Job ID = 11245139 sra ファイルのダウンロード中... Completed: 495806K bytes transferred in 7 seconds (520180K 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 8598203 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669590/SRR7818164.sra Written 8598203 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669590/SRR7818164.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: 00:06:24 8598203 reads; of these: 8598203 (100.00%) were paired; of these: 1036247 (12.05%) aligned concordantly 0 times 6575209 (76.47%) aligned concordantly exactly 1 time 986747 (11.48%) aligned concordantly >1 times ---- 1036247 pairs aligned concordantly 0 times; of these: 15406 (1.49%) aligned discordantly 1 time ---- 1020841 pairs aligned 0 times concordantly or discordantly; of these: 2041682 mates make up the pairs; of these: 1874735 (91.82%) aligned 0 times 88054 (4.31%) aligned exactly 1 time 78893 (3.86%) aligned >1 times 89.10% overall alignment rate Time searching: 00:06:24 Overall time: 00:06:24 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] 1588505 / 7575294 = 0.2097 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 23:42:56: # Command line: callpeak -t SRX4669590.bam -f BAM -g 12100000 -n SRX4669590.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669590.20 # format = BAM # ChIP-seq file = ['SRX4669590.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 23:42:56: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:42:56: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:42:56: # Command line: callpeak -t SRX4669590.bam -f BAM -g 12100000 -n SRX4669590.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669590.05 # format = BAM # ChIP-seq file = ['SRX4669590.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 23:42:56: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:42:56: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:42:56: # Command line: callpeak -t SRX4669590.bam -f BAM -g 12100000 -n SRX4669590.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669590.10 # format = BAM # ChIP-seq file = ['SRX4669590.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 23:42:56: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:42:56: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:43:02: 1000000 INFO @ Tue, 09 Oct 2018 23:43:03: 1000000 INFO @ Tue, 09 Oct 2018 23:43:03: 1000000 INFO @ Tue, 09 Oct 2018 23:43:08: 2000000 INFO @ Tue, 09 Oct 2018 23:43:10: 2000000 INFO @ Tue, 09 Oct 2018 23:43:10: 2000000 INFO @ Tue, 09 Oct 2018 23:43:15: 3000000 INFO @ Tue, 09 Oct 2018 23:43:17: 3000000 INFO @ Tue, 09 Oct 2018 23:43:17: 3000000 INFO @ Tue, 09 Oct 2018 23:43:21: 4000000 INFO @ Tue, 09 Oct 2018 23:43:23: 4000000 INFO @ Tue, 09 Oct 2018 23:43:24: 4000000 INFO @ Tue, 09 Oct 2018 23:43:28: 5000000 INFO @ Tue, 09 Oct 2018 23:43:30: 5000000 INFO @ Tue, 09 Oct 2018 23:43:30: 5000000 INFO @ Tue, 09 Oct 2018 23:43:34: 6000000 INFO @ Tue, 09 Oct 2018 23:43:37: 6000000 INFO @ Tue, 09 Oct 2018 23:43:37: 6000000 INFO @ Tue, 09 Oct 2018 23:43:40: 7000000 INFO @ Tue, 09 Oct 2018 23:43:44: 7000000 INFO @ Tue, 09 Oct 2018 23:43:44: 7000000 INFO @ Tue, 09 Oct 2018 23:43:47: 8000000 INFO @ Tue, 09 Oct 2018 23:43:50: 8000000 INFO @ Tue, 09 Oct 2018 23:43:50: 8000000 INFO @ Tue, 09 Oct 2018 23:43:53: 9000000 INFO @ Tue, 09 Oct 2018 23:43:57: 9000000 INFO @ Tue, 09 Oct 2018 23:43:57: 9000000 INFO @ Tue, 09 Oct 2018 23:43:59: 10000000 INFO @ Tue, 09 Oct 2018 23:44:04: 10000000 INFO @ Tue, 09 Oct 2018 23:44:04: 10000000 INFO @ Tue, 09 Oct 2018 23:44:06: 11000000 INFO @ Tue, 09 Oct 2018 23:44:11: 11000000 INFO @ Tue, 09 Oct 2018 23:44:11: 11000000 INFO @ Tue, 09 Oct 2018 23:44:12: 12000000 INFO @ Tue, 09 Oct 2018 23:44:13: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:44:13: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:44:13: #1 total tags in treatment: 5975518 INFO @ Tue, 09 Oct 2018 23:44:13: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:44:13: #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 23:44:13: #1 tags after filtering in treatment: 4787917 INFO @ Tue, 09 Oct 2018 23:44:13: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 09 Oct 2018 23:44:13: #1 finished! INFO @ Tue, 09 Oct 2018 23:44:13: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:44:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:44:14: #2 number of paired peaks: 26 WARNING @ Tue, 09 Oct 2018 23:44:14: Too few paired peaks (26) 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 23:44:14: Process for pairing-model is terminated! cat: SRX4669590.20_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 `SRX4669590.20_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 `SRX4669590.20_*.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 `SRX4669590.20_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 23:44:17: 12000000 INFO @ Tue, 09 Oct 2018 23:44:17: 12000000 INFO @ Tue, 09 Oct 2018 23:44:18: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:44:18: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:44:18: #1 total tags in treatment: 5975518 INFO @ Tue, 09 Oct 2018 23:44:18: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:44:18: #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 23:44:18: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:44:18: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:44:18: #1 total tags in treatment: 5975518 INFO @ Tue, 09 Oct 2018 23:44:18: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:44:18: #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 23:44:18: #1 tags after filtering in treatment: 4787917 INFO @ Tue, 09 Oct 2018 23:44:18: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 09 Oct 2018 23:44:18: #1 finished! INFO @ Tue, 09 Oct 2018 23:44:18: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:44:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:44:18: #1 tags after filtering in treatment: 4787917 INFO @ Tue, 09 Oct 2018 23:44:18: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 09 Oct 2018 23:44:18: #1 finished! INFO @ Tue, 09 Oct 2018 23:44:18: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:44:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:44:19: #2 number of paired peaks: 26 WARNING @ Tue, 09 Oct 2018 23:44:19: Too few paired peaks (26) 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 23:44:19: Process for pairing-model is terminated! INFO @ Tue, 09 Oct 2018 23:44:19: #2 number of paired peaks: 26 WARNING @ Tue, 09 Oct 2018 23:44:19: Too few paired peaks (26) 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 23:44:19: Process for pairing-model is terminated! cat: SRX4669590.05_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: SRX4669590.10_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) pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669590.05_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 `SRX4669590.05_*.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 `SRX4669590.05_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 `SRX4669590.10_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 `SRX4669590.10_*.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 `SRX4669590.10_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。