Job ID = 11245180 sra ファイルのダウンロード中... Completed: 24641K bytes transferred in 3 seconds (65979K bits/sec), in 1 file. Completed: 206599K bytes transferred in 4 seconds (346122K 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 527909 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669623/SRR7818214.sra Written 527909 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669623/SRR7818214.sra Read 5588255 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669623/SRR7818215.sra Written 5588255 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669623/SRR7818215.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: 00:04:33 6116164 reads; of these: 6116164 (100.00%) were paired; of these: 684037 (11.18%) aligned concordantly 0 times 4744369 (77.57%) aligned concordantly exactly 1 time 687758 (11.24%) aligned concordantly >1 times ---- 684037 pairs aligned concordantly 0 times; of these: 26736 (3.91%) aligned discordantly 1 time ---- 657301 pairs aligned 0 times concordantly or discordantly; of these: 1314602 mates make up the pairs; of these: 1089964 (82.91%) aligned 0 times 153829 (11.70%) aligned exactly 1 time 70809 (5.39%) aligned >1 times 91.09% overall alignment rate Time searching: 00:04:33 Overall time: 00:04:33 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] 1057959 / 5454973 = 0.1939 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 23:51:12: # Command line: callpeak -t SRX4669623.bam -f BAM -g 12100000 -n SRX4669623.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669623.05 # format = BAM # ChIP-seq file = ['SRX4669623.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 23:51:12: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:51:12: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:51:12: # Command line: callpeak -t SRX4669623.bam -f BAM -g 12100000 -n SRX4669623.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669623.10 # format = BAM # ChIP-seq file = ['SRX4669623.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 23:51:12: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:51:12: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:51:12: # Command line: callpeak -t SRX4669623.bam -f BAM -g 12100000 -n SRX4669623.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669623.20 # format = BAM # ChIP-seq file = ['SRX4669623.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 23:51:12: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:51:12: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:51:17: 1000000 INFO @ Tue, 09 Oct 2018 23:51:17: 1000000 INFO @ Tue, 09 Oct 2018 23:51:17: 1000000 INFO @ Tue, 09 Oct 2018 23:51:22: 2000000 INFO @ Tue, 09 Oct 2018 23:51:23: 2000000 INFO @ Tue, 09 Oct 2018 23:51:23: 2000000 INFO @ Tue, 09 Oct 2018 23:51:29: 3000000 INFO @ Tue, 09 Oct 2018 23:51:30: 3000000 INFO @ Tue, 09 Oct 2018 23:51:30: 3000000 INFO @ Tue, 09 Oct 2018 23:51:35: 4000000 INFO @ Tue, 09 Oct 2018 23:51:37: 4000000 INFO @ Tue, 09 Oct 2018 23:51:37: 4000000 INFO @ Tue, 09 Oct 2018 23:51:42: 5000000 INFO @ Tue, 09 Oct 2018 23:51:44: 5000000 INFO @ Tue, 09 Oct 2018 23:51:44: 5000000 INFO @ Tue, 09 Oct 2018 23:51:48: 6000000 INFO @ Tue, 09 Oct 2018 23:51:51: 6000000 INFO @ Tue, 09 Oct 2018 23:51:51: 6000000 INFO @ Tue, 09 Oct 2018 23:51:55: 7000000 INFO @ Tue, 09 Oct 2018 23:51:58: 7000000 INFO @ Tue, 09 Oct 2018 23:51:58: 7000000 INFO @ Tue, 09 Oct 2018 23:52:01: 8000000 INFO @ Tue, 09 Oct 2018 23:52:05: 8000000 INFO @ Tue, 09 Oct 2018 23:52:05: 8000000 INFO @ Tue, 09 Oct 2018 23:52:08: 9000000 INFO @ Tue, 09 Oct 2018 23:52:08: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:52:08: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:52:08: #1 total tags in treatment: 4378930 INFO @ Tue, 09 Oct 2018 23:52:08: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:52:08: #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 23:52:08: #1 tags after filtering in treatment: 3642840 INFO @ Tue, 09 Oct 2018 23:52:08: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 09 Oct 2018 23:52:08: #1 finished! INFO @ Tue, 09 Oct 2018 23:52:08: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:52:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:52:08: #2 number of paired peaks: 35 WARNING @ Tue, 09 Oct 2018 23:52:08: Too few paired peaks (35) 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 23:52:08: Process for pairing-model is terminated! cat: SRX4669623.05_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 `SRX4669623.05_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 `SRX4669623.05_*.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 `SRX4669623.05_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 23:52:12: 9000000 INFO @ Tue, 09 Oct 2018 23:52:12: 9000000 INFO @ Tue, 09 Oct 2018 23:52:13: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:52:13: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:52:13: #1 total tags in treatment: 4378930 INFO @ Tue, 09 Oct 2018 23:52:13: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:52:13: #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 23:52:13: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:52:13: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:52:13: #1 total tags in treatment: 4378930 INFO @ Tue, 09 Oct 2018 23:52:13: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:52:13: #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 23:52:13: #1 tags after filtering in treatment: 3642840 INFO @ Tue, 09 Oct 2018 23:52:13: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 09 Oct 2018 23:52:13: #1 finished! INFO @ Tue, 09 Oct 2018 23:52:13: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:52:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:52:13: #1 tags after filtering in treatment: 3642840 INFO @ Tue, 09 Oct 2018 23:52:13: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 09 Oct 2018 23:52:13: #1 finished! INFO @ Tue, 09 Oct 2018 23:52:13: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:52:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:52:13: #2 number of paired peaks: 35 WARNING @ Tue, 09 Oct 2018 23:52:13: Too few paired peaks (35) 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 23:52:13: Process for pairing-model is terminated! cat: SRX4669623.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Tue, 09 Oct 2018 23:52:13: #2 number of paired peaks: 35 WARNING @ Tue, 09 Oct 2018 23:52:13: Too few paired peaks (35) 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 23:52:13: Process for pairing-model is terminated! cat: SRX4669623.20_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669623.10_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 `SRX4669623.10_*.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 `SRX4669623.10_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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669623.20_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 `SRX4669623.20_*.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 `SRX4669623.20_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。