Job ID = 9302890 sra ファイルのダウンロード中... Completed: 351819K bytes transferred in 10 seconds (284283K bits/sec), in 1 file, 2 directories. 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... Written 6361502 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2745547/SRR5457484.sra Written 6361502 spots total 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: 00:07:03 6361502 reads; of these: 6361502 (100.00%) were paired; of these: 1005077 (15.80%) aligned concordantly 0 times 4526025 (71.15%) aligned concordantly exactly 1 time 830400 (13.05%) aligned concordantly >1 times ---- 1005077 pairs aligned concordantly 0 times; of these: 516864 (51.43%) aligned discordantly 1 time ---- 488213 pairs aligned 0 times concordantly or discordantly; of these: 976426 mates make up the pairs; of these: 703623 (72.06%) aligned 0 times 70357 (7.21%) aligned exactly 1 time 202446 (20.73%) aligned >1 times 94.47% overall alignment rate Time searching: 00:07:03 Overall time: 00:07:03 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] 75117 / 5868772 = 0.0128 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 @ Fri, 28 Jul 2017 11:40:46: # Command line: callpeak -t SRX2745547.bam -f BAM -g 12100000 -n SRX2745547.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2745547.05 # format = BAM # ChIP-seq file = ['SRX2745547.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 @ Fri, 28 Jul 2017 11:40:46: #1 read tag files... INFO @ Fri, 28 Jul 2017 11:40:46: #1 read treatment tags... INFO @ Fri, 28 Jul 2017 11:40:46: # Command line: callpeak -t SRX2745547.bam -f BAM -g 12100000 -n SRX2745547.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2745547.20 # format = BAM # ChIP-seq file = ['SRX2745547.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 @ Fri, 28 Jul 2017 11:40:46: #1 read tag files... INFO @ Fri, 28 Jul 2017 11:40:46: #1 read treatment tags... INFO @ Fri, 28 Jul 2017 11:40:46: # Command line: callpeak -t SRX2745547.bam -f BAM -g 12100000 -n SRX2745547.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2745547.10 # format = BAM # ChIP-seq file = ['SRX2745547.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 @ Fri, 28 Jul 2017 11:40:46: #1 read tag files... INFO @ Fri, 28 Jul 2017 11:40:46: #1 read treatment tags... INFO @ Fri, 28 Jul 2017 11:40:52: 1000000 INFO @ Fri, 28 Jul 2017 11:40:52: 1000000 INFO @ Fri, 28 Jul 2017 11:40:52: 1000000 INFO @ Fri, 28 Jul 2017 11:40:58: 2000000 INFO @ Fri, 28 Jul 2017 11:40:58: 2000000 INFO @ Fri, 28 Jul 2017 11:40:58: 2000000 INFO @ Fri, 28 Jul 2017 11:41:04: 3000000 INFO @ Fri, 28 Jul 2017 11:41:04: 3000000 INFO @ Fri, 28 Jul 2017 11:41:05: 3000000 INFO @ Fri, 28 Jul 2017 11:41:10: 4000000 INFO @ Fri, 28 Jul 2017 11:41:11: 4000000 INFO @ Fri, 28 Jul 2017 11:41:11: 4000000 INFO @ Fri, 28 Jul 2017 11:41:16: 5000000 INFO @ Fri, 28 Jul 2017 11:41:17: 5000000 INFO @ Fri, 28 Jul 2017 11:41:17: 5000000 INFO @ Fri, 28 Jul 2017 11:41:22: 6000000 INFO @ Fri, 28 Jul 2017 11:41:23: 6000000 INFO @ Fri, 28 Jul 2017 11:41:23: 6000000 INFO @ Fri, 28 Jul 2017 11:41:28: 7000000 INFO @ Fri, 28 Jul 2017 11:41:29: 7000000 INFO @ Fri, 28 Jul 2017 11:41:30: 7000000 INFO @ Fri, 28 Jul 2017 11:41:34: 8000000 INFO @ Fri, 28 Jul 2017 11:41:35: 8000000 INFO @ Fri, 28 Jul 2017 11:41:36: 8000000 INFO @ Fri, 28 Jul 2017 11:41:40: 9000000 INFO @ Fri, 28 Jul 2017 11:41:42: 9000000 INFO @ Fri, 28 Jul 2017 11:41:43: 9000000 INFO @ Fri, 28 Jul 2017 11:41:46: 10000000 INFO @ Fri, 28 Jul 2017 11:41:48: 10000000 INFO @ Fri, 28 Jul 2017 11:41:49: 10000000 INFO @ Fri, 28 Jul 2017 11:41:52: 11000000 INFO @ Fri, 28 Jul 2017 11:41:55: 11000000 INFO @ Fri, 28 Jul 2017 11:41:56: 11000000 INFO @ Fri, 28 Jul 2017 11:41:57: #1 tag size is determined as 75 bps INFO @ Fri, 28 Jul 2017 11:41:57: #1 tag size = 75 INFO @ Fri, 28 Jul 2017 11:41:57: #1 total tags in treatment: 5283914 INFO @ Fri, 28 Jul 2017 11:41:57: #1 user defined the maximum tags... INFO @ Fri, 28 Jul 2017 11:41:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 28 Jul 2017 11:41:57: #1 tags after filtering in treatment: 4267145 INFO @ Fri, 28 Jul 2017 11:41:57: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 28 Jul 2017 11:41:57: #1 finished! INFO @ Fri, 28 Jul 2017 11:41:57: #2 Build Peak Model... INFO @ Fri, 28 Jul 2017 11:41:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 28 Jul 2017 11:41:57: #2 number of paired peaks: 28 WARNING @ Fri, 28 Jul 2017 11:41:57: Too few paired peaks (28) 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 @ Fri, 28 Jul 2017 11:41:57: Process for pairing-model is terminated! cat: SRX2745547.10_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 `SRX2745547.10_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 `SRX2745547.10_*.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 `SRX2745547.10_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 @ Fri, 28 Jul 2017 11:42:01: #1 tag size is determined as 75 bps INFO @ Fri, 28 Jul 2017 11:42:01: #1 tag size = 75 INFO @ Fri, 28 Jul 2017 11:42:01: #1 total tags in treatment: 5283914 INFO @ Fri, 28 Jul 2017 11:42:01: #1 user defined the maximum tags... INFO @ Fri, 28 Jul 2017 11:42:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 28 Jul 2017 11:42:01: #1 tags after filtering in treatment: 4267145 INFO @ Fri, 28 Jul 2017 11:42:01: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 28 Jul 2017 11:42:01: #1 finished! INFO @ Fri, 28 Jul 2017 11:42:01: #2 Build Peak Model... INFO @ Fri, 28 Jul 2017 11:42:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 28 Jul 2017 11:42:01: #2 number of paired peaks: 28 WARNING @ Fri, 28 Jul 2017 11:42:01: Too few paired peaks (28) 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 @ Fri, 28 Jul 2017 11:42:01: Process for pairing-model is terminated! cat: SRX2745547.05_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 `SRX2745547.05_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 `SRX2745547.05_*.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 `SRX2745547.05_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 INFO @ Fri, 28 Jul 2017 11:42:01: #1 tag size is determined as 75 bps INFO @ Fri, 28 Jul 2017 11:42:01: #1 tag size = 75 INFO @ Fri, 28 Jul 2017 11:42:01: #1 total tags in treatment: 5283914 INFO @ Fri, 28 Jul 2017 11:42:01: #1 user defined the maximum tags... INFO @ Fri, 28 Jul 2017 11:42:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 28 Jul 2017 11:42:02: #1 tags after filtering in treatment: 4267145 INFO @ Fri, 28 Jul 2017 11:42:02: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 28 Jul 2017 11:42:02: #1 finished! INFO @ Fri, 28 Jul 2017 11:42:02: #2 Build Peak Model... INFO @ Fri, 28 Jul 2017 11:42:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 28 Jul 2017 11:42:02: #2 number of paired peaks: 28 WARNING @ Fri, 28 Jul 2017 11:42:02: Too few paired peaks (28) 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 @ Fri, 28 Jul 2017 11:42:02: Process for pairing-model is terminated! cat: SRX2745547.20_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 `SRX2745547.20_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 `SRX2745547.20_*.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 `SRX2745547.20_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。