Job ID = 11245165 sra ファイルのダウンロード中... Completed: 276712K bytes transferred in 5 seconds (379633K 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 5708545 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669612/SRR7818195.sra Written 5708545 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669612/SRR7818195.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: 00:03:58 5708545 reads; of these: 5708545 (100.00%) were paired; of these: 587051 (10.28%) aligned concordantly 0 times 4519544 (79.17%) aligned concordantly exactly 1 time 601950 (10.54%) aligned concordantly >1 times ---- 587051 pairs aligned concordantly 0 times; of these: 25382 (4.32%) aligned discordantly 1 time ---- 561669 pairs aligned 0 times concordantly or discordantly; of these: 1123338 mates make up the pairs; of these: 903913 (80.47%) aligned 0 times 152957 (13.62%) aligned exactly 1 time 66468 (5.92%) aligned >1 times 92.08% overall alignment rate Time searching: 00:03:58 Overall time: 00:03:58 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] 58001 / 5136758 = 0.0113 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 23:46:28: # Command line: callpeak -t SRX4669612.bam -f BAM -g 12100000 -n SRX4669612.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669612.10 # format = BAM # ChIP-seq file = ['SRX4669612.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 23:46:28: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:46:28: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:46:28: # Command line: callpeak -t SRX4669612.bam -f BAM -g 12100000 -n SRX4669612.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669612.20 # format = BAM # ChIP-seq file = ['SRX4669612.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 23:46:28: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:46:28: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:46:28: # Command line: callpeak -t SRX4669612.bam -f BAM -g 12100000 -n SRX4669612.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669612.05 # format = BAM # ChIP-seq file = ['SRX4669612.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 23:46:28: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:46:28: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:46:34: 1000000 INFO @ Tue, 09 Oct 2018 23:46:34: 1000000 INFO @ Tue, 09 Oct 2018 23:46:34: 1000000 INFO @ Tue, 09 Oct 2018 23:46:40: 2000000 INFO @ Tue, 09 Oct 2018 23:46:40: 2000000 INFO @ Tue, 09 Oct 2018 23:46:40: 2000000 INFO @ Tue, 09 Oct 2018 23:46:46: 3000000 INFO @ Tue, 09 Oct 2018 23:46:46: 3000000 INFO @ Tue, 09 Oct 2018 23:46:47: 3000000 INFO @ Tue, 09 Oct 2018 23:46:51: 4000000 INFO @ Tue, 09 Oct 2018 23:46:52: 4000000 INFO @ Tue, 09 Oct 2018 23:46:53: 4000000 INFO @ Tue, 09 Oct 2018 23:46:57: 5000000 INFO @ Tue, 09 Oct 2018 23:46:58: 5000000 INFO @ Tue, 09 Oct 2018 23:47:00: 5000000 INFO @ Tue, 09 Oct 2018 23:47:03: 6000000 INFO @ Tue, 09 Oct 2018 23:47:05: 6000000 INFO @ Tue, 09 Oct 2018 23:47:06: 6000000 INFO @ Tue, 09 Oct 2018 23:47:08: 7000000 INFO @ Tue, 09 Oct 2018 23:47:11: 7000000 INFO @ Tue, 09 Oct 2018 23:47:13: 7000000 INFO @ Tue, 09 Oct 2018 23:47:14: 8000000 INFO @ Tue, 09 Oct 2018 23:47:17: 8000000 INFO @ Tue, 09 Oct 2018 23:47:19: 8000000 INFO @ Tue, 09 Oct 2018 23:47:20: 9000000 INFO @ Tue, 09 Oct 2018 23:47:23: 9000000 INFO @ Tue, 09 Oct 2018 23:47:25: 10000000 INFO @ Tue, 09 Oct 2018 23:47:25: 9000000 INFO @ Tue, 09 Oct 2018 23:47:28: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:47:28: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:47:28: #1 total tags in treatment: 5063786 INFO @ Tue, 09 Oct 2018 23:47:28: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:47:28: #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 23:47:28: #1 tags after filtering in treatment: 4226348 INFO @ Tue, 09 Oct 2018 23:47:28: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 09 Oct 2018 23:47:28: #1 finished! INFO @ Tue, 09 Oct 2018 23:47:28: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:47:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:47:28: #2 number of paired peaks: 33 WARNING @ Tue, 09 Oct 2018 23:47:28: Too few paired peaks (33) 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 23:47:28: Process for pairing-model is terminated! cat: SRX4669612.20_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 `SRX4669612.20_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 `SRX4669612.20_*.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 `SRX4669612.20_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 @ Tue, 09 Oct 2018 23:47:28: 10000000 INFO @ Tue, 09 Oct 2018 23:47:31: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:47:31: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:47:31: #1 total tags in treatment: 5063786 INFO @ Tue, 09 Oct 2018 23:47:31: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:47:31: #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 23:47:31: #1 tags after filtering in treatment: 4226348 INFO @ Tue, 09 Oct 2018 23:47:31: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 09 Oct 2018 23:47:31: #1 finished! INFO @ Tue, 09 Oct 2018 23:47:31: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:47:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:47:31: #2 number of paired peaks: 33 WARNING @ Tue, 09 Oct 2018 23:47:31: Too few paired peaks (33) 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 23:47:31: Process for pairing-model is terminated! cat: SRX4669612.10_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 `SRX4669612.10_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 `SRX4669612.10_*.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 `SRX4669612.10_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 23:47:32: 10000000 INFO @ Tue, 09 Oct 2018 23:47:34: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:47:34: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:47:34: #1 total tags in treatment: 5063786 INFO @ Tue, 09 Oct 2018 23:47:34: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:47:34: #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 23:47:34: #1 tags after filtering in treatment: 4226348 INFO @ Tue, 09 Oct 2018 23:47:34: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 09 Oct 2018 23:47:34: #1 finished! INFO @ Tue, 09 Oct 2018 23:47:34: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:47:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:47:34: #2 number of paired peaks: 33 WARNING @ Tue, 09 Oct 2018 23:47:34: Too few paired peaks (33) 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 23:47:34: Process for pairing-model is terminated! cat: SRX4669612.05_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 `SRX4669612.05_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 `SRX4669612.05_*.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 `SRX4669612.05_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。