Job ID = 11245212 sra ファイルのダウンロード中... Completed: 411807K bytes transferred in 7 seconds (469091K bits/sec), in 1 file. Completed: 412898K bytes transferred in 6 seconds (483723K bits/sec), in 1 file. Completed: 332742K bytes transferred in 6 seconds (435223K 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 3183608 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669663/SRR7818300.sra Written 3183608 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669663/SRR7818300.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669663/SRR7818299.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669663/SRR7818299.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669663/SRR7818298.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669663/SRR7818298.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: 00:10:16 11183608 reads; of these: 11183608 (100.00%) were paired; of these: 1935963 (17.31%) aligned concordantly 0 times 8077880 (72.23%) aligned concordantly exactly 1 time 1169765 (10.46%) aligned concordantly >1 times ---- 1935963 pairs aligned concordantly 0 times; of these: 137542 (7.10%) aligned discordantly 1 time ---- 1798421 pairs aligned 0 times concordantly or discordantly; of these: 3596842 mates make up the pairs; of these: 3073995 (85.46%) aligned 0 times 395519 (11.00%) aligned exactly 1 time 127328 (3.54%) aligned >1 times 86.26% overall alignment rate Time searching: 00:10:16 Overall time: 00:10:16 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] 168178 / 9348247 = 0.0180 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 00:08:28: # Command line: callpeak -t SRX4669663.bam -f BAM -g 12100000 -n SRX4669663.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669663.05 # format = BAM # ChIP-seq file = ['SRX4669663.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 00:08:28: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:08:28: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:08:28: # Command line: callpeak -t SRX4669663.bam -f BAM -g 12100000 -n SRX4669663.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669663.20 # format = BAM # ChIP-seq file = ['SRX4669663.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 00:08:28: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:08:28: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:08:28: # Command line: callpeak -t SRX4669663.bam -f BAM -g 12100000 -n SRX4669663.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669663.10 # format = BAM # ChIP-seq file = ['SRX4669663.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 00:08:28: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:08:28: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:08:36: 1000000 INFO @ Wed, 10 Oct 2018 00:08:36: 1000000 INFO @ Wed, 10 Oct 2018 00:08:36: 1000000 INFO @ Wed, 10 Oct 2018 00:08:44: 2000000 INFO @ Wed, 10 Oct 2018 00:08:44: 2000000 INFO @ Wed, 10 Oct 2018 00:08:44: 2000000 INFO @ Wed, 10 Oct 2018 00:08:52: 3000000 INFO @ Wed, 10 Oct 2018 00:08:52: 3000000 INFO @ Wed, 10 Oct 2018 00:08:52: 3000000 INFO @ Wed, 10 Oct 2018 00:09:00: 4000000 INFO @ Wed, 10 Oct 2018 00:09:00: 4000000 INFO @ Wed, 10 Oct 2018 00:09:00: 4000000 INFO @ Wed, 10 Oct 2018 00:09:07: 5000000 INFO @ Wed, 10 Oct 2018 00:09:08: 5000000 INFO @ Wed, 10 Oct 2018 00:09:08: 5000000 INFO @ Wed, 10 Oct 2018 00:09:15: 6000000 INFO @ Wed, 10 Oct 2018 00:09:15: 6000000 INFO @ Wed, 10 Oct 2018 00:09:15: 6000000 INFO @ Wed, 10 Oct 2018 00:09:23: 7000000 INFO @ Wed, 10 Oct 2018 00:09:23: 7000000 INFO @ Wed, 10 Oct 2018 00:09:23: 7000000 INFO @ Wed, 10 Oct 2018 00:09:31: 8000000 INFO @ Wed, 10 Oct 2018 00:09:31: 8000000 INFO @ Wed, 10 Oct 2018 00:09:31: 8000000 INFO @ Wed, 10 Oct 2018 00:09:38: 9000000 INFO @ Wed, 10 Oct 2018 00:09:39: 9000000 INFO @ Wed, 10 Oct 2018 00:09:39: 9000000 INFO @ Wed, 10 Oct 2018 00:09:46: 10000000 INFO @ Wed, 10 Oct 2018 00:09:47: 10000000 INFO @ Wed, 10 Oct 2018 00:09:47: 10000000 INFO @ Wed, 10 Oct 2018 00:09:54: 11000000 INFO @ Wed, 10 Oct 2018 00:09:55: 11000000 INFO @ Wed, 10 Oct 2018 00:09:55: 11000000 INFO @ Wed, 10 Oct 2018 00:10:01: 12000000 INFO @ Wed, 10 Oct 2018 00:10:02: 12000000 INFO @ Wed, 10 Oct 2018 00:10:02: 12000000 INFO @ Wed, 10 Oct 2018 00:10:09: 13000000 INFO @ Wed, 10 Oct 2018 00:10:10: 13000000 INFO @ Wed, 10 Oct 2018 00:10:10: 13000000 INFO @ Wed, 10 Oct 2018 00:10:17: 14000000 INFO @ Wed, 10 Oct 2018 00:10:18: 14000000 INFO @ Wed, 10 Oct 2018 00:10:18: 14000000 INFO @ Wed, 10 Oct 2018 00:10:24: 15000000 INFO @ Wed, 10 Oct 2018 00:10:26: 15000000 INFO @ Wed, 10 Oct 2018 00:10:26: 15000000 INFO @ Wed, 10 Oct 2018 00:10:32: 16000000 INFO @ Wed, 10 Oct 2018 00:10:34: 16000000 INFO @ Wed, 10 Oct 2018 00:10:34: 16000000 INFO @ Wed, 10 Oct 2018 00:10:40: 17000000 INFO @ Wed, 10 Oct 2018 00:10:41: 17000000 INFO @ Wed, 10 Oct 2018 00:10:41: 17000000 INFO @ Wed, 10 Oct 2018 00:10:47: 18000000 INFO @ Wed, 10 Oct 2018 00:10:49: 18000000 INFO @ Wed, 10 Oct 2018 00:10:49: 18000000 INFO @ Wed, 10 Oct 2018 00:10:55: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:10:55: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:10:55: #1 total tags in treatment: 9080475 INFO @ Wed, 10 Oct 2018 00:10:55: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:10:55: #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 00:10:55: #1 tags after filtering in treatment: 6941161 INFO @ Wed, 10 Oct 2018 00:10:55: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 10 Oct 2018 00:10:55: #1 finished! INFO @ Wed, 10 Oct 2018 00:10:55: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:10:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:10:55: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:10:55: 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 00:10:55: Process for pairing-model is terminated! cat: SRX4669663.10_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 `SRX4669663.10_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 `SRX4669663.10_*.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 `SRX4669663.10_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 00:10:57: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:10:57: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:10:57: #1 total tags in treatment: 9080475 INFO @ Wed, 10 Oct 2018 00:10:57: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:10:57: #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 00:10:57: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:10:57: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:10:57: #1 total tags in treatment: 9080475 INFO @ Wed, 10 Oct 2018 00:10:57: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:10:57: #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 00:10:57: #1 tags after filtering in treatment: 6941161 INFO @ Wed, 10 Oct 2018 00:10:57: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 10 Oct 2018 00:10:57: #1 finished! INFO @ Wed, 10 Oct 2018 00:10:57: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:10:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:10:57: #1 tags after filtering in treatment: 6941161 INFO @ Wed, 10 Oct 2018 00:10:57: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 10 Oct 2018 00:10:57: #1 finished! INFO @ Wed, 10 Oct 2018 00:10:57: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:10:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:10:57: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:10:57: 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 00:10:57: Process for pairing-model is terminated! INFO @ Wed, 10 Oct 2018 00:10:57: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:10:57: 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 00:10:57: Process for pairing-model is terminated! cat: SRX4669663.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX4669663.20_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) pass1 - making usageList (0 chroms): 2 millis rm: cannot remove `SRX4669663.05_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 `SRX4669663.05_*.xls': そのようなファイルやディレクトリはありません needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669663.05_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 rm: cannot remove `SRX4669663.20_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 `SRX4669663.20_*.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 `SRX4669663.20_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。