Job ID = 11245199 sra ファイルのダウンロード中... Completed: 411384K bytes transferred in 7 seconds (458721K bits/sec), in 1 file. Completed: 411859K bytes transferred in 7 seconds (472403K bits/sec), in 1 file. Completed: 415050K bytes transferred in 6 seconds (488580K bits/sec), in 1 file. Completed: 74276K bytes transferred in 3 seconds (159643K 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 695274 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669653/SRR7818273.sra Written 695274 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669653/SRR7818273.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669653/SRR7818271.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669653/SRR7818271.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669653/SRR7818272.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669653/SRR7818272.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669653/SRR7818270.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669653/SRR7818270.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 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: 00:12:27 12695274 reads; of these: 12695274 (100.00%) were paired; of these: 1269924 (10.00%) aligned concordantly 0 times 10581016 (83.35%) aligned concordantly exactly 1 time 844334 (6.65%) aligned concordantly >1 times ---- 1269924 pairs aligned concordantly 0 times; of these: 145591 (11.46%) aligned discordantly 1 time ---- 1124333 pairs aligned 0 times concordantly or discordantly; of these: 2248666 mates make up the pairs; of these: 1853317 (82.42%) aligned 0 times 295180 (13.13%) aligned exactly 1 time 100169 (4.45%) aligned >1 times 92.70% overall alignment rate Time searching: 00:12:27 Overall time: 00:12:27 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] 118587 / 11537004 = 0.0103 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, 10 Oct 2018 00:10:19: # Command line: callpeak -t SRX4669653.bam -f BAM -g 12100000 -n SRX4669653.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669653.05 # format = BAM # ChIP-seq file = ['SRX4669653.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, 10 Oct 2018 00:10:19: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:10:19: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:10:19: # Command line: callpeak -t SRX4669653.bam -f BAM -g 12100000 -n SRX4669653.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669653.20 # format = BAM # ChIP-seq file = ['SRX4669653.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, 10 Oct 2018 00:10:19: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:10:19: # Command line: callpeak -t SRX4669653.bam -f BAM -g 12100000 -n SRX4669653.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669653.10 # format = BAM # ChIP-seq file = ['SRX4669653.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, 10 Oct 2018 00:10:19: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:10:19: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:10:19: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:10:25: 1000000 INFO @ Wed, 10 Oct 2018 00:10:25: 1000000 INFO @ Wed, 10 Oct 2018 00:10:25: 1000000 INFO @ Wed, 10 Oct 2018 00:10:32: 2000000 INFO @ Wed, 10 Oct 2018 00:10:32: 2000000 INFO @ Wed, 10 Oct 2018 00:10:32: 2000000 INFO @ Wed, 10 Oct 2018 00:10:38: 3000000 INFO @ Wed, 10 Oct 2018 00:10:38: 3000000 INFO @ Wed, 10 Oct 2018 00:10:38: 3000000 INFO @ Wed, 10 Oct 2018 00:10:44: 4000000 INFO @ Wed, 10 Oct 2018 00:10:44: 4000000 INFO @ Wed, 10 Oct 2018 00:10:45: 4000000 INFO @ Wed, 10 Oct 2018 00:10:50: 5000000 INFO @ Wed, 10 Oct 2018 00:10:51: 5000000 INFO @ Wed, 10 Oct 2018 00:10:51: 5000000 INFO @ Wed, 10 Oct 2018 00:10:57: 6000000 INFO @ Wed, 10 Oct 2018 00:10:57: 6000000 INFO @ Wed, 10 Oct 2018 00:10:58: 6000000 INFO @ Wed, 10 Oct 2018 00:11:03: 7000000 INFO @ Wed, 10 Oct 2018 00:11:04: 7000000 INFO @ Wed, 10 Oct 2018 00:11:04: 7000000 INFO @ Wed, 10 Oct 2018 00:11:11: 8000000 INFO @ Wed, 10 Oct 2018 00:11:11: 8000000 INFO @ Wed, 10 Oct 2018 00:11:12: 8000000 INFO @ Wed, 10 Oct 2018 00:11:18: 9000000 INFO @ Wed, 10 Oct 2018 00:11:18: 9000000 INFO @ Wed, 10 Oct 2018 00:11:19: 9000000 INFO @ Wed, 10 Oct 2018 00:11:25: 10000000 INFO @ Wed, 10 Oct 2018 00:11:26: 10000000 INFO @ Wed, 10 Oct 2018 00:11:26: 10000000 INFO @ Wed, 10 Oct 2018 00:11:33: 11000000 INFO @ Wed, 10 Oct 2018 00:11:33: 11000000 INFO @ Wed, 10 Oct 2018 00:11:34: 11000000 INFO @ Wed, 10 Oct 2018 00:11:40: 12000000 INFO @ Wed, 10 Oct 2018 00:11:41: 12000000 INFO @ Wed, 10 Oct 2018 00:11:42: 12000000 INFO @ Wed, 10 Oct 2018 00:11:47: 13000000 INFO @ Wed, 10 Oct 2018 00:11:48: 13000000 INFO @ Wed, 10 Oct 2018 00:11:50: 13000000 INFO @ Wed, 10 Oct 2018 00:11:55: 14000000 INFO @ Wed, 10 Oct 2018 00:11:55: 14000000 INFO @ Wed, 10 Oct 2018 00:11:58: 14000000 INFO @ Wed, 10 Oct 2018 00:12:02: 15000000 INFO @ Wed, 10 Oct 2018 00:12:03: 15000000 INFO @ Wed, 10 Oct 2018 00:12:06: 15000000 INFO @ Wed, 10 Oct 2018 00:12:08: 16000000 INFO @ Wed, 10 Oct 2018 00:12:09: 16000000 INFO @ Wed, 10 Oct 2018 00:12:13: 16000000 INFO @ Wed, 10 Oct 2018 00:12:15: 17000000 INFO @ Wed, 10 Oct 2018 00:12:16: 17000000 INFO @ Wed, 10 Oct 2018 00:12:19: 17000000 INFO @ Wed, 10 Oct 2018 00:12:21: 18000000 INFO @ Wed, 10 Oct 2018 00:12:23: 18000000 INFO @ Wed, 10 Oct 2018 00:12:26: 18000000 INFO @ Wed, 10 Oct 2018 00:12:27: 19000000 INFO @ Wed, 10 Oct 2018 00:12:29: 19000000 INFO @ Wed, 10 Oct 2018 00:12:32: 19000000 INFO @ Wed, 10 Oct 2018 00:12:33: 20000000 INFO @ Wed, 10 Oct 2018 00:12:36: 20000000 INFO @ Wed, 10 Oct 2018 00:12:39: 20000000 INFO @ Wed, 10 Oct 2018 00:12:39: 21000000 INFO @ Wed, 10 Oct 2018 00:12:42: 21000000 INFO @ Wed, 10 Oct 2018 00:12:46: 22000000 INFO @ Wed, 10 Oct 2018 00:12:46: 21000000 INFO @ Wed, 10 Oct 2018 00:12:49: 22000000 INFO @ Wed, 10 Oct 2018 00:12:52: 23000000 INFO @ Wed, 10 Oct 2018 00:12:52: 22000000 INFO @ Wed, 10 Oct 2018 00:12:54: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:12:54: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:12:54: #1 total tags in treatment: 11307575 INFO @ Wed, 10 Oct 2018 00:12:54: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:12:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:12:54: #1 tags after filtering in treatment: 8136819 INFO @ Wed, 10 Oct 2018 00:12:54: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 10 Oct 2018 00:12:54: #1 finished! INFO @ Wed, 10 Oct 2018 00:12:54: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:12:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:12:55: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:12:55: 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, 10 Oct 2018 00:12:55: Process for pairing-model is terminated! cat: SRX4669653.20_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 `SRX4669653.20_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 `SRX4669653.20_*.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 `SRX4669653.20_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 @ Wed, 10 Oct 2018 00:12:55: 23000000 INFO @ Wed, 10 Oct 2018 00:12:57: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:12:57: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:12:57: #1 total tags in treatment: 11307575 INFO @ Wed, 10 Oct 2018 00:12:57: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:12:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:12:57: #1 tags after filtering in treatment: 8136819 INFO @ Wed, 10 Oct 2018 00:12:57: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 10 Oct 2018 00:12:57: #1 finished! INFO @ Wed, 10 Oct 2018 00:12:57: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:12:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:12:58: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:12:58: 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, 10 Oct 2018 00:12:58: Process for pairing-model is terminated! cat: SRX4669653.05_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 `SRX4669653.05_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 `SRX4669653.05_*.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 `SRX4669653.05_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, 10 Oct 2018 00:12:59: 23000000 INFO @ Wed, 10 Oct 2018 00:13:01: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:13:01: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:13:01: #1 total tags in treatment: 11307575 INFO @ Wed, 10 Oct 2018 00:13:01: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:13:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:13:01: #1 tags after filtering in treatment: 8136819 INFO @ Wed, 10 Oct 2018 00:13:01: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 10 Oct 2018 00:13:01: #1 finished! INFO @ Wed, 10 Oct 2018 00:13:01: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:13:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:13:02: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:13:02: 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, 10 Oct 2018 00:13:02: Process for pairing-model is terminated! cat: SRX4669653.10_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 `SRX4669653.10_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 `SRX4669653.10_*.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 `SRX4669653.10_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。