Job ID = 11244991 sra ファイルのダウンロード中... Completed: 282653K bytes transferred in 8 seconds (277572K 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 8924740 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554703/SRR7696376.sra Written 8924740 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554703/SRR7696376.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: 00:04:49 8924740 reads; of these: 8924740 (100.00%) were paired; of these: 6692753 (74.99%) aligned concordantly 0 times 1971617 (22.09%) aligned concordantly exactly 1 time 260370 (2.92%) aligned concordantly >1 times ---- 6692753 pairs aligned concordantly 0 times; of these: 2131 (0.03%) aligned discordantly 1 time ---- 6690622 pairs aligned 0 times concordantly or discordantly; of these: 13381244 mates make up the pairs; of these: 9053376 (67.66%) aligned 0 times 3866848 (28.90%) aligned exactly 1 time 461020 (3.45%) aligned >1 times 49.28% overall alignment rate Time searching: 00:04:49 Overall time: 00:04:49 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_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] 765832 / 2233413 = 0.3429 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 23:08:54: # Command line: callpeak -t SRX4554703.bam -f BAM -g 12100000 -n SRX4554703.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554703.20 # format = BAM # ChIP-seq file = ['SRX4554703.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 23:08:54: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:08:54: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:08:54: # Command line: callpeak -t SRX4554703.bam -f BAM -g 12100000 -n SRX4554703.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554703.10 # format = BAM # ChIP-seq file = ['SRX4554703.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 23:08:54: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:08:54: # Command line: callpeak -t SRX4554703.bam -f BAM -g 12100000 -n SRX4554703.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554703.05 # format = BAM # ChIP-seq file = ['SRX4554703.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 23:08:54: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:08:54: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:08:54: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:09:00: 1000000 INFO @ Tue, 09 Oct 2018 23:09:00: 1000000 INFO @ Tue, 09 Oct 2018 23:09:00: 1000000 INFO @ Tue, 09 Oct 2018 23:09:06: 2000000 INFO @ Tue, 09 Oct 2018 23:09:07: 2000000 INFO @ Tue, 09 Oct 2018 23:09:07: 2000000 INFO @ Tue, 09 Oct 2018 23:09:13: 3000000 INFO @ Tue, 09 Oct 2018 23:09:14: 3000000 INFO @ Tue, 09 Oct 2018 23:09:14: 3000000 INFO @ Tue, 09 Oct 2018 23:09:20: 4000000 INFO @ Tue, 09 Oct 2018 23:09:21: 4000000 INFO @ Tue, 09 Oct 2018 23:09:21: 4000000 INFO @ Tue, 09 Oct 2018 23:09:25: 5000000 INFO @ Tue, 09 Oct 2018 23:09:27: 5000000 INFO @ Tue, 09 Oct 2018 23:09:27: 5000000 INFO @ Tue, 09 Oct 2018 23:09:31: 6000000 INFO @ Tue, 09 Oct 2018 23:09:33: 6000000 INFO @ Tue, 09 Oct 2018 23:09:33: 6000000 INFO @ Tue, 09 Oct 2018 23:09:36: 7000000 INFO @ Tue, 09 Oct 2018 23:09:37: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:09:37: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:09:37: #1 total tags in treatment: 1466233 INFO @ Tue, 09 Oct 2018 23:09:37: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:09:37: #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 23:09:37: #1 tags after filtering in treatment: 1088415 INFO @ Tue, 09 Oct 2018 23:09:37: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 09 Oct 2018 23:09:37: #1 finished! INFO @ Tue, 09 Oct 2018 23:09:37: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:09:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:09:37: #2 number of paired peaks: 8 WARNING @ Tue, 09 Oct 2018 23:09:37: Too few paired peaks (8) 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 23:09:37: Process for pairing-model is terminated! cat: SRX4554703.20_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 `SRX4554703.20_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 `SRX4554703.20_*.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 `SRX4554703.20_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 23:09:38: 7000000 INFO @ Tue, 09 Oct 2018 23:09:38: 7000000 INFO @ Tue, 09 Oct 2018 23:09:40: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:09:40: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:09:40: #1 total tags in treatment: 1466233 INFO @ Tue, 09 Oct 2018 23:09:40: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:09:40: #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 23:09:40: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:09:40: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:09:40: #1 total tags in treatment: 1466233 INFO @ Tue, 09 Oct 2018 23:09:40: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:09:40: #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 23:09:40: #1 tags after filtering in treatment: 1088415 INFO @ Tue, 09 Oct 2018 23:09:40: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 09 Oct 2018 23:09:40: #1 finished! INFO @ Tue, 09 Oct 2018 23:09:40: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:09:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:09:40: #1 tags after filtering in treatment: 1088415 INFO @ Tue, 09 Oct 2018 23:09:40: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 09 Oct 2018 23:09:40: #1 finished! INFO @ Tue, 09 Oct 2018 23:09:40: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:09:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:09:40: #2 number of paired peaks: 8 WARNING @ Tue, 09 Oct 2018 23:09:40: Too few paired peaks (8) 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 23:09:40: Process for pairing-model is terminated! cat: SRX4554703.10_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 23:09:40: #2 number of paired peaks: 8 WARNING @ Tue, 09 Oct 2018 23:09:40: Too few paired peaks (8) 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 23:09:40: Process for pairing-model is terminated! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4554703.10_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 `SRX4554703.10_*.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 `SRX4554703.10_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: SRX4554703.05_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 `SRX4554703.05_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 `SRX4554703.05_*.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 `SRX4554703.05_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。