Job ID = 9302917 sra ファイルのダウンロード中... Completed: 321694K bytes transferred in 8 seconds (321303K 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 5754811 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2745549/SRR5457486.sra Written 5754811 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: 00:06:06 5754811 reads; of these: 5754811 (100.00%) were paired; of these: 920736 (16.00%) aligned concordantly 0 times 4158106 (72.25%) aligned concordantly exactly 1 time 675969 (11.75%) aligned concordantly >1 times ---- 920736 pairs aligned concordantly 0 times; of these: 521820 (56.67%) aligned discordantly 1 time ---- 398916 pairs aligned 0 times concordantly or discordantly; of these: 797832 mates make up the pairs; of these: 551605 (69.14%) aligned 0 times 69076 (8.66%) aligned exactly 1 time 177151 (22.20%) aligned >1 times 95.21% overall alignment rate Time searching: 00:06:06 Overall time: 00:06:06 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] 44288 / 5351923 = 0.0083 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 11:38:42: # Command line: callpeak -t SRX2745549.bam -f BAM -g 12100000 -n SRX2745549.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2745549.10 # format = BAM # ChIP-seq file = ['SRX2745549.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 11:38:42: #1 read tag files... INFO @ Fri, 28 Jul 2017 11:38:42: #1 read treatment tags... INFO @ Fri, 28 Jul 2017 11:38:42: # Command line: callpeak -t SRX2745549.bam -f BAM -g 12100000 -n SRX2745549.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2745549.05 # format = BAM # ChIP-seq file = ['SRX2745549.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 11:38:42: #1 read tag files... INFO @ Fri, 28 Jul 2017 11:38:42: #1 read treatment tags... INFO @ Fri, 28 Jul 2017 11:38:42: # Command line: callpeak -t SRX2745549.bam -f BAM -g 12100000 -n SRX2745549.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2745549.20 # format = BAM # ChIP-seq file = ['SRX2745549.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 11:38:42: #1 read tag files... INFO @ Fri, 28 Jul 2017 11:38:42: #1 read treatment tags... INFO @ Fri, 28 Jul 2017 11:38:50: 1000000 INFO @ Fri, 28 Jul 2017 11:38:50: 1000000 INFO @ Fri, 28 Jul 2017 11:38:50: 1000000 INFO @ Fri, 28 Jul 2017 11:38:57: 2000000 INFO @ Fri, 28 Jul 2017 11:38:58: 2000000 INFO @ Fri, 28 Jul 2017 11:38:59: 2000000 INFO @ Fri, 28 Jul 2017 11:39:04: 3000000 INFO @ Fri, 28 Jul 2017 11:39:06: 3000000 INFO @ Fri, 28 Jul 2017 11:39:07: 3000000 INFO @ Fri, 28 Jul 2017 11:39:11: 4000000 INFO @ Fri, 28 Jul 2017 11:39:14: 4000000 INFO @ Fri, 28 Jul 2017 11:39:16: 4000000 INFO @ Fri, 28 Jul 2017 11:39:19: 5000000 INFO @ Fri, 28 Jul 2017 11:39:23: 5000000 INFO @ Fri, 28 Jul 2017 11:39:25: 5000000 INFO @ Fri, 28 Jul 2017 11:39:26: 6000000 INFO @ Fri, 28 Jul 2017 11:39:31: 6000000 INFO @ Fri, 28 Jul 2017 11:39:33: 7000000 INFO @ Fri, 28 Jul 2017 11:39:34: 6000000 INFO @ Fri, 28 Jul 2017 11:39:39: 7000000 INFO @ Fri, 28 Jul 2017 11:39:41: 8000000 INFO @ Fri, 28 Jul 2017 11:39:43: 7000000 INFO @ Fri, 28 Jul 2017 11:39:47: 8000000 INFO @ Fri, 28 Jul 2017 11:39:48: 9000000 INFO @ Fri, 28 Jul 2017 11:39:51: 8000000 INFO @ Fri, 28 Jul 2017 11:39:55: 10000000 INFO @ Fri, 28 Jul 2017 11:39:55: 9000000 INFO @ Fri, 28 Jul 2017 11:40:00: 9000000 INFO @ Fri, 28 Jul 2017 11:40:01: #1 tag size is determined as 75 bps INFO @ Fri, 28 Jul 2017 11:40:01: #1 tag size = 75 INFO @ Fri, 28 Jul 2017 11:40:01: #1 total tags in treatment: 4791428 INFO @ Fri, 28 Jul 2017 11:40:01: #1 user defined the maximum tags... INFO @ Fri, 28 Jul 2017 11:40:01: #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 11:40:01: #1 tags after filtering in treatment: 3983021 INFO @ Fri, 28 Jul 2017 11:40:01: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 28 Jul 2017 11:40:01: #1 finished! INFO @ Fri, 28 Jul 2017 11:40:01: #2 Build Peak Model... INFO @ Fri, 28 Jul 2017 11:40:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 28 Jul 2017 11:40:01: #2 number of paired peaks: 28 WARNING @ Fri, 28 Jul 2017 11:40:01: 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 11:40:01: Process for pairing-model is terminated! cat: SRX2745549.05_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 `SRX2745549.05_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 `SRX2745549.05_*.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 `SRX2745549.05_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 11:40:04: 10000000 INFO @ Fri, 28 Jul 2017 11:40:08: 10000000 INFO @ Fri, 28 Jul 2017 11:40:11: #1 tag size is determined as 75 bps INFO @ Fri, 28 Jul 2017 11:40:11: #1 tag size = 75 INFO @ Fri, 28 Jul 2017 11:40:11: #1 total tags in treatment: 4791428 INFO @ Fri, 28 Jul 2017 11:40:11: #1 user defined the maximum tags... INFO @ Fri, 28 Jul 2017 11:40:11: #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 11:40:11: #1 tags after filtering in treatment: 3983021 INFO @ Fri, 28 Jul 2017 11:40:11: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 28 Jul 2017 11:40:11: #1 finished! INFO @ Fri, 28 Jul 2017 11:40:11: #2 Build Peak Model... INFO @ Fri, 28 Jul 2017 11:40:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 28 Jul 2017 11:40:11: #2 number of paired peaks: 28 WARNING @ Fri, 28 Jul 2017 11:40:11: 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 11:40:11: Process for pairing-model is terminated! cat: SRX2745549.10_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 `SRX2745549.10_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 `SRX2745549.10_*.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 `SRX2745549.10_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 11:40:15: #1 tag size is determined as 75 bps INFO @ Fri, 28 Jul 2017 11:40:15: #1 tag size = 75 INFO @ Fri, 28 Jul 2017 11:40:15: #1 total tags in treatment: 4791428 INFO @ Fri, 28 Jul 2017 11:40:15: #1 user defined the maximum tags... INFO @ Fri, 28 Jul 2017 11:40:15: #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 11:40:15: #1 tags after filtering in treatment: 3983021 INFO @ Fri, 28 Jul 2017 11:40:15: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 28 Jul 2017 11:40:15: #1 finished! INFO @ Fri, 28 Jul 2017 11:40:15: #2 Build Peak Model... INFO @ Fri, 28 Jul 2017 11:40:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 28 Jul 2017 11:40:15: #2 number of paired peaks: 28 WARNING @ Fri, 28 Jul 2017 11:40:15: 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 11:40:15: Process for pairing-model is terminated! cat: SRX2745549.20_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 `SRX2745549.20_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 `SRX2745549.20_*.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 `SRX2745549.20_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。