Job ID = 11245138 sra ファイルのダウンロード中... Completed: 510192K bytes transferred in 8 seconds (513931K 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 8988215 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669589/SRR7818163.sra Written 8988215 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669589/SRR7818163.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: 00:07:13 8988215 reads; of these: 8988215 (100.00%) were paired; of these: 937727 (10.43%) aligned concordantly 0 times 7132638 (79.36%) aligned concordantly exactly 1 time 917850 (10.21%) aligned concordantly >1 times ---- 937727 pairs aligned concordantly 0 times; of these: 24531 (2.62%) aligned discordantly 1 time ---- 913196 pairs aligned 0 times concordantly or discordantly; of these: 1826392 mates make up the pairs; of these: 1636427 (89.60%) aligned 0 times 98475 (5.39%) aligned exactly 1 time 91490 (5.01%) aligned >1 times 90.90% overall alignment rate Time searching: 00:07:13 Overall time: 00:07:13 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] 1185568 / 8072611 = 0.1469 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 23:44:04: # Command line: callpeak -t SRX4669589.bam -f BAM -g 12100000 -n SRX4669589.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669589.10 # format = BAM # ChIP-seq file = ['SRX4669589.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 23:44:04: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:44:04: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:44:04: # Command line: callpeak -t SRX4669589.bam -f BAM -g 12100000 -n SRX4669589.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669589.05 # format = BAM # ChIP-seq file = ['SRX4669589.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 23:44:04: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:44:04: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:44:04: # Command line: callpeak -t SRX4669589.bam -f BAM -g 12100000 -n SRX4669589.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669589.20 # format = BAM # ChIP-seq file = ['SRX4669589.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 23:44:04: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:44:04: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:44:09: 1000000 INFO @ Tue, 09 Oct 2018 23:44:10: 1000000 INFO @ Tue, 09 Oct 2018 23:44:10: 1000000 INFO @ Tue, 09 Oct 2018 23:44:15: 2000000 INFO @ Tue, 09 Oct 2018 23:44:17: 2000000 INFO @ Tue, 09 Oct 2018 23:44:17: 2000000 INFO @ Tue, 09 Oct 2018 23:44:20: 3000000 INFO @ Tue, 09 Oct 2018 23:44:24: 3000000 INFO @ Tue, 09 Oct 2018 23:44:24: 3000000 INFO @ Tue, 09 Oct 2018 23:44:26: 4000000 INFO @ Tue, 09 Oct 2018 23:44:30: 4000000 INFO @ Tue, 09 Oct 2018 23:44:30: 4000000 INFO @ Tue, 09 Oct 2018 23:44:32: 5000000 INFO @ Tue, 09 Oct 2018 23:44:37: 5000000 INFO @ Tue, 09 Oct 2018 23:44:37: 5000000 INFO @ Tue, 09 Oct 2018 23:44:37: 6000000 INFO @ Tue, 09 Oct 2018 23:44:43: 7000000 INFO @ Tue, 09 Oct 2018 23:44:44: 6000000 INFO @ Tue, 09 Oct 2018 23:44:44: 6000000 INFO @ Tue, 09 Oct 2018 23:44:49: 8000000 INFO @ Tue, 09 Oct 2018 23:44:50: 7000000 INFO @ Tue, 09 Oct 2018 23:44:50: 7000000 INFO @ Tue, 09 Oct 2018 23:44:54: 9000000 INFO @ Tue, 09 Oct 2018 23:44:57: 8000000 INFO @ Tue, 09 Oct 2018 23:44:57: 8000000 INFO @ Tue, 09 Oct 2018 23:45:00: 10000000 INFO @ Tue, 09 Oct 2018 23:45:04: 9000000 INFO @ Tue, 09 Oct 2018 23:45:04: 9000000 INFO @ Tue, 09 Oct 2018 23:45:05: 11000000 INFO @ Tue, 09 Oct 2018 23:45:10: 10000000 INFO @ Tue, 09 Oct 2018 23:45:10: 10000000 INFO @ Tue, 09 Oct 2018 23:45:11: 12000000 INFO @ Tue, 09 Oct 2018 23:45:17: 13000000 INFO @ Tue, 09 Oct 2018 23:45:17: 11000000 INFO @ Tue, 09 Oct 2018 23:45:17: 11000000 INFO @ Tue, 09 Oct 2018 23:45:22: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:45:22: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:45:22: #1 total tags in treatment: 6867096 INFO @ Tue, 09 Oct 2018 23:45:22: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:45:22: #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 23:45:22: #1 tags after filtering in treatment: 5449817 INFO @ Tue, 09 Oct 2018 23:45:22: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 09 Oct 2018 23:45:22: #1 finished! INFO @ Tue, 09 Oct 2018 23:45:22: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:45:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:45:23: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:45:23: 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 @ Tue, 09 Oct 2018 23:45:23: Process for pairing-model is terminated! cat: SRX4669589.20_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 `SRX4669589.20_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 `SRX4669589.20_*.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 `SRX4669589.20_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 23:45:24: 12000000 INFO @ Tue, 09 Oct 2018 23:45:24: 12000000 INFO @ Tue, 09 Oct 2018 23:45:31: 13000000 INFO @ Tue, 09 Oct 2018 23:45:31: 13000000 INFO @ Tue, 09 Oct 2018 23:45:37: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:45:37: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:45:37: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:45:37: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:45:37: #1 total tags in treatment: 6867096 INFO @ Tue, 09 Oct 2018 23:45:37: #1 total tags in treatment: 6867096 INFO @ Tue, 09 Oct 2018 23:45:37: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:45:37: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:45:37: #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 23:45:37: #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 23:45:37: #1 tags after filtering in treatment: 5449817 INFO @ Tue, 09 Oct 2018 23:45:37: #1 tags after filtering in treatment: 5449817 INFO @ Tue, 09 Oct 2018 23:45:37: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 09 Oct 2018 23:45:37: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 09 Oct 2018 23:45:37: #1 finished! INFO @ Tue, 09 Oct 2018 23:45:37: #1 finished! INFO @ Tue, 09 Oct 2018 23:45:37: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:45:37: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:45:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:45:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:45:38: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:45:38: 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 @ Tue, 09 Oct 2018 23:45:38: Process for pairing-model is terminated! INFO @ Tue, 09 Oct 2018 23:45:38: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:45:38: 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 @ Tue, 09 Oct 2018 23:45:38: Process for pairing-model is terminated! cat: SRX4669589.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX4669589.05_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 `SRX4669589.10_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 `SRX4669589.10_*.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 `SRX4669589.10_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 `SRX4669589.05_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 `SRX4669589.05_*.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 `SRX4669589.05_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。