Job ID = 11244863 sra ファイルのダウンロード中... Completed: 632936K bytes transferred in 9 seconds (554500K 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 6597383 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3765655/SRR6807378.sra Written 6597383 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3765655/SRR6807378.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: 00:08:10 6597383 reads; of these: 6597383 (100.00%) were paired; of these: 465467 (7.06%) aligned concordantly 0 times 5266905 (79.83%) aligned concordantly exactly 1 time 865011 (13.11%) aligned concordantly >1 times ---- 465467 pairs aligned concordantly 0 times; of these: 40066 (8.61%) aligned discordantly 1 time ---- 425401 pairs aligned 0 times concordantly or discordantly; of these: 850802 mates make up the pairs; of these: 767344 (90.19%) aligned 0 times 60043 (7.06%) aligned exactly 1 time 23415 (2.75%) aligned >1 times 94.18% overall alignment rate Time searching: 00:08:10 Overall time: 00:08:10 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] 1521051 / 6137150 = 0.2478 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 22:24:42: # Command line: callpeak -t SRX3765655.bam -f BAM -g 12100000 -n SRX3765655.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3765655.10 # format = BAM # ChIP-seq file = ['SRX3765655.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 22:24:42: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:24:42: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:24:42: # Command line: callpeak -t SRX3765655.bam -f BAM -g 12100000 -n SRX3765655.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3765655.20 # format = BAM # ChIP-seq file = ['SRX3765655.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 22:24:42: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:24:42: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:24:42: # Command line: callpeak -t SRX3765655.bam -f BAM -g 12100000 -n SRX3765655.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3765655.05 # format = BAM # ChIP-seq file = ['SRX3765655.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 22:24:42: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:24:42: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:24:51: 1000000 INFO @ Tue, 09 Oct 2018 22:24:51: 1000000 INFO @ Tue, 09 Oct 2018 22:24:51: 1000000 INFO @ Tue, 09 Oct 2018 22:25:01: 2000000 INFO @ Tue, 09 Oct 2018 22:25:01: 2000000 INFO @ Tue, 09 Oct 2018 22:25:01: 2000000 INFO @ Tue, 09 Oct 2018 22:25:10: 3000000 INFO @ Tue, 09 Oct 2018 22:25:11: 3000000 INFO @ Tue, 09 Oct 2018 22:25:11: 3000000 INFO @ Tue, 09 Oct 2018 22:25:19: 4000000 INFO @ Tue, 09 Oct 2018 22:25:20: 4000000 INFO @ Tue, 09 Oct 2018 22:25:20: 4000000 INFO @ Tue, 09 Oct 2018 22:25:29: 5000000 INFO @ Tue, 09 Oct 2018 22:25:30: 5000000 INFO @ Tue, 09 Oct 2018 22:25:30: 5000000 INFO @ Tue, 09 Oct 2018 22:25:38: 6000000 INFO @ Tue, 09 Oct 2018 22:25:39: 6000000 INFO @ Tue, 09 Oct 2018 22:25:39: 6000000 INFO @ Tue, 09 Oct 2018 22:25:48: 7000000 INFO @ Tue, 09 Oct 2018 22:25:49: 7000000 INFO @ Tue, 09 Oct 2018 22:25:49: 7000000 INFO @ Tue, 09 Oct 2018 22:25:57: 8000000 INFO @ Tue, 09 Oct 2018 22:25:59: 8000000 INFO @ Tue, 09 Oct 2018 22:25:59: 8000000 INFO @ Tue, 09 Oct 2018 22:26:06: 9000000 INFO @ Tue, 09 Oct 2018 22:26:08: 9000000 INFO @ Tue, 09 Oct 2018 22:26:08: 9000000 INFO @ Tue, 09 Oct 2018 22:26:10: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:26:10: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:26:10: #1 total tags in treatment: 4613139 INFO @ Tue, 09 Oct 2018 22:26:10: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:26:10: #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 22:26:10: #1 tags after filtering in treatment: 3127743 INFO @ Tue, 09 Oct 2018 22:26:10: #1 Redundant rate of treatment: 0.32 INFO @ Tue, 09 Oct 2018 22:26:10: #1 finished! INFO @ Tue, 09 Oct 2018 22:26:10: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:26:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:26:10: #2 number of paired peaks: 31 WARNING @ Tue, 09 Oct 2018 22:26:10: Too few paired peaks (31) 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 22:26:10: Process for pairing-model is terminated! cat: SRX3765655.10_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 `SRX3765655.10_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 `SRX3765655.10_*.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 `SRX3765655.10_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 22:26:12: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:26:12: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:26:12: #1 total tags in treatment: 4613139 INFO @ Tue, 09 Oct 2018 22:26:12: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:26:12: #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 22:26:12: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:26:12: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:26:12: #1 total tags in treatment: 4613139 INFO @ Tue, 09 Oct 2018 22:26:12: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:26:12: #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 22:26:12: #1 tags after filtering in treatment: 3127743 INFO @ Tue, 09 Oct 2018 22:26:12: #1 Redundant rate of treatment: 0.32 INFO @ Tue, 09 Oct 2018 22:26:12: #1 finished! INFO @ Tue, 09 Oct 2018 22:26:12: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:26:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:26:12: #1 tags after filtering in treatment: 3127743 INFO @ Tue, 09 Oct 2018 22:26:12: #1 Redundant rate of treatment: 0.32 INFO @ Tue, 09 Oct 2018 22:26:12: #1 finished! INFO @ Tue, 09 Oct 2018 22:26:12: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:26:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:26:12: #2 number of paired peaks: 31 WARNING @ Tue, 09 Oct 2018 22:26:12: Too few paired peaks (31) 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 22:26:12: Process for pairing-model is terminated! INFO @ Tue, 09 Oct 2018 22:26:12: #2 number of paired peaks: 31 WARNING @ Tue, 09 Oct 2018 22:26:12: Too few paired peaks (31) 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 22:26:12: Process for pairing-model is terminated! cat: SRX3765655.05_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: SRX3765655.20_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 `SRX3765655.05_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 `SRX3765655.05_*.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 `SRX3765655.05_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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3765655.20_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 `SRX3765655.20_*.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 `SRX3765655.20_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。