Job ID = 11245217 sra ファイルのダウンロード中... Completed: 415066K bytes transferred in 7 seconds (482512K bits/sec), in 1 file. Completed: 415273K bytes transferred in 7 seconds (466039K bits/sec), in 1 file. Completed: 417675K bytes transferred in 6 seconds (496185K bits/sec), in 1 file. Completed: 18540K bytes transferred in 3 seconds (44137K 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 170566 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669666/SRR7818312.sra Written 170566 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669666/SRR7818312.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669666/SRR7818309.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669666/SRR7818309.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669666/SRR7818310.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669666/SRR7818310.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669666/SRR7818311.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669666/SRR7818311.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 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: 00:10:06 12170566 reads; of these: 12170566 (100.00%) were paired; of these: 2681149 (22.03%) aligned concordantly 0 times 8284482 (68.07%) aligned concordantly exactly 1 time 1204935 (9.90%) aligned concordantly >1 times ---- 2681149 pairs aligned concordantly 0 times; of these: 137353 (5.12%) aligned discordantly 1 time ---- 2543796 pairs aligned 0 times concordantly or discordantly; of these: 5087592 mates make up the pairs; of these: 4633973 (91.08%) aligned 0 times 328512 (6.46%) aligned exactly 1 time 125107 (2.46%) aligned >1 times 80.96% overall alignment rate Time searching: 00:10:06 Overall time: 00:10:06 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 12 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] 159406 / 9597278 = 0.0166 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, 10 Oct 2018 00:09:13: # Command line: callpeak -t SRX4669666.bam -f BAM -g 12100000 -n SRX4669666.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669666.20 # format = BAM # ChIP-seq file = ['SRX4669666.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, 10 Oct 2018 00:09:13: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:09:13: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:09:13: # Command line: callpeak -t SRX4669666.bam -f BAM -g 12100000 -n SRX4669666.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669666.05 # format = BAM # ChIP-seq file = ['SRX4669666.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, 10 Oct 2018 00:09:13: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:09:13: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:09:13: # Command line: callpeak -t SRX4669666.bam -f BAM -g 12100000 -n SRX4669666.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669666.10 # format = BAM # ChIP-seq file = ['SRX4669666.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, 10 Oct 2018 00:09:13: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:09:13: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:09:19: 1000000 INFO @ Wed, 10 Oct 2018 00:09:19: 1000000 INFO @ Wed, 10 Oct 2018 00:09:20: 1000000 INFO @ Wed, 10 Oct 2018 00:09:26: 2000000 INFO @ Wed, 10 Oct 2018 00:09:26: 2000000 INFO @ Wed, 10 Oct 2018 00:09:27: 2000000 INFO @ Wed, 10 Oct 2018 00:09:33: 3000000 INFO @ Wed, 10 Oct 2018 00:09:33: 3000000 INFO @ Wed, 10 Oct 2018 00:09:34: 3000000 INFO @ Wed, 10 Oct 2018 00:09:40: 4000000 INFO @ Wed, 10 Oct 2018 00:09:40: 4000000 INFO @ Wed, 10 Oct 2018 00:09:41: 4000000 INFO @ Wed, 10 Oct 2018 00:09:46: 5000000 INFO @ Wed, 10 Oct 2018 00:09:47: 5000000 INFO @ Wed, 10 Oct 2018 00:09:48: 5000000 INFO @ Wed, 10 Oct 2018 00:09:53: 6000000 INFO @ Wed, 10 Oct 2018 00:09:54: 6000000 INFO @ Wed, 10 Oct 2018 00:09:56: 6000000 INFO @ Wed, 10 Oct 2018 00:09:59: 7000000 INFO @ Wed, 10 Oct 2018 00:10:01: 7000000 INFO @ Wed, 10 Oct 2018 00:10:03: 7000000 INFO @ Wed, 10 Oct 2018 00:10:06: 8000000 INFO @ Wed, 10 Oct 2018 00:10:07: 8000000 INFO @ Wed, 10 Oct 2018 00:10:10: 8000000 INFO @ Wed, 10 Oct 2018 00:10:12: 9000000 INFO @ Wed, 10 Oct 2018 00:10:14: 9000000 INFO @ Wed, 10 Oct 2018 00:10:17: 9000000 INFO @ Wed, 10 Oct 2018 00:10:18: 10000000 INFO @ Wed, 10 Oct 2018 00:10:21: 10000000 INFO @ Wed, 10 Oct 2018 00:10:24: 10000000 INFO @ Wed, 10 Oct 2018 00:10:25: 11000000 INFO @ Wed, 10 Oct 2018 00:10:28: 11000000 INFO @ Wed, 10 Oct 2018 00:10:31: 11000000 INFO @ Wed, 10 Oct 2018 00:10:31: 12000000 INFO @ Wed, 10 Oct 2018 00:10:35: 12000000 INFO @ Wed, 10 Oct 2018 00:10:38: 13000000 INFO @ Wed, 10 Oct 2018 00:10:38: 12000000 INFO @ Wed, 10 Oct 2018 00:10:41: 13000000 INFO @ Wed, 10 Oct 2018 00:10:45: 14000000 INFO @ Wed, 10 Oct 2018 00:10:45: 13000000 INFO @ Wed, 10 Oct 2018 00:10:48: 14000000 INFO @ Wed, 10 Oct 2018 00:10:51: 15000000 INFO @ Wed, 10 Oct 2018 00:10:53: 14000000 INFO @ Wed, 10 Oct 2018 00:10:54: 15000000 INFO @ Wed, 10 Oct 2018 00:10:58: 16000000 INFO @ Wed, 10 Oct 2018 00:11:00: 15000000 INFO @ Wed, 10 Oct 2018 00:11:01: 16000000 INFO @ Wed, 10 Oct 2018 00:11:05: 17000000 INFO @ Wed, 10 Oct 2018 00:11:07: 16000000 INFO @ Wed, 10 Oct 2018 00:11:07: 17000000 INFO @ Wed, 10 Oct 2018 00:11:12: 18000000 INFO @ Wed, 10 Oct 2018 00:11:14: 18000000 INFO @ Wed, 10 Oct 2018 00:11:14: 17000000 INFO @ Wed, 10 Oct 2018 00:11:18: 19000000 INFO @ Wed, 10 Oct 2018 00:11:20: 19000000 INFO @ Wed, 10 Oct 2018 00:11:21: 18000000 INFO @ Wed, 10 Oct 2018 00:11:21: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:11:21: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:11:21: #1 total tags in treatment: 9330885 INFO @ Wed, 10 Oct 2018 00:11:21: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:11:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:11:21: #1 tags after filtering in treatment: 7123285 INFO @ Wed, 10 Oct 2018 00:11:21: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 10 Oct 2018 00:11:21: #1 finished! INFO @ Wed, 10 Oct 2018 00:11:21: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:11:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:11:22: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:11:22: 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, 10 Oct 2018 00:11:22: Process for pairing-model is terminated! cat: SRX4669666.05_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 `SRX4669666.05_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 `SRX4669666.05_*.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 `SRX4669666.05_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 @ Wed, 10 Oct 2018 00:11:23: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:11:23: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:11:23: #1 total tags in treatment: 9330885 INFO @ Wed, 10 Oct 2018 00:11:23: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:11:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:11:23: #1 tags after filtering in treatment: 7123285 INFO @ Wed, 10 Oct 2018 00:11:23: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 10 Oct 2018 00:11:23: #1 finished! INFO @ Wed, 10 Oct 2018 00:11:23: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:11:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:11:24: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:11:24: 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, 10 Oct 2018 00:11:24: Process for pairing-model is terminated! cat: SRX4669666.10_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 `SRX4669666.10_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 `SRX4669666.10_*.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 `SRX4669666.10_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, 10 Oct 2018 00:11:28: 19000000 INFO @ Wed, 10 Oct 2018 00:11:30: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:11:30: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:11:30: #1 total tags in treatment: 9330885 INFO @ Wed, 10 Oct 2018 00:11:30: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:11:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:11:31: #1 tags after filtering in treatment: 7123285 INFO @ Wed, 10 Oct 2018 00:11:31: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 10 Oct 2018 00:11:31: #1 finished! INFO @ Wed, 10 Oct 2018 00:11:31: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:11:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:11:31: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:11:31: 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, 10 Oct 2018 00:11:31: Process for pairing-model is terminated! cat: SRX4669666.20_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 `SRX4669666.20_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 `SRX4669666.20_*.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 `SRX4669666.20_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。