Job ID = 11244924 sra ファイルのダウンロード中... Completed: 664148K bytes transferred in 11 seconds (462458K 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 20464725 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554664/SRR7696337.sra Written 20464725 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554664/SRR7696337.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: 00:13:08 20464725 reads; of these: 20464725 (100.00%) were paired; of these: 3079807 (15.05%) aligned concordantly 0 times 14549004 (71.09%) aligned concordantly exactly 1 time 2835914 (13.86%) aligned concordantly >1 times ---- 3079807 pairs aligned concordantly 0 times; of these: 457774 (14.86%) aligned discordantly 1 time ---- 2622033 pairs aligned 0 times concordantly or discordantly; of these: 5244066 mates make up the pairs; of these: 4503015 (85.87%) aligned 0 times 443528 (8.46%) aligned exactly 1 time 297523 (5.67%) aligned >1 times 89.00% overall alignment rate Time searching: 00:13:08 Overall time: 00:13:08 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] 1056767 / 17749204 = 0.0595 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 @ Tue, 09 Oct 2018 23:15:55: # Command line: callpeak -t SRX4554664.bam -f BAM -g 12100000 -n SRX4554664.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554664.20 # format = BAM # ChIP-seq file = ['SRX4554664.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 @ Tue, 09 Oct 2018 23:15:55: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:15:55: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:15:55: # Command line: callpeak -t SRX4554664.bam -f BAM -g 12100000 -n SRX4554664.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554664.10 # format = BAM # ChIP-seq file = ['SRX4554664.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 @ Tue, 09 Oct 2018 23:15:55: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:15:55: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:15:55: # Command line: callpeak -t SRX4554664.bam -f BAM -g 12100000 -n SRX4554664.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554664.05 # format = BAM # ChIP-seq file = ['SRX4554664.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 @ Tue, 09 Oct 2018 23:15:55: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:15:55: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:16:02: 1000000 INFO @ Tue, 09 Oct 2018 23:16:02: 1000000 INFO @ Tue, 09 Oct 2018 23:16:02: 1000000 INFO @ Tue, 09 Oct 2018 23:16:10: 2000000 INFO @ Tue, 09 Oct 2018 23:16:10: 2000000 INFO @ Tue, 09 Oct 2018 23:16:10: 2000000 INFO @ Tue, 09 Oct 2018 23:16:17: 3000000 INFO @ Tue, 09 Oct 2018 23:16:17: 3000000 INFO @ Tue, 09 Oct 2018 23:16:17: 3000000 INFO @ Tue, 09 Oct 2018 23:16:24: 4000000 INFO @ Tue, 09 Oct 2018 23:16:24: 4000000 INFO @ Tue, 09 Oct 2018 23:16:24: 4000000 INFO @ Tue, 09 Oct 2018 23:16:31: 5000000 INFO @ Tue, 09 Oct 2018 23:16:32: 5000000 INFO @ Tue, 09 Oct 2018 23:16:32: 5000000 INFO @ Tue, 09 Oct 2018 23:16:39: 6000000 INFO @ Tue, 09 Oct 2018 23:16:39: 6000000 INFO @ Tue, 09 Oct 2018 23:16:39: 6000000 INFO @ Tue, 09 Oct 2018 23:16:46: 7000000 INFO @ Tue, 09 Oct 2018 23:16:46: 7000000 INFO @ Tue, 09 Oct 2018 23:16:46: 7000000 INFO @ Tue, 09 Oct 2018 23:16:53: 8000000 INFO @ Tue, 09 Oct 2018 23:16:54: 8000000 INFO @ Tue, 09 Oct 2018 23:16:54: 8000000 INFO @ Tue, 09 Oct 2018 23:17:00: 9000000 INFO @ Tue, 09 Oct 2018 23:17:01: 9000000 INFO @ Tue, 09 Oct 2018 23:17:01: 9000000 INFO @ Tue, 09 Oct 2018 23:17:07: 10000000 INFO @ Tue, 09 Oct 2018 23:17:08: 10000000 INFO @ Tue, 09 Oct 2018 23:17:08: 10000000 INFO @ Tue, 09 Oct 2018 23:17:14: 11000000 INFO @ Tue, 09 Oct 2018 23:17:15: 11000000 INFO @ Tue, 09 Oct 2018 23:17:15: 11000000 INFO @ Tue, 09 Oct 2018 23:17:21: 12000000 INFO @ Tue, 09 Oct 2018 23:17:22: 12000000 INFO @ Tue, 09 Oct 2018 23:17:22: 12000000 INFO @ Tue, 09 Oct 2018 23:17:28: 13000000 INFO @ Tue, 09 Oct 2018 23:17:29: 13000000 INFO @ Tue, 09 Oct 2018 23:17:29: 13000000 INFO @ Tue, 09 Oct 2018 23:17:36: 14000000 INFO @ Tue, 09 Oct 2018 23:17:37: 14000000 INFO @ Tue, 09 Oct 2018 23:17:37: 14000000 INFO @ Tue, 09 Oct 2018 23:17:43: 15000000 INFO @ Tue, 09 Oct 2018 23:17:44: 15000000 INFO @ Tue, 09 Oct 2018 23:17:44: 15000000 INFO @ Tue, 09 Oct 2018 23:17:50: 16000000 INFO @ Tue, 09 Oct 2018 23:17:51: 16000000 INFO @ Tue, 09 Oct 2018 23:17:51: 16000000 INFO @ Tue, 09 Oct 2018 23:17:57: 17000000 INFO @ Tue, 09 Oct 2018 23:17:59: 17000000 INFO @ Tue, 09 Oct 2018 23:17:59: 17000000 INFO @ Tue, 09 Oct 2018 23:18:04: 18000000 INFO @ Tue, 09 Oct 2018 23:18:06: 18000000 INFO @ Tue, 09 Oct 2018 23:18:06: 18000000 INFO @ Tue, 09 Oct 2018 23:18:11: 19000000 INFO @ Tue, 09 Oct 2018 23:18:13: 19000000 INFO @ Tue, 09 Oct 2018 23:18:13: 19000000 INFO @ Tue, 09 Oct 2018 23:18:18: 20000000 INFO @ Tue, 09 Oct 2018 23:18:21: 20000000 INFO @ Tue, 09 Oct 2018 23:18:21: 20000000 INFO @ Tue, 09 Oct 2018 23:18:25: 21000000 INFO @ Tue, 09 Oct 2018 23:18:28: 21000000 INFO @ Tue, 09 Oct 2018 23:18:28: 21000000 INFO @ Tue, 09 Oct 2018 23:18:32: 22000000 INFO @ Tue, 09 Oct 2018 23:18:35: 22000000 INFO @ Tue, 09 Oct 2018 23:18:35: 22000000 INFO @ Tue, 09 Oct 2018 23:18:39: 23000000 INFO @ Tue, 09 Oct 2018 23:18:43: 23000000 INFO @ Tue, 09 Oct 2018 23:18:43: 23000000 INFO @ Tue, 09 Oct 2018 23:18:46: 24000000 INFO @ Tue, 09 Oct 2018 23:18:50: 24000000 INFO @ Tue, 09 Oct 2018 23:18:50: 24000000 INFO @ Tue, 09 Oct 2018 23:18:53: 25000000 INFO @ Tue, 09 Oct 2018 23:18:57: 25000000 INFO @ Tue, 09 Oct 2018 23:18:57: 25000000 INFO @ Tue, 09 Oct 2018 23:19:00: 26000000 INFO @ Tue, 09 Oct 2018 23:19:04: 26000000 INFO @ Tue, 09 Oct 2018 23:19:04: 26000000 INFO @ Tue, 09 Oct 2018 23:19:07: 27000000 INFO @ Tue, 09 Oct 2018 23:19:12: 27000000 INFO @ Tue, 09 Oct 2018 23:19:12: 27000000 INFO @ Tue, 09 Oct 2018 23:19:14: 28000000 INFO @ Tue, 09 Oct 2018 23:19:19: 28000000 INFO @ Tue, 09 Oct 2018 23:19:19: 28000000 INFO @ Tue, 09 Oct 2018 23:19:21: 29000000 INFO @ Tue, 09 Oct 2018 23:19:26: 29000000 INFO @ Tue, 09 Oct 2018 23:19:26: 29000000 INFO @ Tue, 09 Oct 2018 23:19:28: 30000000 INFO @ Tue, 09 Oct 2018 23:19:34: 30000000 INFO @ Tue, 09 Oct 2018 23:19:34: 30000000 INFO @ Tue, 09 Oct 2018 23:19:35: 31000000 INFO @ Tue, 09 Oct 2018 23:19:41: 31000000 INFO @ Tue, 09 Oct 2018 23:19:41: 31000000 INFO @ Tue, 09 Oct 2018 23:19:42: 32000000 INFO @ Tue, 09 Oct 2018 23:19:48: 32000000 INFO @ Tue, 09 Oct 2018 23:19:48: 32000000 INFO @ Tue, 09 Oct 2018 23:19:49: 33000000 INFO @ Tue, 09 Oct 2018 23:19:56: 33000000 INFO @ Tue, 09 Oct 2018 23:19:56: 33000000 INFO @ Tue, 09 Oct 2018 23:19:56: 34000000 INFO @ Tue, 09 Oct 2018 23:19:58: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:19:58: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:19:58: #1 total tags in treatment: 16347281 INFO @ Tue, 09 Oct 2018 23:19:58: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:19:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:19:59: #1 tags after filtering in treatment: 9466006 INFO @ Tue, 09 Oct 2018 23:19:59: #1 Redundant rate of treatment: 0.42 INFO @ Tue, 09 Oct 2018 23:19:59: #1 finished! INFO @ Tue, 09 Oct 2018 23:19:59: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:19:59: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 09 Oct 2018 23:19:59: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:19:59: 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 @ Tue, 09 Oct 2018 23:19:59: Process for pairing-model is terminated! cat: SRX4554664.10_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 `SRX4554664.10_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 `SRX4554664.10_*.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 `SRX4554664.10_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 @ Tue, 09 Oct 2018 23:20:03: 34000000 INFO @ Tue, 09 Oct 2018 23:20:03: 34000000 INFO @ Tue, 09 Oct 2018 23:20:06: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:20:06: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:20:06: #1 total tags in treatment: 16347281 INFO @ Tue, 09 Oct 2018 23:20:06: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:20:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:20:06: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:20:06: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:20:06: #1 total tags in treatment: 16347281 INFO @ Tue, 09 Oct 2018 23:20:06: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:20:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:20:06: #1 tags after filtering in treatment: 9466006 INFO @ Tue, 09 Oct 2018 23:20:06: #1 Redundant rate of treatment: 0.42 INFO @ Tue, 09 Oct 2018 23:20:06: #1 finished! INFO @ Tue, 09 Oct 2018 23:20:06: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:20:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:20:06: #1 tags after filtering in treatment: 9466006 INFO @ Tue, 09 Oct 2018 23:20:06: #1 Redundant rate of treatment: 0.42 INFO @ Tue, 09 Oct 2018 23:20:06: #1 finished! INFO @ Tue, 09 Oct 2018 23:20:06: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:20:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:20:07: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:20:07: 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 @ Tue, 09 Oct 2018 23:20:07: Process for pairing-model is terminated! cat: SRX4554664.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Tue, 09 Oct 2018 23:20:07: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:20:07: 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 @ Tue, 09 Oct 2018 23:20:07: Process for pairing-model is terminated! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) cat: SRX4554664.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません rm: cannot remove `SRX4554664.05_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 `SRX4554664.05_*.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 `SRX4554664.05_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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4554664.20_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 `SRX4554664.20_*.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 `SRX4554664.20_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 BigWig に変換しました。