Job ID = 10845224 sra ファイルのダウンロード中... Completed: 815136K bytes transferred in 46 seconds (144006K 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 16035148 spots for /home/okishinya/chipatlas/results/dm3/SRX3632922/SRR6655574.sra Written 16035148 spots for /home/okishinya/chipatlas/results/dm3/SRX3632922/SRR6655574.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: 00:33:19 16035148 reads; of these: 16035148 (100.00%) were paired; of these: 1211624 (7.56%) aligned concordantly 0 times 12474297 (77.79%) aligned concordantly exactly 1 time 2349227 (14.65%) aligned concordantly >1 times ---- 1211624 pairs aligned concordantly 0 times; of these: 314796 (25.98%) aligned discordantly 1 time ---- 896828 pairs aligned 0 times concordantly or discordantly; of these: 1793656 mates make up the pairs; of these: 1264055 (70.47%) aligned 0 times 353502 (19.71%) aligned exactly 1 time 176099 (9.82%) aligned >1 times 96.06% overall alignment rate Time searching: 00:33:19 Overall time: 00:33:19 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 713607 / 15077683 = 0.0473 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, 04 Jul 2018 10:13:54: # Command line: callpeak -t SRX3632922.bam -f BAM -g dm -n SRX3632922.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3632922.05 # format = BAM # ChIP-seq file = ['SRX3632922.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 04 Jul 2018 10:13:54: #1 read tag files... INFO @ Wed, 04 Jul 2018 10:13:54: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 10:13:54: # Command line: callpeak -t SRX3632922.bam -f BAM -g dm -n SRX3632922.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3632922.10 # format = BAM # ChIP-seq file = ['SRX3632922.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 04 Jul 2018 10:13:54: #1 read tag files... INFO @ Wed, 04 Jul 2018 10:13:54: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 10:13:54: # Command line: callpeak -t SRX3632922.bam -f BAM -g dm -n SRX3632922.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3632922.20 # format = BAM # ChIP-seq file = ['SRX3632922.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 04 Jul 2018 10:13:54: #1 read tag files... INFO @ Wed, 04 Jul 2018 10:13:54: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 10:14:00: 1000000 INFO @ Wed, 04 Jul 2018 10:14:00: 1000000 INFO @ Wed, 04 Jul 2018 10:14:00: 1000000 INFO @ Wed, 04 Jul 2018 10:14:06: 2000000 INFO @ Wed, 04 Jul 2018 10:14:07: 2000000 INFO @ Wed, 04 Jul 2018 10:14:07: 2000000 INFO @ Wed, 04 Jul 2018 10:14:13: 3000000 INFO @ Wed, 04 Jul 2018 10:14:13: 3000000 INFO @ Wed, 04 Jul 2018 10:14:13: 3000000 INFO @ Wed, 04 Jul 2018 10:14:19: 4000000 INFO @ Wed, 04 Jul 2018 10:14:19: 4000000 INFO @ Wed, 04 Jul 2018 10:14:20: 4000000 INFO @ Wed, 04 Jul 2018 10:14:25: 5000000 INFO @ Wed, 04 Jul 2018 10:14:26: 5000000 INFO @ Wed, 04 Jul 2018 10:14:26: 5000000 INFO @ Wed, 04 Jul 2018 10:14:32: 6000000 INFO @ Wed, 04 Jul 2018 10:14:32: 6000000 INFO @ Wed, 04 Jul 2018 10:14:32: 6000000 INFO @ Wed, 04 Jul 2018 10:14:38: 7000000 INFO @ Wed, 04 Jul 2018 10:14:39: 7000000 INFO @ Wed, 04 Jul 2018 10:14:39: 7000000 INFO @ Wed, 04 Jul 2018 10:14:44: 8000000 INFO @ Wed, 04 Jul 2018 10:14:45: 8000000 INFO @ Wed, 04 Jul 2018 10:14:45: 8000000 INFO @ Wed, 04 Jul 2018 10:14:50: 9000000 INFO @ Wed, 04 Jul 2018 10:14:51: 9000000 INFO @ Wed, 04 Jul 2018 10:14:51: 9000000 INFO @ Wed, 04 Jul 2018 10:14:57: 10000000 INFO @ Wed, 04 Jul 2018 10:14:57: 10000000 INFO @ Wed, 04 Jul 2018 10:14:58: 10000000 INFO @ Wed, 04 Jul 2018 10:15:03: 11000000 INFO @ Wed, 04 Jul 2018 10:15:04: 11000000 INFO @ Wed, 04 Jul 2018 10:15:04: 11000000 INFO @ Wed, 04 Jul 2018 10:15:09: 12000000 INFO @ Wed, 04 Jul 2018 10:15:10: 12000000 INFO @ Wed, 04 Jul 2018 10:15:10: 12000000 INFO @ Wed, 04 Jul 2018 10:15:15: 13000000 INFO @ Wed, 04 Jul 2018 10:15:16: 13000000 INFO @ Wed, 04 Jul 2018 10:15:16: 13000000 INFO @ Wed, 04 Jul 2018 10:15:21: 14000000 INFO @ Wed, 04 Jul 2018 10:15:23: 14000000 INFO @ Wed, 04 Jul 2018 10:15:23: 14000000 INFO @ Wed, 04 Jul 2018 10:15:28: 15000000 INFO @ Wed, 04 Jul 2018 10:15:29: 15000000 INFO @ Wed, 04 Jul 2018 10:15:29: 15000000 INFO @ Wed, 04 Jul 2018 10:15:34: 16000000 INFO @ Wed, 04 Jul 2018 10:15:35: 16000000 INFO @ Wed, 04 Jul 2018 10:15:35: 16000000 INFO @ Wed, 04 Jul 2018 10:15:40: 17000000 INFO @ Wed, 04 Jul 2018 10:15:41: 17000000 INFO @ Wed, 04 Jul 2018 10:15:42: 17000000 INFO @ Wed, 04 Jul 2018 10:15:46: 18000000 INFO @ Wed, 04 Jul 2018 10:15:48: 18000000 INFO @ Wed, 04 Jul 2018 10:15:48: 18000000 INFO @ Wed, 04 Jul 2018 10:15:52: 19000000 INFO @ Wed, 04 Jul 2018 10:15:54: 19000000 INFO @ Wed, 04 Jul 2018 10:15:54: 19000000 INFO @ Wed, 04 Jul 2018 10:15:58: 20000000 INFO @ Wed, 04 Jul 2018 10:16:00: 20000000 INFO @ Wed, 04 Jul 2018 10:16:01: 20000000 INFO @ Wed, 04 Jul 2018 10:16:05: 21000000 INFO @ Wed, 04 Jul 2018 10:16:07: 21000000 INFO @ Wed, 04 Jul 2018 10:16:07: 21000000 INFO @ Wed, 04 Jul 2018 10:16:11: 22000000 INFO @ Wed, 04 Jul 2018 10:16:13: 22000000 INFO @ Wed, 04 Jul 2018 10:16:13: 22000000 INFO @ Wed, 04 Jul 2018 10:16:17: 23000000 INFO @ Wed, 04 Jul 2018 10:16:19: 23000000 INFO @ Wed, 04 Jul 2018 10:16:20: 23000000 INFO @ Wed, 04 Jul 2018 10:16:23: 24000000 INFO @ Wed, 04 Jul 2018 10:16:25: 24000000 INFO @ Wed, 04 Jul 2018 10:16:26: 24000000 INFO @ Wed, 04 Jul 2018 10:16:29: 25000000 INFO @ Wed, 04 Jul 2018 10:16:32: 25000000 INFO @ Wed, 04 Jul 2018 10:16:32: 25000000 INFO @ Wed, 04 Jul 2018 10:16:36: 26000000 INFO @ Wed, 04 Jul 2018 10:16:38: 26000000 INFO @ Wed, 04 Jul 2018 10:16:39: 26000000 INFO @ Wed, 04 Jul 2018 10:16:42: 27000000 INFO @ Wed, 04 Jul 2018 10:16:45: 27000000 INFO @ Wed, 04 Jul 2018 10:16:45: 27000000 INFO @ Wed, 04 Jul 2018 10:16:48: 28000000 INFO @ Wed, 04 Jul 2018 10:16:51: 28000000 INFO @ Wed, 04 Jul 2018 10:16:52: 28000000 INFO @ Wed, 04 Jul 2018 10:16:54: 29000000 INFO @ Wed, 04 Jul 2018 10:16:57: #1 tag size is determined as 75 bps INFO @ Wed, 04 Jul 2018 10:16:57: #1 tag size = 75 INFO @ Wed, 04 Jul 2018 10:16:57: #1 total tags in treatment: 14117094 INFO @ Wed, 04 Jul 2018 10:16:57: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 10:16:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 10:16:57: #1 tags after filtering in treatment: 12568157 INFO @ Wed, 04 Jul 2018 10:16:57: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 04 Jul 2018 10:16:57: #1 finished! INFO @ Wed, 04 Jul 2018 10:16:57: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 10:16:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 10:16:58: 29000000 INFO @ Wed, 04 Jul 2018 10:16:58: #2 number of paired peaks: 3 WARNING @ Wed, 04 Jul 2018 10:16:58: Too few paired peaks (3) 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, 04 Jul 2018 10:16:58: Process for pairing-model is terminated! cat: SRX3632922.20_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 `SRX3632922.20_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 `SRX3632922.20_*.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 `SRX3632922.20_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, 04 Jul 2018 10:16:58: 29000000 INFO @ Wed, 04 Jul 2018 10:17:00: #1 tag size is determined as 75 bps INFO @ Wed, 04 Jul 2018 10:17:00: #1 tag size = 75 INFO @ Wed, 04 Jul 2018 10:17:00: #1 total tags in treatment: 14117094 INFO @ Wed, 04 Jul 2018 10:17:00: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 10:17:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 10:17:00: #1 tags after filtering in treatment: 12568157 INFO @ Wed, 04 Jul 2018 10:17:00: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 04 Jul 2018 10:17:00: #1 finished! INFO @ Wed, 04 Jul 2018 10:17:00: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 10:17:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 10:17:01: #1 tag size is determined as 75 bps INFO @ Wed, 04 Jul 2018 10:17:01: #1 tag size = 75 INFO @ Wed, 04 Jul 2018 10:17:01: #1 total tags in treatment: 14117094 INFO @ Wed, 04 Jul 2018 10:17:01: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 10:17:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 10:17:01: #1 tags after filtering in treatment: 12568157 INFO @ Wed, 04 Jul 2018 10:17:01: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 04 Jul 2018 10:17:01: #1 finished! INFO @ Wed, 04 Jul 2018 10:17:01: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 10:17:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 10:17:01: #2 number of paired peaks: 3 WARNING @ Wed, 04 Jul 2018 10:17:01: Too few paired peaks (3) 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, 04 Jul 2018 10:17:01: Process for pairing-model is terminated! cat: SRX3632922.05_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 `SRX3632922.05_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 `SRX3632922.05_*.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 `SRX3632922.05_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, 04 Jul 2018 10:17:02: #2 number of paired peaks: 3 WARNING @ Wed, 04 Jul 2018 10:17:02: Too few paired peaks (3) 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, 04 Jul 2018 10:17:02: Process for pairing-model is terminated! cat: SRX3632922.10_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 `SRX3632922.10_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 `SRX3632922.10_*.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 `SRX3632922.10_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。