Job ID = 11193127 sra ファイルのダウンロード中... Completed: 608557K bytes transferred in 17 seconds (285465K 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 17655092 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337719/SRR7467884.sra Written 17655092 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337719/SRR7467884.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: 00:06:17 17655092 reads; of these: 17655092 (100.00%) were paired; of these: 16075636 (91.05%) aligned concordantly 0 times 1372842 (7.78%) aligned concordantly exactly 1 time 206614 (1.17%) aligned concordantly >1 times ---- 16075636 pairs aligned concordantly 0 times; of these: 1647611 (10.25%) aligned discordantly 1 time ---- 14428025 pairs aligned 0 times concordantly or discordantly; of these: 28856050 mates make up the pairs; of these: 24658124 (85.45%) aligned 0 times 3371291 (11.68%) aligned exactly 1 time 826635 (2.86%) aligned >1 times 30.17% overall alignment rate Time searching: 00:06:17 Overall time: 00:06:17 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_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] 883572 / 2926381 = 0.3019 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 @ Sat, 15 Sep 2018 11:09:53: # Command line: callpeak -t SRX4337719.bam -f BAM -g 12100000 -n SRX4337719.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4337719.20 # format = BAM # ChIP-seq file = ['SRX4337719.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 @ Sat, 15 Sep 2018 11:09:53: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:09:53: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:09:53: # Command line: callpeak -t SRX4337719.bam -f BAM -g 12100000 -n SRX4337719.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4337719.05 # format = BAM # ChIP-seq file = ['SRX4337719.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 @ Sat, 15 Sep 2018 11:09:53: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:09:53: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:09:53: # Command line: callpeak -t SRX4337719.bam -f BAM -g 12100000 -n SRX4337719.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4337719.10 # format = BAM # ChIP-seq file = ['SRX4337719.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 @ Sat, 15 Sep 2018 11:09:53: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:09:53: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:09:58: 1000000 INFO @ Sat, 15 Sep 2018 11:09:59: 1000000 INFO @ Sat, 15 Sep 2018 11:09:59: 1000000 INFO @ Sat, 15 Sep 2018 11:10:03: 2000000 INFO @ Sat, 15 Sep 2018 11:10:04: 2000000 INFO @ Sat, 15 Sep 2018 11:10:04: 2000000 INFO @ Sat, 15 Sep 2018 11:10:08: 3000000 INFO @ Sat, 15 Sep 2018 11:10:08: 3000000 INFO @ Sat, 15 Sep 2018 11:10:09: 3000000 INFO @ Sat, 15 Sep 2018 11:10:13: 4000000 INFO @ Sat, 15 Sep 2018 11:10:14: 4000000 INFO @ Sat, 15 Sep 2018 11:10:14: 4000000 INFO @ Sat, 15 Sep 2018 11:10:18: 5000000 INFO @ Sat, 15 Sep 2018 11:10:19: 5000000 INFO @ Sat, 15 Sep 2018 11:10:19: 5000000 INFO @ Sat, 15 Sep 2018 11:10:23: 6000000 INFO @ Sat, 15 Sep 2018 11:10:24: 6000000 INFO @ Sat, 15 Sep 2018 11:10:25: 6000000 INFO @ Sat, 15 Sep 2018 11:10:28: 7000000 INFO @ Sat, 15 Sep 2018 11:10:29: 7000000 INFO @ Sat, 15 Sep 2018 11:10:30: 7000000 INFO @ Sat, 15 Sep 2018 11:10:33: 8000000 INFO @ Sat, 15 Sep 2018 11:10:34: 8000000 INFO @ Sat, 15 Sep 2018 11:10:35: 8000000 INFO @ Sat, 15 Sep 2018 11:10:38: #1 tag size is determined as 44 bps INFO @ Sat, 15 Sep 2018 11:10:38: #1 tag size = 44 INFO @ Sat, 15 Sep 2018 11:10:38: #1 total tags in treatment: 1141998 INFO @ Sat, 15 Sep 2018 11:10:38: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:10:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:10:38: #1 tags after filtering in treatment: 980807 INFO @ Sat, 15 Sep 2018 11:10:38: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Sep 2018 11:10:38: #1 finished! INFO @ Sat, 15 Sep 2018 11:10:38: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:10:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:10:38: #2 number of paired peaks: 81 WARNING @ Sat, 15 Sep 2018 11:10:38: Too few paired peaks (81) 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 @ Sat, 15 Sep 2018 11:10:38: Process for pairing-model is terminated! cat: SRX4337719.20_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4337719.20_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 `SRX4337719.20_*.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 `SRX4337719.20_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 @ Sat, 15 Sep 2018 11:10:38: #1 tag size is determined as 44 bps INFO @ Sat, 15 Sep 2018 11:10:38: #1 tag size = 44 INFO @ Sat, 15 Sep 2018 11:10:38: #1 total tags in treatment: 1141998 INFO @ Sat, 15 Sep 2018 11:10:38: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:10:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:10:38: #1 tags after filtering in treatment: 980807 INFO @ Sat, 15 Sep 2018 11:10:38: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Sep 2018 11:10:38: #1 finished! INFO @ Sat, 15 Sep 2018 11:10:38: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:10:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:10:38: #2 number of paired peaks: 81 WARNING @ Sat, 15 Sep 2018 11:10:38: Too few paired peaks (81) 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 @ Sat, 15 Sep 2018 11:10:38: Process for pairing-model is terminated! cat: SRX4337719.05_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4337719.05_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 `SRX4337719.05_*.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 `SRX4337719.05_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 @ Sat, 15 Sep 2018 11:10:40: #1 tag size is determined as 44 bps INFO @ Sat, 15 Sep 2018 11:10:40: #1 tag size = 44 INFO @ Sat, 15 Sep 2018 11:10:40: #1 total tags in treatment: 1141998 INFO @ Sat, 15 Sep 2018 11:10:40: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:10:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:10:40: #1 tags after filtering in treatment: 980807 INFO @ Sat, 15 Sep 2018 11:10:40: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Sep 2018 11:10:40: #1 finished! INFO @ Sat, 15 Sep 2018 11:10:40: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:10:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:10:40: #2 number of paired peaks: 81 WARNING @ Sat, 15 Sep 2018 11:10:40: Too few paired peaks (81) 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 @ Sat, 15 Sep 2018 11:10:40: Process for pairing-model is terminated! cat: SRX4337719.10_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 `SRX4337719.10_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 `SRX4337719.10_*.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 `SRX4337719.10_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。