57000000 INFO @ Sun, 03 Jun 2018 14:11:02: 54000000 INFO @ Sun, 03 Jun 2018 14:11:04: 57000000 INFO @ Sun, 03 Jun 2018 14:11:07: 58000000 INFO @ Sun, 03 Jun 2018 14:11:08: 55000000 INFO @ Sun, 03 Jun 2018 14:11:09: 58000000 INFO @ Sun, 03 Jun 2018 14:11:12: 59000000 INFO @ Sun, 03 Jun 2018 14:11:14: 56000000 INFO @ Sun, 03 Jun 2018 14:11:15: 59000000 INFO @ Sun, 03 Jun 2018 14:11:17: 60000000 INFO @ Sun, 03 Jun 2018 14:11:20: 57000000 INFO @ Sun, 03 Jun 2018 14:11:20: 60000000 INFO @ Sun, 03 Jun 2018 14:11:23: 61000000 INFO @ Sun, 03 Jun 2018 14:11:25: 61000000 INFO @ Sun, 03 Jun 2018 14:11:25: 58000000 INFO @ Sun, 03 Jun 2018 14:11:28: 62000000 INFO @ Sun, 03 Jun 2018 14:11:31: 62000000 INFO @ Sun, 03 Jun 2018 14:11:31: 59000000 INFO @ Sun, 03 Jun 2018 14:11:33: 63000000 INFO @ Sun, 03 Jun 2018 14:11:36: 63000000 INFO @ Sun, 03 Jun 2018 14:11:37: 60000000 INFO @ Sun, 03 Jun 2018 14:11:39: 64000000 INFO @ Sun, 03 Jun 2018 14:11:42: 64000000 INFO @ Sun, 03 Jun 2018 14:11:43: 61000000 INFO @ Sun, 03 Jun 2018 14:11:44: 65000000 INFO @ Sun, 03 Jun 2018 14:11:47: 65000000 INFO @ Sun, 03 Jun 2018 14:11:49: 62000000 INFO @ Sun, 03 Jun 2018 14:11:49: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 14:11:49: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 14:11:49: #1 total tags in treatment: 31958369 INFO @ Sun, 03 Jun 2018 14:11:49: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 14:11:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 14:11:50: #1 tags after filtering in treatment: 25010987 INFO @ Sun, 03 Jun 2018 14:11:50: #1 Redundant rate of treatment: 0.22 INFO @ Sun, 03 Jun 2018 14:11:50: #1 finished! INFO @ Sun, 03 Jun 2018 14:11:50: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 14:11:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 14:11:51: #2 number of paired peaks: 62 WARNING @ Sun, 03 Jun 2018 14:11:51: Too few paired peaks (62) 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 Jun 2018 14:11:51: Process for pairing-model is terminated! cat: SRX4085431.20_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 `SRX4085431.20_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 `SRX4085431.20_*.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 `SRX4085431.20_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 @ Sun, 03 Jun 2018 14:11:52: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 14:11:52: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 14:11:52: #1 total tags in treatment: 31958369 INFO @ Sun, 03 Jun 2018 14:11:52: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 14:11:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 14:11:53: #1 tags after filtering in treatment: 25010987 INFO @ Sun, 03 Jun 2018 14:11:53: #1 Redundant rate of treatment: 0.22 INFO @ Sun, 03 Jun 2018 14:11:53: #1 finished! INFO @ Sun, 03 Jun 2018 14:11:53: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 14:11:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 14:11:54: 63000000 INFO @ Sun, 03 Jun 2018 14:11:55: #2 number of paired peaks: 62 WARNING @ Sun, 03 Jun 2018 14:11:55: Too few paired peaks (62) 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 Jun 2018 14:11:55: Process for pairing-model is terminated! cat: SRX4085431.10_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 `SRX4085431.10_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 `SRX4085431.10_*.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 `SRX4085431.10_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 Jun 2018 14:12:00: 64000000 INFO @ Sun, 03 Jun 2018 14:12:06: 65000000 INFO @ Sun, 03 Jun 2018 14:12:11: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 14:12:11: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 14:12:11: #1 total tags in treatment: 31958369 INFO @ Sun, 03 Jun 2018 14:12:11: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 14:12:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 14:12:12: #1 tags after filtering in treatment: 25010987 INFO @ Sun, 03 Jun 2018 14:12:12: #1 Redundant rate of treatment: 0.22 INFO @ Sun, 03 Jun 2018 14:12:12: #1 finished! INFO @ Sun, 03 Jun 2018 14:12:12: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 14:12:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 14:12:13: #2 number of paired peaks: 62 WARNING @ Sun, 03 Jun 2018 14:12:13: Too few paired peaks (62) 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 Jun 2018 14:12:13: Process for pairing-model is terminated! cat: SRX4085431.05_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 `SRX4085431.05_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 `SRX4085431.05_*.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 `SRX4085431.05_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。