Job ID = 11245206 sra ファイルのダウンロード中... Completed: 410181K bytes transferred in 7 seconds (428057K bits/sec), in 1 file. Completed: 345361K bytes transferred in 7 seconds (381335K 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 3330126 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669658/SRR7818285.sra Written 3330126 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669658/SRR7818285.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669658/SRR7818284.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669658/SRR7818284.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: 00:06:49 7330126 reads; of these: 7330126 (100.00%) were paired; of these: 1359670 (18.55%) aligned concordantly 0 times 5320167 (72.58%) aligned concordantly exactly 1 time 650289 (8.87%) aligned concordantly >1 times ---- 1359670 pairs aligned concordantly 0 times; of these: 90621 (6.66%) aligned discordantly 1 time ---- 1269049 pairs aligned 0 times concordantly or discordantly; of these: 2538098 mates make up the pairs; of these: 2193851 (86.44%) aligned 0 times 270486 (10.66%) aligned exactly 1 time 73761 (2.91%) aligned >1 times 85.04% overall alignment rate Time searching: 00:06:49 Overall time: 00:06:49 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] 66259 / 6041833 = 0.0110 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 00:01:46: # Command line: callpeak -t SRX4669658.bam -f BAM -g 12100000 -n SRX4669658.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669658.20 # format = BAM # ChIP-seq file = ['SRX4669658.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 00:01:46: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:01:46: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:01:46: # Command line: callpeak -t SRX4669658.bam -f BAM -g 12100000 -n SRX4669658.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669658.05 # format = BAM # ChIP-seq file = ['SRX4669658.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 00:01:46: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:01:46: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:01:46: # Command line: callpeak -t SRX4669658.bam -f BAM -g 12100000 -n SRX4669658.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669658.10 # format = BAM # ChIP-seq file = ['SRX4669658.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 00:01:46: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:01:46: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:01:54: 1000000 INFO @ Wed, 10 Oct 2018 00:01:55: 1000000 INFO @ Wed, 10 Oct 2018 00:01:55: 1000000 INFO @ Wed, 10 Oct 2018 00:02:01: 2000000 INFO @ Wed, 10 Oct 2018 00:02:04: 2000000 INFO @ Wed, 10 Oct 2018 00:02:04: 2000000 INFO @ Wed, 10 Oct 2018 00:02:08: 3000000 INFO @ Wed, 10 Oct 2018 00:02:13: 3000000 INFO @ Wed, 10 Oct 2018 00:02:13: 3000000 INFO @ Wed, 10 Oct 2018 00:02:16: 4000000 INFO @ Wed, 10 Oct 2018 00:02:21: 4000000 INFO @ Wed, 10 Oct 2018 00:02:21: 4000000 INFO @ Wed, 10 Oct 2018 00:02:23: 5000000 INFO @ Wed, 10 Oct 2018 00:02:30: 5000000 INFO @ Wed, 10 Oct 2018 00:02:30: 5000000 INFO @ Wed, 10 Oct 2018 00:02:30: 6000000 INFO @ Wed, 10 Oct 2018 00:02:38: 7000000 INFO @ Wed, 10 Oct 2018 00:02:39: 6000000 INFO @ Wed, 10 Oct 2018 00:02:39: 6000000 INFO @ Wed, 10 Oct 2018 00:02:45: 8000000 INFO @ Wed, 10 Oct 2018 00:02:48: 7000000 INFO @ Wed, 10 Oct 2018 00:02:48: 7000000 INFO @ Wed, 10 Oct 2018 00:02:52: 9000000 INFO @ Wed, 10 Oct 2018 00:02:56: 8000000 INFO @ Wed, 10 Oct 2018 00:02:56: 8000000 INFO @ Wed, 10 Oct 2018 00:03:00: 10000000 INFO @ Wed, 10 Oct 2018 00:03:05: 9000000 INFO @ Wed, 10 Oct 2018 00:03:05: 9000000 INFO @ Wed, 10 Oct 2018 00:03:08: 11000000 INFO @ Wed, 10 Oct 2018 00:03:15: 10000000 INFO @ Wed, 10 Oct 2018 00:03:15: 10000000 INFO @ Wed, 10 Oct 2018 00:03:17: 12000000 INFO @ Wed, 10 Oct 2018 00:03:19: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:03:19: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:03:19: #1 total tags in treatment: 5904734 INFO @ Wed, 10 Oct 2018 00:03:19: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:03:19: #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 00:03:20: #1 tags after filtering in treatment: 4821298 INFO @ Wed, 10 Oct 2018 00:03:20: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 10 Oct 2018 00:03:20: #1 finished! INFO @ Wed, 10 Oct 2018 00:03:20: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:03:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:03:20: #2 number of paired peaks: 23 WARNING @ Wed, 10 Oct 2018 00:03:20: Too few paired peaks (23) 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 00:03:20: Process for pairing-model is terminated! cat: SRX4669658.20_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): 12 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669658.20_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 `SRX4669658.20_*.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 `SRX4669658.20_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 @ Wed, 10 Oct 2018 00:03:24: 11000000 INFO @ Wed, 10 Oct 2018 00:03:24: 11000000 INFO @ Wed, 10 Oct 2018 00:03:33: 12000000 INFO @ Wed, 10 Oct 2018 00:03:34: 12000000 INFO @ Wed, 10 Oct 2018 00:03:36: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:03:36: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:03:36: #1 total tags in treatment: 5904734 INFO @ Wed, 10 Oct 2018 00:03:36: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:03:36: #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 00:03:36: #1 tags after filtering in treatment: 4821298 INFO @ Wed, 10 Oct 2018 00:03:36: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 10 Oct 2018 00:03:36: #1 finished! INFO @ Wed, 10 Oct 2018 00:03:36: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:03:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:03:36: #2 number of paired peaks: 23 WARNING @ Wed, 10 Oct 2018 00:03:36: Too few paired peaks (23) 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 00:03:36: Process for pairing-model is terminated! cat: SRX4669658.10_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 `SRX4669658.10_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 `SRX4669658.10_*.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 `SRX4669658.10_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 00:03:37: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:03:37: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:03:37: #1 total tags in treatment: 5904734 INFO @ Wed, 10 Oct 2018 00:03:37: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:03:37: #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 00:03:37: #1 tags after filtering in treatment: 4821298 INFO @ Wed, 10 Oct 2018 00:03:37: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 10 Oct 2018 00:03:37: #1 finished! INFO @ Wed, 10 Oct 2018 00:03:37: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:03:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:03:37: #2 number of paired peaks: 23 WARNING @ Wed, 10 Oct 2018 00:03:37: Too few paired peaks (23) 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 00:03:37: Process for pairing-model is terminated! cat: SRX4669658.05_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): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669658.05_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 `SRX4669658.05_*.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 `SRX4669658.05_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。