Job ID = 9161736 sra ファイルのダウンロード中... Completed: 1567397K bytes transferred in 16 seconds (758464K 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 10733466 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1004439/SRR1986257.sra Written 10733466 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: 00:12:45 10733466 reads; of these: 10733466 (100.00%) were paired; of these: 4175958 (38.91%) aligned concordantly 0 times 5978609 (55.70%) aligned concordantly exactly 1 time 578899 (5.39%) aligned concordantly >1 times ---- 4175958 pairs aligned concordantly 0 times; of these: 1204767 (28.85%) aligned discordantly 1 time ---- 2971191 pairs aligned 0 times concordantly or discordantly; of these: 5942382 mates make up the pairs; of these: 5387294 (90.66%) aligned 0 times 285519 (4.80%) aligned exactly 1 time 269569 (4.54%) aligned >1 times 74.90% overall alignment rate Time searching: 00:12:45 Overall time: 00:12:45 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] 367725 / 7702771 = 0.0477 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 @ Wed, 28 Jun 2017 04:47:35: # Command line: callpeak -t SRX1004439.bam -f BAM -g 12100000 -n SRX1004439.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1004439.10 # format = BAM # ChIP-seq file = ['SRX1004439.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 @ Wed, 28 Jun 2017 04:47:35: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:47:35: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:47:35: # Command line: callpeak -t SRX1004439.bam -f BAM -g 12100000 -n SRX1004439.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1004439.05 # format = BAM # ChIP-seq file = ['SRX1004439.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 @ Wed, 28 Jun 2017 04:47:35: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:47:35: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:47:35: # Command line: callpeak -t SRX1004439.bam -f BAM -g 12100000 -n SRX1004439.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1004439.20 # format = BAM # ChIP-seq file = ['SRX1004439.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 @ Wed, 28 Jun 2017 04:47:35: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:47:35: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:47:42: 1000000 INFO @ Wed, 28 Jun 2017 04:47:42: 1000000 INFO @ Wed, 28 Jun 2017 04:47:42: 1000000 INFO @ Wed, 28 Jun 2017 04:47:50: 2000000 INFO @ Wed, 28 Jun 2017 04:47:50: 2000000 INFO @ Wed, 28 Jun 2017 04:47:50: 2000000 INFO @ Wed, 28 Jun 2017 04:47:57: 3000000 INFO @ Wed, 28 Jun 2017 04:47:57: 3000000 INFO @ Wed, 28 Jun 2017 04:47:57: 3000000 INFO @ Wed, 28 Jun 2017 04:48:04: 4000000 INFO @ Wed, 28 Jun 2017 04:48:04: 4000000 INFO @ Wed, 28 Jun 2017 04:48:04: 4000000 INFO @ Wed, 28 Jun 2017 04:48:11: 5000000 INFO @ Wed, 28 Jun 2017 04:48:11: 5000000 INFO @ Wed, 28 Jun 2017 04:48:12: 5000000 INFO @ Wed, 28 Jun 2017 04:48:19: 6000000 INFO @ Wed, 28 Jun 2017 04:48:19: 6000000 INFO @ Wed, 28 Jun 2017 04:48:19: 6000000 INFO @ Wed, 28 Jun 2017 04:48:26: 7000000 INFO @ Wed, 28 Jun 2017 04:48:26: 7000000 INFO @ Wed, 28 Jun 2017 04:48:26: 7000000 INFO @ Wed, 28 Jun 2017 04:48:33: 8000000 INFO @ Wed, 28 Jun 2017 04:48:33: 8000000 INFO @ Wed, 28 Jun 2017 04:48:34: 8000000 INFO @ Wed, 28 Jun 2017 04:48:40: 9000000 INFO @ Wed, 28 Jun 2017 04:48:40: 9000000 INFO @ Wed, 28 Jun 2017 04:48:41: 9000000 INFO @ Wed, 28 Jun 2017 04:48:48: 10000000 INFO @ Wed, 28 Jun 2017 04:48:48: 10000000 INFO @ Wed, 28 Jun 2017 04:48:48: 10000000 INFO @ Wed, 28 Jun 2017 04:48:55: 11000000 INFO @ Wed, 28 Jun 2017 04:48:55: 11000000 INFO @ Wed, 28 Jun 2017 04:48:55: 11000000 INFO @ Wed, 28 Jun 2017 04:49:02: 12000000 INFO @ Wed, 28 Jun 2017 04:49:02: 12000000 INFO @ Wed, 28 Jun 2017 04:49:02: 12000000 INFO @ Wed, 28 Jun 2017 04:49:10: 13000000 INFO @ Wed, 28 Jun 2017 04:49:10: 13000000 INFO @ Wed, 28 Jun 2017 04:49:10: 13000000 INFO @ Wed, 28 Jun 2017 04:49:17: 14000000 INFO @ Wed, 28 Jun 2017 04:49:17: 14000000 INFO @ Wed, 28 Jun 2017 04:49:18: 14000000 INFO @ Wed, 28 Jun 2017 04:49:26: 15000000 INFO @ Wed, 28 Jun 2017 04:49:26: 15000000 INFO @ Wed, 28 Jun 2017 04:49:26: 15000000 INFO @ Wed, 28 Jun 2017 04:49:29: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 04:49:29: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 04:49:29: #1 total tags in treatment: 6243141 INFO @ Wed, 28 Jun 2017 04:49:29: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:49:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 04:49:29: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 04:49:29: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 04:49:29: #1 total tags in treatment: 6243141 INFO @ Wed, 28 Jun 2017 04:49:29: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:49:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 04:49:29: #1 tags after filtering in treatment: 4130820 INFO @ Wed, 28 Jun 2017 04:49:29: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 28 Jun 2017 04:49:29: #1 finished! INFO @ Wed, 28 Jun 2017 04:49:29: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:49:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:49:29: #1 tags after filtering in treatment: 4130820 INFO @ Wed, 28 Jun 2017 04:49:29: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 28 Jun 2017 04:49:29: #1 finished! INFO @ Wed, 28 Jun 2017 04:49:29: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:49:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:49:29: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 04:49:29: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 04:49:29: #1 total tags in treatment: 6243141 INFO @ Wed, 28 Jun 2017 04:49:29: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:49:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 04:49:29: #1 tags after filtering in treatment: 4130820 INFO @ Wed, 28 Jun 2017 04:49:29: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 28 Jun 2017 04:49:29: #1 finished! INFO @ Wed, 28 Jun 2017 04:49:29: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:49:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:49:29: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 04:49:29: 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 @ Wed, 28 Jun 2017 04:49:29: Process for pairing-model is terminated! cat: SRX1004439.05_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 `SRX1004439.05_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 `SRX1004439.05_*.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 `SRX1004439.05_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 @ Wed, 28 Jun 2017 04:49:29: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 04:49:29: 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 @ Wed, 28 Jun 2017 04:49:29: Process for pairing-model is terminated! cat: SRX1004439.10_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 `SRX1004439.10_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 `SRX1004439.10_*.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 `SRX1004439.10_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 @ Wed, 28 Jun 2017 04:49:30: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 04:49:30: 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 @ Wed, 28 Jun 2017 04:49:30: Process for pairing-model is terminated! cat: SRX1004439.20_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 `SRX1004439.20_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 `SRX1004439.20_*.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 `SRX1004439.20_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。