Job ID = 11388948 sra ファイルのダウンロード中... Completed: 567528K bytes transferred in 12 seconds (384680K 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 6962727 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017466/SRR8198089.sra Written 6962727 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017466/SRR8198089.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: 00:15:53 6962727 reads; of these: 6962727 (100.00%) were paired; of these: 2057369 (29.55%) aligned concordantly 0 times 4334171 (62.25%) aligned concordantly exactly 1 time 571187 (8.20%) aligned concordantly >1 times ---- 2057369 pairs aligned concordantly 0 times; of these: 60101 (2.92%) aligned discordantly 1 time ---- 1997268 pairs aligned 0 times concordantly or discordantly; of these: 3994536 mates make up the pairs; of these: 3430300 (85.87%) aligned 0 times 477523 (11.95%) aligned exactly 1 time 86713 (2.17%) aligned >1 times 75.37% overall alignment rate Time searching: 00:15:53 Overall time: 00:15:53 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 8 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] 32364 / 4929702 = 0.0066 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 @ Thu, 13 Dec 2018 00:43:51: # Command line: callpeak -t SRX5017466.bam -f BAM -g 12100000 -n SRX5017466.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5017466.05 # format = BAM # ChIP-seq file = ['SRX5017466.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 @ Thu, 13 Dec 2018 00:43:51: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:43:51: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:43:51: # Command line: callpeak -t SRX5017466.bam -f BAM -g 12100000 -n SRX5017466.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5017466.20 # format = BAM # ChIP-seq file = ['SRX5017466.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 @ Thu, 13 Dec 2018 00:43:51: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:43:51: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:43:51: # Command line: callpeak -t SRX5017466.bam -f BAM -g 12100000 -n SRX5017466.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5017466.10 # format = BAM # ChIP-seq file = ['SRX5017466.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 @ Thu, 13 Dec 2018 00:43:51: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:43:51: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:44:05: 1000000 INFO @ Thu, 13 Dec 2018 00:44:07: 1000000 INFO @ Thu, 13 Dec 2018 00:44:07: 1000000 INFO @ Thu, 13 Dec 2018 00:44:20: 2000000 INFO @ Thu, 13 Dec 2018 00:44:20: 2000000 INFO @ Thu, 13 Dec 2018 00:44:20: 2000000 INFO @ Thu, 13 Dec 2018 00:44:33: 3000000 INFO @ Thu, 13 Dec 2018 00:44:33: 3000000 INFO @ Thu, 13 Dec 2018 00:44:34: 3000000 INFO @ Thu, 13 Dec 2018 00:44:49: 4000000 INFO @ Thu, 13 Dec 2018 00:44:49: 4000000 INFO @ Thu, 13 Dec 2018 00:44:54: 4000000 INFO @ Thu, 13 Dec 2018 00:45:05: 5000000 INFO @ Thu, 13 Dec 2018 00:45:06: 5000000 INFO @ Thu, 13 Dec 2018 00:45:13: 5000000 INFO @ Thu, 13 Dec 2018 00:45:21: 6000000 INFO @ Thu, 13 Dec 2018 00:45:26: 6000000 INFO @ Thu, 13 Dec 2018 00:45:38: 6000000 INFO @ Thu, 13 Dec 2018 00:45:40: 7000000 INFO @ Thu, 13 Dec 2018 00:45:48: 7000000 INFO @ Thu, 13 Dec 2018 00:45:55: 7000000 INFO @ Thu, 13 Dec 2018 00:46:04: 8000000 INFO @ Thu, 13 Dec 2018 00:46:08: 8000000 INFO @ Thu, 13 Dec 2018 00:46:09: 8000000 INFO @ Thu, 13 Dec 2018 00:46:23: 9000000 INFO @ Thu, 13 Dec 2018 00:46:27: 9000000 INFO @ Thu, 13 Dec 2018 00:46:31: 9000000 INFO @ Thu, 13 Dec 2018 00:46:43: 10000000 INFO @ Thu, 13 Dec 2018 00:46:48: 10000000 INFO @ Thu, 13 Dec 2018 00:46:51: #1 tag size is determined as 100 bps INFO @ Thu, 13 Dec 2018 00:46:51: #1 tag size = 100 INFO @ Thu, 13 Dec 2018 00:46:51: #1 total tags in treatment: 4873001 INFO @ Thu, 13 Dec 2018 00:46:51: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:46:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 00:46:52: #1 tags after filtering in treatment: 4100597 INFO @ Thu, 13 Dec 2018 00:46:52: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 13 Dec 2018 00:46:52: #1 finished! INFO @ Thu, 13 Dec 2018 00:46:52: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:46:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:46:52: #2 number of paired peaks: 28 WARNING @ Thu, 13 Dec 2018 00:46:52: Too few paired peaks (28) 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 @ Thu, 13 Dec 2018 00:46:52: Process for pairing-model is terminated! cat: SRX5017466.05_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): 5 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017466.05_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 `SRX5017466.05_*.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 `SRX5017466.05_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 @ Thu, 13 Dec 2018 00:46:54: 10000000 INFO @ Thu, 13 Dec 2018 00:46:57: #1 tag size is determined as 100 bps INFO @ Thu, 13 Dec 2018 00:46:57: #1 tag size = 100 INFO @ Thu, 13 Dec 2018 00:46:57: #1 total tags in treatment: 4873001 INFO @ Thu, 13 Dec 2018 00:46:57: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:46:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 00:46:57: #1 tags after filtering in treatment: 4100597 INFO @ Thu, 13 Dec 2018 00:46:57: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 13 Dec 2018 00:46:57: #1 finished! INFO @ Thu, 13 Dec 2018 00:46:57: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:46:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:46:58: #2 number of paired peaks: 28 WARNING @ Thu, 13 Dec 2018 00:46:58: Too few paired peaks (28) 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 @ Thu, 13 Dec 2018 00:46:58: Process for pairing-model is terminated! cat: SRX5017466.20_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): 5 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017466.20_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 `SRX5017466.20_*.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 `SRX5017466.20_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 @ Thu, 13 Dec 2018 00:47:03: #1 tag size is determined as 100 bps INFO @ Thu, 13 Dec 2018 00:47:03: #1 tag size = 100 INFO @ Thu, 13 Dec 2018 00:47:03: #1 total tags in treatment: 4873001 INFO @ Thu, 13 Dec 2018 00:47:03: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:47:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 00:47:03: #1 tags after filtering in treatment: 4100597 INFO @ Thu, 13 Dec 2018 00:47:03: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 13 Dec 2018 00:47:03: #1 finished! INFO @ Thu, 13 Dec 2018 00:47:03: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:47:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:47:04: #2 number of paired peaks: 28 WARNING @ Thu, 13 Dec 2018 00:47:04: Too few paired peaks (28) 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 @ Thu, 13 Dec 2018 00:47:04: Process for pairing-model is terminated! cat: SRX5017466.10_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): 5 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017466.10_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 `SRX5017466.10_*.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 `SRX5017466.10_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。