Job ID = 10937541 sra ファイルのダウンロード中... Completed: 530379K bytes transferred in 74 seconds (58688K bits/sec), in 1 file. 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... Read 5389393 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010334/SRR5833333.sra Written 5389393 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010334/SRR5833333.sra rm: cannot remove `[DSE]RX*': 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 `[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: 00:06:52 5389393 reads; of these: 5389393 (100.00%) were paired; of these: 264423 (4.91%) aligned concordantly 0 times 4085833 (75.81%) aligned concordantly exactly 1 time 1039137 (19.28%) aligned concordantly >1 times ---- 264423 pairs aligned concordantly 0 times; of these: 22704 (8.59%) aligned discordantly 1 time ---- 241719 pairs aligned 0 times concordantly or discordantly; of these: 483438 mates make up the pairs; of these: 412201 (85.26%) aligned 0 times 43806 (9.06%) aligned exactly 1 time 27431 (5.67%) aligned >1 times 96.18% overall alignment rate Time searching: 00:06:52 Overall time: 00:06:52 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] 174195 / 5134472 = 0.0339 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, 10 Aug 2018 02:46:10: # Command line: callpeak -t SRX3010334.bam -f BAM -g 12100000 -n SRX3010334.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3010334.20 # format = BAM # ChIP-seq file = ['SRX3010334.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, 10 Aug 2018 02:46:10: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:46:10: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:46:10: # Command line: callpeak -t SRX3010334.bam -f BAM -g 12100000 -n SRX3010334.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3010334.10 # format = BAM # ChIP-seq file = ['SRX3010334.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, 10 Aug 2018 02:46:10: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:46:10: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:46:10: # Command line: callpeak -t SRX3010334.bam -f BAM -g 12100000 -n SRX3010334.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3010334.05 # format = BAM # ChIP-seq file = ['SRX3010334.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, 10 Aug 2018 02:46:10: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:46:10: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:46:17: 1000000 INFO @ Fri, 10 Aug 2018 02:46:18: 1000000 INFO @ Fri, 10 Aug 2018 02:46:18: 1000000 INFO @ Fri, 10 Aug 2018 02:46:24: 2000000 INFO @ Fri, 10 Aug 2018 02:46:25: 2000000 INFO @ Fri, 10 Aug 2018 02:46:25: 2000000 INFO @ Fri, 10 Aug 2018 02:46:31: 3000000 INFO @ Fri, 10 Aug 2018 02:46:31: 3000000 INFO @ Fri, 10 Aug 2018 02:46:32: 3000000 INFO @ Fri, 10 Aug 2018 02:46:38: 4000000 INFO @ Fri, 10 Aug 2018 02:46:38: 4000000 INFO @ Fri, 10 Aug 2018 02:46:40: 4000000 INFO @ Fri, 10 Aug 2018 02:46:45: 5000000 INFO @ Fri, 10 Aug 2018 02:46:45: 5000000 INFO @ Fri, 10 Aug 2018 02:46:48: 5000000 INFO @ Fri, 10 Aug 2018 02:46:51: 6000000 INFO @ Fri, 10 Aug 2018 02:46:52: 6000000 INFO @ Fri, 10 Aug 2018 02:46:55: 6000000 INFO @ Fri, 10 Aug 2018 02:46:58: 7000000 INFO @ Fri, 10 Aug 2018 02:46:58: 7000000 INFO @ Fri, 10 Aug 2018 02:47:03: 7000000 INFO @ Fri, 10 Aug 2018 02:47:05: 8000000 INFO @ Fri, 10 Aug 2018 02:47:05: 8000000 INFO @ Fri, 10 Aug 2018 02:47:11: 8000000 INFO @ Fri, 10 Aug 2018 02:47:11: 9000000 INFO @ Fri, 10 Aug 2018 02:47:12: 9000000 INFO @ Fri, 10 Aug 2018 02:47:18: 10000000 INFO @ Fri, 10 Aug 2018 02:47:18: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:47:18: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:47:18: #1 total tags in treatment: 4950816 INFO @ Fri, 10 Aug 2018 02:47:18: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:47:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:47:18: #1 tags after filtering in treatment: 3809211 INFO @ Fri, 10 Aug 2018 02:47:18: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 10 Aug 2018 02:47:18: #1 finished! INFO @ Fri, 10 Aug 2018 02:47:18: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:47:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:47:19: #2 number of paired peaks: 49 WARNING @ Fri, 10 Aug 2018 02:47:19: Too few paired peaks (49) 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, 10 Aug 2018 02:47:19: Process for pairing-model is terminated! cat: SRX3010334.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Fri, 10 Aug 2018 02:47:19: 10000000 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3010334.20_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 `SRX3010334.20_*.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 `SRX3010334.20_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 @ Fri, 10 Aug 2018 02:47:19: 9000000 INFO @ Fri, 10 Aug 2018 02:47:19: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:47:19: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:47:19: #1 total tags in treatment: 4950816 INFO @ Fri, 10 Aug 2018 02:47:19: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:47:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:47:19: #1 tags after filtering in treatment: 3809211 INFO @ Fri, 10 Aug 2018 02:47:19: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 10 Aug 2018 02:47:19: #1 finished! INFO @ Fri, 10 Aug 2018 02:47:19: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:47:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:47:19: #2 number of paired peaks: 49 WARNING @ Fri, 10 Aug 2018 02:47:19: Too few paired peaks (49) 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, 10 Aug 2018 02:47:19: Process for pairing-model is terminated! cat: SRX3010334.05_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): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3010334.05_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 `SRX3010334.05_*.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 `SRX3010334.05_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, 10 Aug 2018 02:47:26: 10000000 INFO @ Fri, 10 Aug 2018 02:47:26: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:47:26: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:47:26: #1 total tags in treatment: 4950816 INFO @ Fri, 10 Aug 2018 02:47:26: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:47:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:47:26: #1 tags after filtering in treatment: 3809211 INFO @ Fri, 10 Aug 2018 02:47:26: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 10 Aug 2018 02:47:26: #1 finished! INFO @ Fri, 10 Aug 2018 02:47:26: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:47:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:47:27: #2 number of paired peaks: 49 WARNING @ Fri, 10 Aug 2018 02:47:27: Too few paired peaks (49) 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, 10 Aug 2018 02:47:27: Process for pairing-model is terminated! cat: SRX3010334.10_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): 5 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3010334.10_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 `SRX3010334.10_*.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 `SRX3010334.10_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。