Job ID = 9161952 sra ファイルのダウンロード中... Completed: 1088563K bytes transferred in 12 seconds (725462K bits/sec), in 1 file, 2 directories. 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 26326214 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1423686/SRR2930975.sra Written 26326214 spots total 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: 00:20:14 26326214 reads; of these: 26326214 (100.00%) were paired; of these: 1025911 (3.90%) aligned concordantly 0 times 21567432 (81.92%) aligned concordantly exactly 1 time 3732871 (14.18%) aligned concordantly >1 times ---- 1025911 pairs aligned concordantly 0 times; of these: 34327 (3.35%) aligned discordantly 1 time ---- 991584 pairs aligned 0 times concordantly or discordantly; of these: 1983168 mates make up the pairs; of these: 1759505 (88.72%) aligned 0 times 166345 (8.39%) aligned exactly 1 time 57318 (2.89%) aligned >1 times 96.66% overall alignment rate Time searching: 00:20:14 Overall time: 00:20:14 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 24 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] 14565635 / 25308622 = 0.5755 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, 28 Jun 2017 05:34:43: # Command line: callpeak -t SRX1423686.bam -f BAM -g 12100000 -n SRX1423686.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1423686.10 # format = BAM # ChIP-seq file = ['SRX1423686.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, 28 Jun 2017 05:34:43: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:34:43: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:34:43: # Command line: callpeak -t SRX1423686.bam -f BAM -g 12100000 -n SRX1423686.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1423686.05 # format = BAM # ChIP-seq file = ['SRX1423686.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, 28 Jun 2017 05:34:43: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:34:43: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:34:43: # Command line: callpeak -t SRX1423686.bam -f BAM -g 12100000 -n SRX1423686.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1423686.20 # format = BAM # ChIP-seq file = ['SRX1423686.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, 28 Jun 2017 05:34:43: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:34:43: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:34:49: 1000000 INFO @ Wed, 28 Jun 2017 05:34:49: 1000000 INFO @ Wed, 28 Jun 2017 05:34:49: 1000000 INFO @ Wed, 28 Jun 2017 05:34:55: 2000000 INFO @ Wed, 28 Jun 2017 05:34:57: 2000000 INFO @ Wed, 28 Jun 2017 05:34:57: 2000000 INFO @ Wed, 28 Jun 2017 05:35:03: 3000000 INFO @ Wed, 28 Jun 2017 05:35:06: 3000000 INFO @ Wed, 28 Jun 2017 05:35:06: 3000000 INFO @ Wed, 28 Jun 2017 05:35:11: 4000000 INFO @ Wed, 28 Jun 2017 05:35:14: 4000000 INFO @ Wed, 28 Jun 2017 05:35:14: 4000000 INFO @ Wed, 28 Jun 2017 05:35:18: 5000000 INFO @ Wed, 28 Jun 2017 05:35:22: 5000000 INFO @ Wed, 28 Jun 2017 05:35:22: 5000000 INFO @ Wed, 28 Jun 2017 05:35:25: 6000000 INFO @ Wed, 28 Jun 2017 05:35:30: 6000000 INFO @ Wed, 28 Jun 2017 05:35:30: 6000000 INFO @ Wed, 28 Jun 2017 05:35:32: 7000000 INFO @ Wed, 28 Jun 2017 05:35:37: 7000000 INFO @ Wed, 28 Jun 2017 05:35:37: 7000000 INFO @ Wed, 28 Jun 2017 05:35:39: 8000000 INFO @ Wed, 28 Jun 2017 05:35:44: 8000000 INFO @ Wed, 28 Jun 2017 05:35:44: 8000000 INFO @ Wed, 28 Jun 2017 05:35:45: 9000000 INFO @ Wed, 28 Jun 2017 05:35:51: 9000000 INFO @ Wed, 28 Jun 2017 05:35:51: 9000000 INFO @ Wed, 28 Jun 2017 05:35:51: 10000000 INFO @ Wed, 28 Jun 2017 05:35:57: 11000000 INFO @ Wed, 28 Jun 2017 05:35:57: 10000000 INFO @ Wed, 28 Jun 2017 05:35:57: 10000000 INFO @ Wed, 28 Jun 2017 05:36:03: 12000000 INFO @ Wed, 28 Jun 2017 05:36:04: 11000000 INFO @ Wed, 28 Jun 2017 05:36:04: 11000000 INFO @ Wed, 28 Jun 2017 05:36:09: 13000000 INFO @ Wed, 28 Jun 2017 05:36:10: 12000000 INFO @ Wed, 28 Jun 2017 05:36:10: 12000000 INFO @ Wed, 28 Jun 2017 05:36:15: 14000000 INFO @ Wed, 28 Jun 2017 05:36:17: 13000000 INFO @ Wed, 28 Jun 2017 05:36:17: 13000000 INFO @ Wed, 28 Jun 2017 05:36:21: 15000000 INFO @ Wed, 28 Jun 2017 05:36:24: 14000000 INFO @ Wed, 28 Jun 2017 05:36:24: 14000000 INFO @ Wed, 28 Jun 2017 05:36:27: 16000000 INFO @ Wed, 28 Jun 2017 05:36:31: 15000000 INFO @ Wed, 28 Jun 2017 05:36:31: 15000000 INFO @ Wed, 28 Jun 2017 05:36:33: 17000000 INFO @ Wed, 28 Jun 2017 05:36:38: 16000000 INFO @ Wed, 28 Jun 2017 05:36:38: 16000000 INFO @ Wed, 28 Jun 2017 05:36:40: 18000000 INFO @ Wed, 28 Jun 2017 05:36:45: 17000000 INFO @ Wed, 28 Jun 2017 05:36:45: 17000000 INFO @ Wed, 28 Jun 2017 05:36:46: 19000000 INFO @ Wed, 28 Jun 2017 05:36:52: 20000000 INFO @ Wed, 28 Jun 2017 05:36:52: 18000000 INFO @ Wed, 28 Jun 2017 05:36:52: 18000000 INFO @ Wed, 28 Jun 2017 05:36:58: 21000000 INFO @ Wed, 28 Jun 2017 05:36:59: 19000000 INFO @ Wed, 28 Jun 2017 05:36:59: 19000000 INFO @ Wed, 28 Jun 2017 05:37:03: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:37:03: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:37:03: #1 total tags in treatment: 10739504 INFO @ Wed, 28 Jun 2017 05:37:03: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:37:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:37:03: #1 tags after filtering in treatment: 7753449 INFO @ Wed, 28 Jun 2017 05:37:03: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 28 Jun 2017 05:37:03: #1 finished! INFO @ Wed, 28 Jun 2017 05:37:03: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:37:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:37:03: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:37:03: 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, 28 Jun 2017 05:37:03: Process for pairing-model is terminated! cat: SRX1423686.10_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 `SRX1423686.10_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 `SRX1423686.10_*.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 `SRX1423686.10_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 @ Wed, 28 Jun 2017 05:37:06: 20000000 INFO @ Wed, 28 Jun 2017 05:37:06: 20000000 INFO @ Wed, 28 Jun 2017 05:37:13: 21000000 INFO @ Wed, 28 Jun 2017 05:37:13: 21000000 INFO @ Wed, 28 Jun 2017 05:37:17: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:37:17: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:37:17: #1 total tags in treatment: 10739504 INFO @ Wed, 28 Jun 2017 05:37:17: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:37:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:37:17: #1 tags after filtering in treatment: 7753449 INFO @ Wed, 28 Jun 2017 05:37:17: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 28 Jun 2017 05:37:17: #1 finished! INFO @ Wed, 28 Jun 2017 05:37:17: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:37:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:37:18: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:37:18: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:37:18: #1 total tags in treatment: 10739504 INFO @ Wed, 28 Jun 2017 05:37:18: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:37:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:37:18: #1 tags after filtering in treatment: 7753449 INFO @ Wed, 28 Jun 2017 05:37:18: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 28 Jun 2017 05:37:18: #1 finished! INFO @ Wed, 28 Jun 2017 05:37:18: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:37:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:37:18: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:37:18: 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, 28 Jun 2017 05:37:18: Process for pairing-model is terminated! cat: SRX1423686.20_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 `SRX1423686.20_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 `SRX1423686.20_*.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 `SRX1423686.20_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, 28 Jun 2017 05:37:18: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:37:18: 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, 28 Jun 2017 05:37:18: Process for pairing-model is terminated! cat: SRX1423686.05_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 `SRX1423686.05_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 `SRX1423686.05_*.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 `SRX1423686.05_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。