Job ID = 11388946 sra ファイルのダウンロード中... Completed: 552326K bytes transferred in 12 seconds (369954K 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 6641993 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017464/SRR8198087.sra Written 6641993 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017464/SRR8198087.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: 00:17:25 6641993 reads; of these: 6641993 (100.00%) were paired; of these: 1620107 (24.39%) aligned concordantly 0 times 4289543 (64.58%) aligned concordantly exactly 1 time 732343 (11.03%) aligned concordantly >1 times ---- 1620107 pairs aligned concordantly 0 times; of these: 137692 (8.50%) aligned discordantly 1 time ---- 1482415 pairs aligned 0 times concordantly or discordantly; of these: 2964830 mates make up the pairs; of these: 2417367 (81.53%) aligned 0 times 363920 (12.27%) aligned exactly 1 time 183543 (6.19%) aligned >1 times 81.80% overall alignment rate Time searching: 00:17:25 Overall time: 00:17:25 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] 66452 / 5156877 = 0.0129 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 00:44:45: # Command line: callpeak -t SRX5017464.bam -f BAM -g 12100000 -n SRX5017464.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5017464.05 # format = BAM # ChIP-seq file = ['SRX5017464.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 00:44:45: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:44:45: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:44:45: # Command line: callpeak -t SRX5017464.bam -f BAM -g 12100000 -n SRX5017464.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5017464.20 # format = BAM # ChIP-seq file = ['SRX5017464.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 00:44:45: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:44:45: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:44:45: # Command line: callpeak -t SRX5017464.bam -f BAM -g 12100000 -n SRX5017464.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5017464.10 # format = BAM # ChIP-seq file = ['SRX5017464.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 00:44:45: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:44:45: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:45:01: 1000000 INFO @ Thu, 13 Dec 2018 00:45:08: 1000000 INFO @ Thu, 13 Dec 2018 00:45:10: 1000000 INFO @ Thu, 13 Dec 2018 00:45:20: 2000000 INFO @ Thu, 13 Dec 2018 00:45:25: 2000000 INFO @ Thu, 13 Dec 2018 00:45:32: 2000000 INFO @ Thu, 13 Dec 2018 00:45:35: 3000000 INFO @ Thu, 13 Dec 2018 00:45:45: 3000000 INFO @ Thu, 13 Dec 2018 00:45:49: 4000000 INFO @ Thu, 13 Dec 2018 00:45:56: 3000000 INFO @ Thu, 13 Dec 2018 00:46:01: 5000000 INFO @ Thu, 13 Dec 2018 00:46:06: 4000000 INFO @ Thu, 13 Dec 2018 00:46:13: 6000000 INFO @ Thu, 13 Dec 2018 00:46:15: 4000000 INFO @ Thu, 13 Dec 2018 00:46:24: 5000000 INFO @ Thu, 13 Dec 2018 00:46:25: 7000000 INFO @ Thu, 13 Dec 2018 00:46:37: 8000000 INFO @ Thu, 13 Dec 2018 00:46:38: 5000000 INFO @ Thu, 13 Dec 2018 00:46:39: 6000000 INFO @ Thu, 13 Dec 2018 00:46:49: 9000000 INFO @ Thu, 13 Dec 2018 00:46:54: 7000000 INFO @ Thu, 13 Dec 2018 00:46:58: 6000000 INFO @ Thu, 13 Dec 2018 00:47:02: 10000000 INFO @ Thu, 13 Dec 2018 00:47:10: 8000000 INFO @ Thu, 13 Dec 2018 00:47:11: #1 tag size is determined as 100 bps INFO @ Thu, 13 Dec 2018 00:47:11: #1 tag size = 100 INFO @ Thu, 13 Dec 2018 00:47:11: #1 total tags in treatment: 4955997 INFO @ Thu, 13 Dec 2018 00:47:11: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:47:11: #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 00:47:11: #1 tags after filtering in treatment: 4030775 INFO @ Thu, 13 Dec 2018 00:47:11: #1 Redundant rate of treatment: 0.19 INFO @ Thu, 13 Dec 2018 00:47:11: #1 finished! INFO @ Thu, 13 Dec 2018 00:47:11: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:47:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:47:12: #2 number of paired peaks: 28 WARNING @ Thu, 13 Dec 2018 00:47:12: 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 00:47:12: Process for pairing-model is terminated! cat: SRX5017464.10_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): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017464.10_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 `SRX5017464.10_*.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 `SRX5017464.10_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 00:47:21: 7000000 INFO @ Thu, 13 Dec 2018 00:47:28: 9000000 INFO @ Thu, 13 Dec 2018 00:47:44: 8000000 INFO @ Thu, 13 Dec 2018 00:47:44: 10000000 INFO @ Thu, 13 Dec 2018 00:47:56: #1 tag size is determined as 100 bps INFO @ Thu, 13 Dec 2018 00:47:56: #1 tag size = 100 INFO @ Thu, 13 Dec 2018 00:47:56: #1 total tags in treatment: 4955997 INFO @ Thu, 13 Dec 2018 00:47:56: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:47:56: #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 00:47:56: #1 tags after filtering in treatment: 4030775 INFO @ Thu, 13 Dec 2018 00:47:56: #1 Redundant rate of treatment: 0.19 INFO @ Thu, 13 Dec 2018 00:47:56: #1 finished! INFO @ Thu, 13 Dec 2018 00:47:56: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:47:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:47:56: #2 number of paired peaks: 28 WARNING @ Thu, 13 Dec 2018 00:47:56: 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 00:47:56: Process for pairing-model is terminated! cat: SRX5017464.05_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): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017464.05_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 `SRX5017464.05_*.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 `SRX5017464.05_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 00:48:09: 9000000 INFO @ Thu, 13 Dec 2018 00:48:31: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 13 Dec 2018 00:48:47: #1 tag size is determined as 100 bps INFO @ Thu, 13 Dec 2018 00:48:47: #1 tag size = 100 INFO @ Thu, 13 Dec 2018 00:48:47: #1 total tags in treatment: 4955997 INFO @ Thu, 13 Dec 2018 00:48:47: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:48:47: #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 00:48:47: #1 tags after filtering in treatment: 4030775 INFO @ Thu, 13 Dec 2018 00:48:47: #1 Redundant rate of treatment: 0.19 INFO @ Thu, 13 Dec 2018 00:48:47: #1 finished! INFO @ Thu, 13 Dec 2018 00:48:47: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:48:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:48:47: #2 number of paired peaks: 28 WARNING @ Thu, 13 Dec 2018 00:48:47: 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 00:48:47: Process for pairing-model is terminated! cat: SRX5017464.20_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): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017464.20_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 `SRX5017464.20_*.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 `SRX5017464.20_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 BigWig に変換しました。