Job ID = 11388936 sra ファイルのダウンロード中... Completed: 1902684K bytes transferred in 36 seconds (422254K 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 33640378 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017455/SRR8198078.sra Written 33640378 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017455/SRR8198078.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: 01:01:59 33640378 reads; of these: 33640378 (100.00%) were paired; of these: 4174568 (12.41%) aligned concordantly 0 times 25357930 (75.38%) aligned concordantly exactly 1 time 4107880 (12.21%) aligned concordantly >1 times ---- 4174568 pairs aligned concordantly 0 times; of these: 1147800 (27.50%) aligned discordantly 1 time ---- 3026768 pairs aligned 0 times concordantly or discordantly; of these: 6053536 mates make up the pairs; of these: 4642522 (76.69%) aligned 0 times 900528 (14.88%) aligned exactly 1 time 510486 (8.43%) aligned >1 times 93.10% overall alignment rate Time searching: 01:01:59 Overall time: 01:01:59 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 28 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] 4879203 / 29941954 = 0.1630 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 @ Thu, 13 Dec 2018 01:49:33: # Command line: callpeak -t SRX5017455.bam -f BAM -g 12100000 -n SRX5017455.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5017455.10 # format = BAM # ChIP-seq file = ['SRX5017455.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 @ Thu, 13 Dec 2018 01:49:33: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:49:33: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:49:33: # Command line: callpeak -t SRX5017455.bam -f BAM -g 12100000 -n SRX5017455.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5017455.05 # format = BAM # ChIP-seq file = ['SRX5017455.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 @ Thu, 13 Dec 2018 01:49:33: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:49:33: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:49:33: # Command line: callpeak -t SRX5017455.bam -f BAM -g 12100000 -n SRX5017455.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5017455.20 # format = BAM # ChIP-seq file = ['SRX5017455.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 @ Thu, 13 Dec 2018 01:49:33: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:49:33: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:49:49: 1000000 INFO @ Thu, 13 Dec 2018 01:49:53: 1000000 INFO @ Thu, 13 Dec 2018 01:49:55: 1000000 INFO @ Thu, 13 Dec 2018 01:50:04: 2000000 INFO @ Thu, 13 Dec 2018 01:50:13: 2000000 INFO @ Thu, 13 Dec 2018 01:50:18: 3000000 INFO @ Thu, 13 Dec 2018 01:50:18: 2000000 INFO @ Thu, 13 Dec 2018 01:50:29: 3000000 INFO @ Thu, 13 Dec 2018 01:50:38: 4000000 INFO @ Thu, 13 Dec 2018 01:50:39: 3000000 INFO @ Thu, 13 Dec 2018 01:50:47: 4000000 INFO @ Thu, 13 Dec 2018 01:50:59: 5000000 INFO @ Thu, 13 Dec 2018 01:51:00: 4000000 INFO @ Thu, 13 Dec 2018 01:51:08: 5000000 INFO @ Thu, 13 Dec 2018 01:51:15: 5000000 INFO @ Thu, 13 Dec 2018 01:51:17: 6000000 INFO @ Thu, 13 Dec 2018 01:51:27: 6000000 INFO @ Thu, 13 Dec 2018 01:51:29: 6000000 INFO @ Thu, 13 Dec 2018 01:51:33: 7000000 INFO @ Thu, 13 Dec 2018 01:51:43: 7000000 INFO @ Thu, 13 Dec 2018 01:51:43: 7000000 INFO @ Thu, 13 Dec 2018 01:51:54: 8000000 INFO @ Thu, 13 Dec 2018 01:52:02: 8000000 INFO @ Thu, 13 Dec 2018 01:52:06: 8000000 INFO @ Thu, 13 Dec 2018 01:52:15: 9000000 INFO @ Thu, 13 Dec 2018 01:52:21: 9000000 INFO @ Thu, 13 Dec 2018 01:52:29: 9000000 INFO @ Thu, 13 Dec 2018 01:52:37: 10000000 INFO @ Thu, 13 Dec 2018 01:52:42: 10000000 INFO @ Thu, 13 Dec 2018 01:52:50: 10000000 INFO @ Thu, 13 Dec 2018 01:52:59: 11000000 INFO @ Thu, 13 Dec 2018 01:53:03: 11000000 INFO @ Thu, 13 Dec 2018 01:53:10: 11000000 INFO @ Thu, 13 Dec 2018 01:53:21: 12000000 INFO @ Thu, 13 Dec 2018 01:53:25: 12000000 INFO @ Thu, 13 Dec 2018 01:53:32: 12000000 INFO @ Thu, 13 Dec 2018 01:53:42: 13000000 INFO @ Thu, 13 Dec 2018 01:53:46: 13000000 INFO @ Thu, 13 Dec 2018 01:53:53: 13000000 INFO @ Thu, 13 Dec 2018 01:54:04: 14000000 INFO @ Thu, 13 Dec 2018 01:54:07: 14000000 INFO @ Thu, 13 Dec 2018 01:54:16: 14000000 INFO @ Thu, 13 Dec 2018 01:54:27: 15000000 INFO @ Thu, 13 Dec 2018 01:54:31: 15000000 INFO @ Thu, 13 Dec 2018 01:54:44: 15000000 INFO @ Thu, 13 Dec 2018 01:54:49: 16000000 INFO @ Thu, 13 Dec 2018 01:54:55: 16000000 INFO @ Thu, 13 Dec 2018 01:55:11: 16000000 INFO @ Thu, 13 Dec 2018 01:55:11: 17000000 INFO @ Thu, 13 Dec 2018 01:55:18: 17000000 INFO @ Thu, 13 Dec 2018 01:55:32: 18000000 INFO @ Thu, 13 Dec 2018 01:55:37: 18000000 INFO @ Thu, 13 Dec 2018 01:55:38: 17000000 INFO @ Thu, 13 Dec 2018 01:55:51: 19000000 INFO @ Thu, 13 Dec 2018 01:56:00: 18000000 INFO @ Thu, 13 Dec 2018 01:56:01: 19000000 INFO @ Thu, 13 Dec 2018 01:56:10: 20000000 INFO @ Thu, 13 Dec 2018 01:56:19: 20000000 INFO @ Thu, 13 Dec 2018 01:56:21: 19000000 INFO @ Thu, 13 Dec 2018 01:56:30: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 13 Dec 2018 01:56:34: 21000000 INFO @ Thu, 13 Dec 2018 01:56:38: 20000000 INFO @ Thu, 13 Dec 2018 01:56:50: 22000000 INFO @ Thu, 13 Dec 2018 01:56:51: 22000000 INFO @ Thu, 13 Dec 2018 01:56:53: 21000000 BigWig に変換しました。 INFO @ Thu, 13 Dec 2018 01:57:08: 23000000 INFO @ Thu, 13 Dec 2018 01:57:10: 22000000 INFO @ Thu, 13 Dec 2018 01:57:11: 23000000 INFO @ Thu, 13 Dec 2018 01:57:26: 23000000 INFO @ Thu, 13 Dec 2018 01:57:30: 24000000 INFO @ Thu, 13 Dec 2018 01:57:31: 24000000 INFO @ Thu, 13 Dec 2018 01:57:41: 24000000 INFO @ Thu, 13 Dec 2018 01:57:52: 25000000 INFO @ Thu, 13 Dec 2018 01:57:55: 25000000 INFO @ Thu, 13 Dec 2018 01:57:57: 25000000 INFO @ Thu, 13 Dec 2018 01:58:12: 26000000 INFO @ Thu, 13 Dec 2018 01:58:12: 26000000 INFO @ Thu, 13 Dec 2018 01:58:19: 26000000 INFO @ Thu, 13 Dec 2018 01:58:27: 27000000 INFO @ Thu, 13 Dec 2018 01:58:31: 27000000 INFO @ Thu, 13 Dec 2018 01:58:42: 27000000 INFO @ Thu, 13 Dec 2018 01:58:42: 28000000 INFO @ Thu, 13 Dec 2018 01:58:45: 28000000 INFO @ Thu, 13 Dec 2018 01:58:58: 29000000 INFO @ Thu, 13 Dec 2018 01:58:59: 29000000 INFO @ Thu, 13 Dec 2018 01:59:07: 28000000 INFO @ Thu, 13 Dec 2018 01:59:16: 30000000 INFO @ Thu, 13 Dec 2018 01:59:16: 30000000 INFO @ Thu, 13 Dec 2018 01:59:31: 29000000 INFO @ Thu, 13 Dec 2018 01:59:32: 31000000 INFO @ Thu, 13 Dec 2018 01:59:33: 31000000 INFO @ Thu, 13 Dec 2018 01:59:47: 32000000 INFO @ Thu, 13 Dec 2018 01:59:49: 32000000 INFO @ Thu, 13 Dec 2018 01:59:53: 30000000 INFO @ Thu, 13 Dec 2018 01:59:58: 33000000 INFO @ Thu, 13 Dec 2018 02:00:03: 33000000 INFO @ Thu, 13 Dec 2018 02:00:09: 34000000 INFO @ Thu, 13 Dec 2018 02:00:18: 31000000 INFO @ Thu, 13 Dec 2018 02:00:20: 34000000 INFO @ Thu, 13 Dec 2018 02:00:22: 35000000 INFO @ Thu, 13 Dec 2018 02:00:33: 36000000 INFO @ Thu, 13 Dec 2018 02:00:38: 35000000 INFO @ Thu, 13 Dec 2018 02:00:43: 32000000 INFO @ Thu, 13 Dec 2018 02:00:46: 37000000 INFO @ Thu, 13 Dec 2018 02:00:55: 36000000 INFO @ Thu, 13 Dec 2018 02:01:01: 38000000 INFO @ Thu, 13 Dec 2018 02:01:05: 33000000 INFO @ Thu, 13 Dec 2018 02:01:13: 37000000 INFO @ Thu, 13 Dec 2018 02:01:17: 39000000 INFO @ Thu, 13 Dec 2018 02:01:24: 34000000 INFO @ Thu, 13 Dec 2018 02:01:31: 38000000 INFO @ Thu, 13 Dec 2018 02:01:34: 40000000 INFO @ Thu, 13 Dec 2018 02:01:40: 35000000 INFO @ Thu, 13 Dec 2018 02:01:48: 39000000 INFO @ Thu, 13 Dec 2018 02:01:49: 41000000 INFO @ Thu, 13 Dec 2018 02:01:54: 36000000 INFO @ Thu, 13 Dec 2018 02:02:03: 42000000 INFO @ Thu, 13 Dec 2018 02:02:06: 40000000 INFO @ Thu, 13 Dec 2018 02:02:11: 37000000 INFO @ Thu, 13 Dec 2018 02:02:17: 43000000 INFO @ Thu, 13 Dec 2018 02:02:26: 41000000 INFO @ Thu, 13 Dec 2018 02:02:30: 38000000 INFO @ Thu, 13 Dec 2018 02:02:36: 44000000 INFO @ Thu, 13 Dec 2018 02:02:45: 42000000 INFO @ Thu, 13 Dec 2018 02:02:51: 39000000 INFO @ Thu, 13 Dec 2018 02:02:56: 45000000 INFO @ Thu, 13 Dec 2018 02:03:05: 43000000 INFO @ Thu, 13 Dec 2018 02:03:13: 40000000 INFO @ Thu, 13 Dec 2018 02:03:16: 46000000 INFO @ Thu, 13 Dec 2018 02:03:25: 44000000 INFO @ Thu, 13 Dec 2018 02:03:35: 47000000 INFO @ Thu, 13 Dec 2018 02:03:36: 41000000 INFO @ Thu, 13 Dec 2018 02:03:46: 45000000 INFO @ Thu, 13 Dec 2018 02:03:55: 42000000 INFO @ Thu, 13 Dec 2018 02:03:57: 48000000 INFO @ Thu, 13 Dec 2018 02:04:04: 46000000 INFO @ Thu, 13 Dec 2018 02:04:12: 43000000 INFO @ Thu, 13 Dec 2018 02:04:15: 49000000 INFO @ Thu, 13 Dec 2018 02:04:22: 47000000 INFO @ Thu, 13 Dec 2018 02:04:33: 50000000 INFO @ Thu, 13 Dec 2018 02:04:33: 44000000 INFO @ Thu, 13 Dec 2018 02:04:39: 48000000 INFO @ Thu, 13 Dec 2018 02:04:49: 45000000 INFO @ Thu, 13 Dec 2018 02:04:53: 51000000 INFO @ Thu, 13 Dec 2018 02:04:59: 49000000 INFO @ Thu, 13 Dec 2018 02:05:05: 46000000 INFO @ Thu, 13 Dec 2018 02:05:15: 52000000 INFO @ Thu, 13 Dec 2018 02:05:17: 50000000 INFO @ Thu, 13 Dec 2018 02:05:22: 47000000 INFO @ Thu, 13 Dec 2018 02:05:28: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 02:05:28: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 02:05:28: #1 total tags in treatment: 24625980 INFO @ Thu, 13 Dec 2018 02:05:28: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 02:05:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 02:05:29: #1 tags after filtering in treatment: 13500128 INFO @ Thu, 13 Dec 2018 02:05:29: #1 Redundant rate of treatment: 0.45 INFO @ Thu, 13 Dec 2018 02:05:29: #1 finished! INFO @ Thu, 13 Dec 2018 02:05:29: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 02:05:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 02:05:30: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 02:05:30: 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 @ Thu, 13 Dec 2018 02:05:30: Process for pairing-model is terminated! cat: SRX5017455.20_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017455.20_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 `SRX5017455.20_*.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 `SRX5017455.20_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 @ Thu, 13 Dec 2018 02:05:34: 51000000 INFO @ Thu, 13 Dec 2018 02:05:41: 48000000 INFO @ Thu, 13 Dec 2018 02:05:55: 52000000 INFO @ Thu, 13 Dec 2018 02:06:01: 49000000 INFO @ Thu, 13 Dec 2018 02:06:13: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 02:06:13: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 02:06:13: #1 total tags in treatment: 24625980 INFO @ Thu, 13 Dec 2018 02:06:13: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 02:06:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 02:06:14: #1 tags after filtering in treatment: 13500128 INFO @ Thu, 13 Dec 2018 02:06:14: #1 Redundant rate of treatment: 0.45 INFO @ Thu, 13 Dec 2018 02:06:14: #1 finished! INFO @ Thu, 13 Dec 2018 02:06:14: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 02:06:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 02:06:15: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 02:06:15: 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 @ Thu, 13 Dec 2018 02:06:15: Process for pairing-model is terminated! cat: SRX5017455.10_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017455.10_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 `SRX5017455.10_*.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 `SRX5017455.10_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 @ Thu, 13 Dec 2018 02:06:19: 50000000 INFO @ Thu, 13 Dec 2018 02:06:35: 51000000 INFO @ Thu, 13 Dec 2018 02:06:53: 52000000 INFO @ Thu, 13 Dec 2018 02:07:08: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 02:07:08: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 02:07:08: #1 total tags in treatment: 24625980 INFO @ Thu, 13 Dec 2018 02:07:08: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 02:07:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 02:07:08: #1 tags after filtering in treatment: 13500128 INFO @ Thu, 13 Dec 2018 02:07:08: #1 Redundant rate of treatment: 0.45 INFO @ Thu, 13 Dec 2018 02:07:08: #1 finished! INFO @ Thu, 13 Dec 2018 02:07:08: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 02:07:08: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 02:07:10: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 02:07:10: 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 @ Thu, 13 Dec 2018 02:07:10: Process for pairing-model is terminated! cat: SRX5017455.05_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017455.05_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 `SRX5017455.05_*.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 `SRX5017455.05_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