Job ID = 10254443 sra ファイルのダウンロード中... Completed: 484686K bytes transferred in 13 seconds (284474K bits/sec), in 1 file. Completed: 320767K bytes transferred in 12 seconds (218339K 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... Written 5008070 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3353381/SRR6246237.sra Written 5008070 spots total Written 7776320 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3353381/SRR6246236.sra Written 7776320 spots total 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: 00:10:37 12784390 reads; of these: 12784390 (100.00%) were paired; of these: 2449182 (19.16%) aligned concordantly 0 times 8600421 (67.27%) aligned concordantly exactly 1 time 1734787 (13.57%) aligned concordantly >1 times ---- 2449182 pairs aligned concordantly 0 times; of these: 1142916 (46.67%) aligned discordantly 1 time ---- 1306266 pairs aligned 0 times concordantly or discordantly; of these: 2612532 mates make up the pairs; of these: 1445965 (55.35%) aligned 0 times 631984 (24.19%) aligned exactly 1 time 534583 (20.46%) aligned >1 times 94.34% overall alignment rate Time searching: 00:10:37 Overall time: 00:10:37 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] 192312 / 11279427 = 0.0170 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, 06 Dec 2017 18:20:02: # Command line: callpeak -t SRX3353381.bam -f BAM -g 12100000 -n SRX3353381.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3353381.05 # format = BAM # ChIP-seq file = ['SRX3353381.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, 06 Dec 2017 18:20:02: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:20:02: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:20:02: # Command line: callpeak -t SRX3353381.bam -f BAM -g 12100000 -n SRX3353381.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3353381.10 # format = BAM # ChIP-seq file = ['SRX3353381.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, 06 Dec 2017 18:20:02: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:20:02: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:20:02: # Command line: callpeak -t SRX3353381.bam -f BAM -g 12100000 -n SRX3353381.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3353381.20 # format = BAM # ChIP-seq file = ['SRX3353381.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, 06 Dec 2017 18:20:02: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:20:02: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:20:09: 1000000 INFO @ Wed, 06 Dec 2017 18:20:09: 1000000 INFO @ Wed, 06 Dec 2017 18:20:09: 1000000 INFO @ Wed, 06 Dec 2017 18:20:15: 2000000 INFO @ Wed, 06 Dec 2017 18:20:15: 2000000 INFO @ Wed, 06 Dec 2017 18:20:16: 2000000 INFO @ Wed, 06 Dec 2017 18:20:22: 3000000 INFO @ Wed, 06 Dec 2017 18:20:22: 3000000 INFO @ Wed, 06 Dec 2017 18:20:23: 3000000 INFO @ Wed, 06 Dec 2017 18:20:29: 4000000 INFO @ Wed, 06 Dec 2017 18:20:29: 4000000 INFO @ Wed, 06 Dec 2017 18:20:30: 4000000 INFO @ Wed, 06 Dec 2017 18:20:35: 5000000 INFO @ Wed, 06 Dec 2017 18:20:35: 5000000 INFO @ Wed, 06 Dec 2017 18:20:37: 5000000 INFO @ Wed, 06 Dec 2017 18:20:42: 6000000 INFO @ Wed, 06 Dec 2017 18:20:42: 6000000 INFO @ Wed, 06 Dec 2017 18:20:44: 6000000 INFO @ Wed, 06 Dec 2017 18:20:48: 7000000 INFO @ Wed, 06 Dec 2017 18:20:48: 7000000 INFO @ Wed, 06 Dec 2017 18:20:51: 7000000 INFO @ Wed, 06 Dec 2017 18:20:55: 8000000 INFO @ Wed, 06 Dec 2017 18:20:55: 8000000 INFO @ Wed, 06 Dec 2017 18:20:58: 8000000 INFO @ Wed, 06 Dec 2017 18:21:02: 9000000 INFO @ Wed, 06 Dec 2017 18:21:02: 9000000 INFO @ Wed, 06 Dec 2017 18:21:06: 9000000 INFO @ Wed, 06 Dec 2017 18:21:08: 10000000 INFO @ Wed, 06 Dec 2017 18:21:08: 10000000 INFO @ Wed, 06 Dec 2017 18:21:13: 10000000 INFO @ Wed, 06 Dec 2017 18:21:15: 11000000 INFO @ Wed, 06 Dec 2017 18:21:15: 11000000 INFO @ Wed, 06 Dec 2017 18:21:20: 11000000 INFO @ Wed, 06 Dec 2017 18:21:22: 12000000 INFO @ Wed, 06 Dec 2017 18:21:22: 12000000 INFO @ Wed, 06 Dec 2017 18:21:27: 12000000 INFO @ Wed, 06 Dec 2017 18:21:28: 13000000 INFO @ Wed, 06 Dec 2017 18:21:28: 13000000 INFO @ Wed, 06 Dec 2017 18:21:34: 13000000 INFO @ Wed, 06 Dec 2017 18:21:35: 14000000 INFO @ Wed, 06 Dec 2017 18:21:35: 14000000 INFO @ Wed, 06 Dec 2017 18:21:41: 14000000 INFO @ Wed, 06 Dec 2017 18:21:42: 15000000 INFO @ Wed, 06 Dec 2017 18:21:42: 15000000 INFO @ Wed, 06 Dec 2017 18:21:48: 15000000 INFO @ Wed, 06 Dec 2017 18:21:48: 16000000 INFO @ Wed, 06 Dec 2017 18:21:48: 16000000 INFO @ Wed, 06 Dec 2017 18:21:55: 17000000 INFO @ Wed, 06 Dec 2017 18:21:55: 17000000 INFO @ Wed, 06 Dec 2017 18:21:55: 16000000 INFO @ Wed, 06 Dec 2017 18:22:02: 18000000 INFO @ Wed, 06 Dec 2017 18:22:02: 18000000 INFO @ Wed, 06 Dec 2017 18:22:02: 17000000 INFO @ Wed, 06 Dec 2017 18:22:08: 19000000 INFO @ Wed, 06 Dec 2017 18:22:08: 19000000 INFO @ Wed, 06 Dec 2017 18:22:09: 18000000 INFO @ Wed, 06 Dec 2017 18:22:15: 20000000 INFO @ Wed, 06 Dec 2017 18:22:15: 20000000 INFO @ Wed, 06 Dec 2017 18:22:16: 19000000 INFO @ Wed, 06 Dec 2017 18:22:21: 21000000 INFO @ Wed, 06 Dec 2017 18:22:21: 21000000 INFO @ Wed, 06 Dec 2017 18:22:23: 20000000 INFO @ Wed, 06 Dec 2017 18:22:28: 22000000 INFO @ Wed, 06 Dec 2017 18:22:28: 22000000 INFO @ Wed, 06 Dec 2017 18:22:30: 21000000 INFO @ Wed, 06 Dec 2017 18:22:35: 23000000 INFO @ Wed, 06 Dec 2017 18:22:35: 23000000 INFO @ Wed, 06 Dec 2017 18:22:37: 22000000 INFO @ Wed, 06 Dec 2017 18:22:40: #1 tag size is determined as 51 bps INFO @ Wed, 06 Dec 2017 18:22:40: #1 tag size = 51 INFO @ Wed, 06 Dec 2017 18:22:40: #1 total tags in treatment: 10145801 INFO @ Wed, 06 Dec 2017 18:22:40: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:22:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 18:22:40: #1 tag size is determined as 51 bps INFO @ Wed, 06 Dec 2017 18:22:40: #1 tag size = 51 INFO @ Wed, 06 Dec 2017 18:22:40: #1 total tags in treatment: 10145801 INFO @ Wed, 06 Dec 2017 18:22:40: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:22:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 18:22:40: #1 tags after filtering in treatment: 7217637 INFO @ Wed, 06 Dec 2017 18:22:40: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 06 Dec 2017 18:22:40: #1 finished! INFO @ Wed, 06 Dec 2017 18:22:40: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:22:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:22:40: #1 tags after filtering in treatment: 7217637 INFO @ Wed, 06 Dec 2017 18:22:40: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 06 Dec 2017 18:22:40: #1 finished! INFO @ Wed, 06 Dec 2017 18:22:40: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:22:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:22:40: #2 number of paired peaks: 0 WARNING @ Wed, 06 Dec 2017 18:22:40: 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, 06 Dec 2017 18:22:40: Process for pairing-model is terminated! cat: SRX3353381.05_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3353381.05_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 `SRX3353381.05_*.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 `SRX3353381.05_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, 06 Dec 2017 18:22:41: #2 number of paired peaks: 0 WARNING @ Wed, 06 Dec 2017 18:22:41: 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, 06 Dec 2017 18:22:41: Process for pairing-model is terminated! cat: SRX3353381.20_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 `SRX3353381.20_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 `SRX3353381.20_*.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 `SRX3353381.20_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, 06 Dec 2017 18:22:44: 23000000 INFO @ Wed, 06 Dec 2017 18:22:48: #1 tag size is determined as 51 bps INFO @ Wed, 06 Dec 2017 18:22:48: #1 tag size = 51 INFO @ Wed, 06 Dec 2017 18:22:48: #1 total tags in treatment: 10145801 INFO @ Wed, 06 Dec 2017 18:22:48: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:22:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 18:22:48: #1 tags after filtering in treatment: 7217637 INFO @ Wed, 06 Dec 2017 18:22:48: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 06 Dec 2017 18:22:48: #1 finished! INFO @ Wed, 06 Dec 2017 18:22:48: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:22:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:22:49: #2 number of paired peaks: 0 WARNING @ Wed, 06 Dec 2017 18:22:49: 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, 06 Dec 2017 18:22:49: Process for pairing-model is terminated! cat: SRX3353381.10_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 `SRX3353381.10_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 `SRX3353381.10_*.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 `SRX3353381.10_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。