Job ID = 11245127 sra ファイルのダウンロード中... Completed: 320468K bytes transferred in 6 seconds (413151K 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 6408619 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669581/SRR7818155.sra Written 6408619 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669581/SRR7818155.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: 00:04:28 6408619 reads; of these: 6408619 (100.00%) were paired; of these: 544490 (8.50%) aligned concordantly 0 times 5100915 (79.59%) aligned concordantly exactly 1 time 763214 (11.91%) aligned concordantly >1 times ---- 544490 pairs aligned concordantly 0 times; of these: 19320 (3.55%) aligned discordantly 1 time ---- 525170 pairs aligned 0 times concordantly or discordantly; of these: 1050340 mates make up the pairs; of these: 897867 (85.48%) aligned 0 times 98955 (9.42%) aligned exactly 1 time 53518 (5.10%) aligned >1 times 92.99% overall alignment rate Time searching: 00:04:28 Overall time: 00:04:28 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] 97560 / 5871243 = 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 @ Tue, 09 Oct 2018 23:37:14: # Command line: callpeak -t SRX4669581.bam -f BAM -g 12100000 -n SRX4669581.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669581.05 # format = BAM # ChIP-seq file = ['SRX4669581.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 @ Tue, 09 Oct 2018 23:37:14: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:37:14: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:37:14: # Command line: callpeak -t SRX4669581.bam -f BAM -g 12100000 -n SRX4669581.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669581.20 # format = BAM # ChIP-seq file = ['SRX4669581.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 @ Tue, 09 Oct 2018 23:37:14: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:37:14: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:37:14: # Command line: callpeak -t SRX4669581.bam -f BAM -g 12100000 -n SRX4669581.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669581.10 # format = BAM # ChIP-seq file = ['SRX4669581.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 @ Tue, 09 Oct 2018 23:37:14: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:37:14: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:37:20: 1000000 INFO @ Tue, 09 Oct 2018 23:37:20: 1000000 INFO @ Tue, 09 Oct 2018 23:37:20: 1000000 INFO @ Tue, 09 Oct 2018 23:37:27: 2000000 INFO @ Tue, 09 Oct 2018 23:37:27: 2000000 INFO @ Tue, 09 Oct 2018 23:37:27: 2000000 INFO @ Tue, 09 Oct 2018 23:37:33: 3000000 INFO @ Tue, 09 Oct 2018 23:37:33: 3000000 INFO @ Tue, 09 Oct 2018 23:37:33: 3000000 INFO @ Tue, 09 Oct 2018 23:37:39: 4000000 INFO @ Tue, 09 Oct 2018 23:37:40: 4000000 INFO @ Tue, 09 Oct 2018 23:37:40: 4000000 INFO @ Tue, 09 Oct 2018 23:37:45: 5000000 INFO @ Tue, 09 Oct 2018 23:37:46: 5000000 INFO @ Tue, 09 Oct 2018 23:37:46: 5000000 INFO @ Tue, 09 Oct 2018 23:37:51: 6000000 INFO @ Tue, 09 Oct 2018 23:37:52: 6000000 INFO @ Tue, 09 Oct 2018 23:37:52: 6000000 INFO @ Tue, 09 Oct 2018 23:37:57: 7000000 INFO @ Tue, 09 Oct 2018 23:37:59: 7000000 INFO @ Tue, 09 Oct 2018 23:37:59: 7000000 INFO @ Tue, 09 Oct 2018 23:38:04: 8000000 INFO @ Tue, 09 Oct 2018 23:38:05: 8000000 INFO @ Tue, 09 Oct 2018 23:38:05: 8000000 INFO @ Tue, 09 Oct 2018 23:38:10: 9000000 INFO @ Tue, 09 Oct 2018 23:38:12: 9000000 INFO @ Tue, 09 Oct 2018 23:38:12: 9000000 INFO @ Tue, 09 Oct 2018 23:38:17: 10000000 INFO @ Tue, 09 Oct 2018 23:38:18: 10000000 INFO @ Tue, 09 Oct 2018 23:38:19: 10000000 INFO @ Tue, 09 Oct 2018 23:38:23: 11000000 INFO @ Tue, 09 Oct 2018 23:38:25: 11000000 INFO @ Tue, 09 Oct 2018 23:38:25: 11000000 INFO @ Tue, 09 Oct 2018 23:38:27: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:38:27: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:38:27: #1 total tags in treatment: 5766693 INFO @ Tue, 09 Oct 2018 23:38:27: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:38:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:38:28: #1 tags after filtering in treatment: 4660684 INFO @ Tue, 09 Oct 2018 23:38:28: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 09 Oct 2018 23:38:28: #1 finished! INFO @ Tue, 09 Oct 2018 23:38:28: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:38:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:38:28: #2 number of paired peaks: 22 WARNING @ Tue, 09 Oct 2018 23:38:28: Too few paired peaks (22) 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 @ Tue, 09 Oct 2018 23:38:28: Process for pairing-model is terminated! cat: SRX4669581.10_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 `SRX4669581.10_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 `SRX4669581.10_*.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 `SRX4669581.10_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 @ Tue, 09 Oct 2018 23:38:29: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:38:29: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:38:29: #1 total tags in treatment: 5766693 INFO @ Tue, 09 Oct 2018 23:38:29: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:38:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:38:29: #1 tags after filtering in treatment: 4660684 INFO @ Tue, 09 Oct 2018 23:38:29: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 09 Oct 2018 23:38:29: #1 finished! INFO @ Tue, 09 Oct 2018 23:38:29: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:38:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:38:29: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:38:29: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:38:29: #1 total tags in treatment: 5766693 INFO @ Tue, 09 Oct 2018 23:38:29: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:38:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:38:29: #1 tags after filtering in treatment: 4660684 INFO @ Tue, 09 Oct 2018 23:38:29: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 09 Oct 2018 23:38:29: #1 finished! INFO @ Tue, 09 Oct 2018 23:38:29: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:38:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:38:30: #2 number of paired peaks: 22 WARNING @ Tue, 09 Oct 2018 23:38:30: Too few paired peaks (22) 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 @ Tue, 09 Oct 2018 23:38:30: Process for pairing-model is terminated! cat: SRX4669581.05_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 `SRX4669581.05_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 `SRX4669581.05_*.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 `SRX4669581.05_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 @ Tue, 09 Oct 2018 23:38:30: #2 number of paired peaks: 22 WARNING @ Tue, 09 Oct 2018 23:38:30: Too few paired peaks (22) 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 @ Tue, 09 Oct 2018 23:38:30: Process for pairing-model is terminated! cat: SRX4669581.20_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 `SRX4669581.20_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 `SRX4669581.20_*.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 `SRX4669581.20_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。