Job ID = 9163055 sra ファイルのダウンロード中... Completed: 857365K bytes transferred in 11 seconds (632738K bits/sec), in 2 files, 3 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 2791537 spots for /home/okishinya/chipatlas/results/sacCer3/SRX475228/SRR1175178.sra Written 2791537 spots total Written 2841811 spots for /home/okishinya/chipatlas/results/sacCer3/SRX475228/SRR1175177.sra Written 2841811 spots total 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: 00:09:03 5633348 reads; of these: 5633348 (100.00%) were paired; of these: 1344838 (23.87%) aligned concordantly 0 times 3177070 (56.40%) aligned concordantly exactly 1 time 1111440 (19.73%) aligned concordantly >1 times ---- 1344838 pairs aligned concordantly 0 times; of these: 631442 (46.95%) aligned discordantly 1 time ---- 713396 pairs aligned 0 times concordantly or discordantly; of these: 1426792 mates make up the pairs; of these: 918895 (64.40%) aligned 0 times 65026 (4.56%) aligned exactly 1 time 442871 (31.04%) aligned >1 times 91.84% overall alignment rate Time searching: 00:09:03 Overall time: 00:09:03 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] 198292 / 4869331 = 0.0407 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 10:01:09: # Command line: callpeak -t SRX475228.bam -f BAM -g 12100000 -n SRX475228.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX475228.20 # format = BAM # ChIP-seq file = ['SRX475228.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 10:01:09: #1 read tag files... INFO @ Wed, 28 Jun 2017 10:01:09: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 10:01:09: # Command line: callpeak -t SRX475228.bam -f BAM -g 12100000 -n SRX475228.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX475228.05 # format = BAM # ChIP-seq file = ['SRX475228.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 10:01:09: #1 read tag files... INFO @ Wed, 28 Jun 2017 10:01:09: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 10:01:09: # Command line: callpeak -t SRX475228.bam -f BAM -g 12100000 -n SRX475228.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX475228.10 # format = BAM # ChIP-seq file = ['SRX475228.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 10:01:09: #1 read tag files... INFO @ Wed, 28 Jun 2017 10:01:09: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 10:01:21: 1000000 INFO @ Wed, 28 Jun 2017 10:01:21: 1000000 INFO @ Wed, 28 Jun 2017 10:01:21: 1000000 INFO @ Wed, 28 Jun 2017 10:01:32: 2000000 INFO @ Wed, 28 Jun 2017 10:01:32: 2000000 INFO @ Wed, 28 Jun 2017 10:01:32: 2000000 INFO @ Wed, 28 Jun 2017 10:01:44: 3000000 INFO @ Wed, 28 Jun 2017 10:01:44: 3000000 INFO @ Wed, 28 Jun 2017 10:01:44: 3000000 INFO @ Wed, 28 Jun 2017 10:01:55: 4000000 INFO @ Wed, 28 Jun 2017 10:01:55: 4000000 INFO @ Wed, 28 Jun 2017 10:01:55: 4000000 INFO @ Wed, 28 Jun 2017 10:02:06: 5000000 INFO @ Wed, 28 Jun 2017 10:02:06: 5000000 INFO @ Wed, 28 Jun 2017 10:02:06: 5000000 INFO @ Wed, 28 Jun 2017 10:02:17: 6000000 INFO @ Wed, 28 Jun 2017 10:02:17: 6000000 INFO @ Wed, 28 Jun 2017 10:02:17: 6000000 INFO @ Wed, 28 Jun 2017 10:02:28: 7000000 INFO @ Wed, 28 Jun 2017 10:02:28: 7000000 INFO @ Wed, 28 Jun 2017 10:02:28: 7000000 INFO @ Wed, 28 Jun 2017 10:02:40: 8000000 INFO @ Wed, 28 Jun 2017 10:02:40: 8000000 INFO @ Wed, 28 Jun 2017 10:02:40: 8000000 INFO @ Wed, 28 Jun 2017 10:02:51: 9000000 INFO @ Wed, 28 Jun 2017 10:02:51: 9000000 INFO @ Wed, 28 Jun 2017 10:02:51: 9000000 INFO @ Wed, 28 Jun 2017 10:03:02: #1 tag size is determined as 126 bps INFO @ Wed, 28 Jun 2017 10:03:02: #1 tag size = 126 INFO @ Wed, 28 Jun 2017 10:03:02: #1 total tags in treatment: 4103350 INFO @ Wed, 28 Jun 2017 10:03:02: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 10:03:02: #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 10:03:02: #1 tag size is determined as 126 bps INFO @ Wed, 28 Jun 2017 10:03:02: #1 tag size = 126 INFO @ Wed, 28 Jun 2017 10:03:02: #1 total tags in treatment: 4103350 INFO @ Wed, 28 Jun 2017 10:03:02: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 10:03:02: #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 10:03:02: #1 tag size is determined as 126 bps INFO @ Wed, 28 Jun 2017 10:03:02: #1 tag size = 126 INFO @ Wed, 28 Jun 2017 10:03:02: #1 total tags in treatment: 4103350 INFO @ Wed, 28 Jun 2017 10:03:02: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 10:03:02: #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 10:03:02: #1 tags after filtering in treatment: 3117440 INFO @ Wed, 28 Jun 2017 10:03:02: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 28 Jun 2017 10:03:02: #1 finished! INFO @ Wed, 28 Jun 2017 10:03:02: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 10:03:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 10:03:02: #1 tags after filtering in treatment: 3117440 INFO @ Wed, 28 Jun 2017 10:03:02: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 28 Jun 2017 10:03:02: #1 finished! INFO @ Wed, 28 Jun 2017 10:03:02: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 10:03:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 10:03:02: #1 tags after filtering in treatment: 3117440 INFO @ Wed, 28 Jun 2017 10:03:02: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 28 Jun 2017 10:03:02: #1 finished! INFO @ Wed, 28 Jun 2017 10:03:02: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 10:03:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 10:03:02: #2 number of paired peaks: 40 WARNING @ Wed, 28 Jun 2017 10:03:02: Too few paired peaks (40) 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 10:03:02: Process for pairing-model is terminated! INFO @ Wed, 28 Jun 2017 10:03:02: #2 number of paired peaks: 40 WARNING @ Wed, 28 Jun 2017 10:03:02: Too few paired peaks (40) 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 10:03:02: Process for pairing-model is terminated! INFO @ Wed, 28 Jun 2017 10:03:02: #2 number of paired peaks: 40 WARNING @ Wed, 28 Jun 2017 10:03:02: Too few paired peaks (40) 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 10:03:02: Process for pairing-model is terminated! cat: SRX475228.10_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: SRX475228.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX475228.05_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 pass1 - making usageList (0 chroms): 1 millis pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX475228.05_model.r'rm: cannot remove `SRX475228.10_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 `SRX475228.20_model.r': そのようなファイルやディレクトリはありません : 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 `SRX475228.05_*.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 `SRX475228.10_*.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 `SRX475228.20_*.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 `SRX475228.05_peaks.narrowPeak': そのようなファイルやディレクトリはありません rm: cannot remove `SRX475228.10_peaks.narrowPeak': そのようなファイルやディレクトリはありません rm: cannot remove `SRX475228.20_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 CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。