Job ID = 9160003 sra ファイルのダウンロード中... Completed: 1173043K bytes transferred in 14 seconds (674699K 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 12394232 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2402728/SRR5085173.sra Written 12394232 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: 00:13:19 12394232 reads; of these: 12394232 (100.00%) were paired; of these: 783130 (6.32%) aligned concordantly 0 times 9131187 (73.67%) aligned concordantly exactly 1 time 2479915 (20.01%) aligned concordantly >1 times ---- 783130 pairs aligned concordantly 0 times; of these: 54035 (6.90%) aligned discordantly 1 time ---- 729095 pairs aligned 0 times concordantly or discordantly; of these: 1458190 mates make up the pairs; of these: 1173355 (80.47%) aligned 0 times 198332 (13.60%) aligned exactly 1 time 86503 (5.93%) aligned >1 times 95.27% overall alignment rate Time searching: 00:13:19 Overall time: 00:13:19 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 12 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] 9129486 / 11655802 = 0.7833 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 01:53:34: # Command line: callpeak -t SRX2402728.bam -f BAM -g 12100000 -n SRX2402728.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2402728.20 # format = BAM # ChIP-seq file = ['SRX2402728.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 01:53:34: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:53:34: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:53:34: # Command line: callpeak -t SRX2402728.bam -f BAM -g 12100000 -n SRX2402728.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2402728.05 # format = BAM # ChIP-seq file = ['SRX2402728.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 01:53:34: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:53:34: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:53:34: # Command line: callpeak -t SRX2402728.bam -f BAM -g 12100000 -n SRX2402728.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2402728.10 # format = BAM # ChIP-seq file = ['SRX2402728.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 01:53:34: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:53:34: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:53:41: 1000000 INFO @ Wed, 28 Jun 2017 01:53:41: 1000000 INFO @ Wed, 28 Jun 2017 01:53:41: 1000000 INFO @ Wed, 28 Jun 2017 01:53:49: 2000000 INFO @ Wed, 28 Jun 2017 01:53:49: 2000000 INFO @ Wed, 28 Jun 2017 01:53:49: 2000000 INFO @ Wed, 28 Jun 2017 01:53:56: 3000000 INFO @ Wed, 28 Jun 2017 01:53:56: 3000000 INFO @ Wed, 28 Jun 2017 01:53:56: 3000000 INFO @ Wed, 28 Jun 2017 01:54:02: 4000000 INFO @ Wed, 28 Jun 2017 01:54:03: 4000000 INFO @ Wed, 28 Jun 2017 01:54:04: 4000000 INFO @ Wed, 28 Jun 2017 01:54:09: 5000000 INFO @ Wed, 28 Jun 2017 01:54:10: 5000000 INFO @ Wed, 28 Jun 2017 01:54:11: 5000000 INFO @ Wed, 28 Jun 2017 01:54:12: #1 tag size is determined as 75 bps INFO @ Wed, 28 Jun 2017 01:54:12: #1 tag size = 75 INFO @ Wed, 28 Jun 2017 01:54:12: #1 total tags in treatment: 2508792 INFO @ Wed, 28 Jun 2017 01:54:12: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:54:12: #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 01:54:12: #1 tags after filtering in treatment: 1866477 INFO @ Wed, 28 Jun 2017 01:54:12: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 28 Jun 2017 01:54:12: #1 finished! INFO @ Wed, 28 Jun 2017 01:54:12: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:54:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:54:12: #2 number of paired peaks: 89 WARNING @ Wed, 28 Jun 2017 01:54:12: Too few paired peaks (89) 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 01:54:12: Process for pairing-model is terminated! cat: SRX2402728.20_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 `SRX2402728.20_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 `SRX2402728.20_*.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 `SRX2402728.20_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 @ Wed, 28 Jun 2017 01:54:13: #1 tag size is determined as 75 bps INFO @ Wed, 28 Jun 2017 01:54:13: #1 tag size = 75 INFO @ Wed, 28 Jun 2017 01:54:13: #1 total tags in treatment: 2508792 INFO @ Wed, 28 Jun 2017 01:54:13: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:54:13: #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 01:54:13: #1 tags after filtering in treatment: 1866477 INFO @ Wed, 28 Jun 2017 01:54:13: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 28 Jun 2017 01:54:13: #1 finished! INFO @ Wed, 28 Jun 2017 01:54:13: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:54:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:54:13: #2 number of paired peaks: 89 WARNING @ Wed, 28 Jun 2017 01:54:13: Too few paired peaks (89) 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 01:54:13: Process for pairing-model is terminated! cat: SRX2402728.05_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 `SRX2402728.05_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 `SRX2402728.05_*.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 `SRX2402728.05_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 01:54:14: #1 tag size is determined as 75 bps INFO @ Wed, 28 Jun 2017 01:54:14: #1 tag size = 75 INFO @ Wed, 28 Jun 2017 01:54:14: #1 total tags in treatment: 2508792 INFO @ Wed, 28 Jun 2017 01:54:14: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:54:14: #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 01:54:14: #1 tags after filtering in treatment: 1866477 INFO @ Wed, 28 Jun 2017 01:54:14: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 28 Jun 2017 01:54:14: #1 finished! INFO @ Wed, 28 Jun 2017 01:54:14: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:54:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:54:14: #2 number of paired peaks: 89 WARNING @ Wed, 28 Jun 2017 01:54:14: Too few paired peaks (89) 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 01:54:14: Process for pairing-model is terminated! cat: SRX2402728.10_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 `SRX2402728.10_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 `SRX2402728.10_*.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 `SRX2402728.10_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。