Job ID = 11388942 sra ファイルのダウンロード中... Completed: 593503K bytes transferred in 12 seconds (401900K 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 7299455 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017460/SRR8198083.sra Written 7299455 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017460/SRR8198083.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: 00:17:26 7299455 reads; of these: 7299455 (100.00%) were paired; of these: 1813241 (24.84%) aligned concordantly 0 times 4719544 (64.66%) aligned concordantly exactly 1 time 766670 (10.50%) aligned concordantly >1 times ---- 1813241 pairs aligned concordantly 0 times; of these: 209169 (11.54%) aligned discordantly 1 time ---- 1604072 pairs aligned 0 times concordantly or discordantly; of these: 3208144 mates make up the pairs; of these: 2597779 (80.97%) aligned 0 times 389028 (12.13%) aligned exactly 1 time 221337 (6.90%) aligned >1 times 82.21% overall alignment rate Time searching: 00:17:26 Overall time: 00:17:26 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] 61170 / 5692167 = 0.0107 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 00:43:41: # Command line: callpeak -t SRX5017460.bam -f BAM -g 12100000 -n SRX5017460.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5017460.10 # format = BAM # ChIP-seq file = ['SRX5017460.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 00:43:41: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:43:41: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:43:41: # Command line: callpeak -t SRX5017460.bam -f BAM -g 12100000 -n SRX5017460.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5017460.20 # format = BAM # ChIP-seq file = ['SRX5017460.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 00:43:41: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:43:41: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:43:41: # Command line: callpeak -t SRX5017460.bam -f BAM -g 12100000 -n SRX5017460.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5017460.05 # format = BAM # ChIP-seq file = ['SRX5017460.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 00:43:41: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:43:41: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:44:05: 1000000 INFO @ Thu, 13 Dec 2018 00:44:06: 1000000 INFO @ Thu, 13 Dec 2018 00:44:08: 1000000 INFO @ Thu, 13 Dec 2018 00:44:32: 2000000 INFO @ Thu, 13 Dec 2018 00:44:37: 2000000 INFO @ Thu, 13 Dec 2018 00:44:38: 2000000 INFO @ Thu, 13 Dec 2018 00:44:56: 3000000 INFO @ Thu, 13 Dec 2018 00:45:04: 3000000 INFO @ Thu, 13 Dec 2018 00:45:05: 3000000 INFO @ Thu, 13 Dec 2018 00:45:19: 4000000 INFO @ Thu, 13 Dec 2018 00:45:30: 4000000 INFO @ Thu, 13 Dec 2018 00:45:38: 4000000 INFO @ Thu, 13 Dec 2018 00:45:43: 5000000 INFO @ Thu, 13 Dec 2018 00:45:58: 5000000 INFO @ Thu, 13 Dec 2018 00:46:09: 6000000 INFO @ Thu, 13 Dec 2018 00:46:12: 5000000 INFO @ Thu, 13 Dec 2018 00:46:23: 6000000 INFO @ Thu, 13 Dec 2018 00:46:36: 7000000 INFO @ Thu, 13 Dec 2018 00:46:42: 7000000 INFO @ Thu, 13 Dec 2018 00:46:45: 6000000 INFO @ Thu, 13 Dec 2018 00:47:00: 8000000 INFO @ Thu, 13 Dec 2018 00:47:01: 7000000 INFO @ Thu, 13 Dec 2018 00:47:03: 8000000 INFO @ Thu, 13 Dec 2018 00:47:14: 8000000 INFO @ Thu, 13 Dec 2018 00:47:21: 9000000 INFO @ Thu, 13 Dec 2018 00:47:28: 9000000 INFO @ Thu, 13 Dec 2018 00:47:30: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 13 Dec 2018 00:47:39: 10000000 INFO @ Thu, 13 Dec 2018 00:47:42: 10000000 BigWig に変換しました。 INFO @ Thu, 13 Dec 2018 00:47:56: 10000000 INFO @ Thu, 13 Dec 2018 00:47:56: 11000000 INFO @ Thu, 13 Dec 2018 00:47:57: 11000000 INFO @ Thu, 13 Dec 2018 00:48:09: #1 tag size is determined as 100 bps INFO @ Thu, 13 Dec 2018 00:48:09: #1 tag size = 100 INFO @ Thu, 13 Dec 2018 00:48:09: #1 total tags in treatment: 5425766 INFO @ Thu, 13 Dec 2018 00:48:09: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:48:09: #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 00:48:09: #1 tags after filtering in treatment: 4392069 INFO @ Thu, 13 Dec 2018 00:48:09: #1 Redundant rate of treatment: 0.19 INFO @ Thu, 13 Dec 2018 00:48:09: #1 finished! INFO @ Thu, 13 Dec 2018 00:48:09: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:48:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:48:10: #2 number of paired peaks: 28 WARNING @ Thu, 13 Dec 2018 00:48:10: 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 00:48:10: Process for pairing-model is terminated! cat: SRX5017460.05_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): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017460.05_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 `SRX5017460.05_*.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 `SRX5017460.05_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 00:48:12: #1 tag size is determined as 100 bps INFO @ Thu, 13 Dec 2018 00:48:12: #1 tag size = 100 INFO @ Thu, 13 Dec 2018 00:48:12: #1 total tags in treatment: 5425766 INFO @ Thu, 13 Dec 2018 00:48:12: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:48:12: #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 00:48:13: #1 tags after filtering in treatment: 4392069 INFO @ Thu, 13 Dec 2018 00:48:13: #1 Redundant rate of treatment: 0.19 INFO @ Thu, 13 Dec 2018 00:48:13: #1 finished! INFO @ Thu, 13 Dec 2018 00:48:13: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:48:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:48:13: #2 number of paired peaks: 28 WARNING @ Thu, 13 Dec 2018 00:48:13: 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 00:48:13: Process for pairing-model is terminated! cat: SRX5017460.10_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017460.10_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 `SRX5017460.10_*.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 `SRX5017460.10_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 @ Thu, 13 Dec 2018 00:48:20: 11000000 INFO @ Thu, 13 Dec 2018 00:48:36: #1 tag size is determined as 100 bps INFO @ Thu, 13 Dec 2018 00:48:36: #1 tag size = 100 INFO @ Thu, 13 Dec 2018 00:48:36: #1 total tags in treatment: 5425766 INFO @ Thu, 13 Dec 2018 00:48:36: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:48:36: #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 00:48:36: #1 tags after filtering in treatment: 4392069 INFO @ Thu, 13 Dec 2018 00:48:36: #1 Redundant rate of treatment: 0.19 INFO @ Thu, 13 Dec 2018 00:48:36: #1 finished! INFO @ Thu, 13 Dec 2018 00:48:36: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:48:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:48:36: #2 number of paired peaks: 28 WARNING @ Thu, 13 Dec 2018 00:48:36: 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 00:48:36: Process for pairing-model is terminated! cat: SRX5017460.20_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017460.20_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 `SRX5017460.20_*.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 `SRX5017460.20_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