Job ID = 11388944 sra ファイルのダウンロード中... Completed: 854453K bytes transferred in 16 seconds (425037K 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 10514669 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017462/SRR8198085.sra Written 10514669 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017462/SRR8198085.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: 00:24:33 10514669 reads; of these: 10514669 (100.00%) were paired; of these: 3041949 (28.93%) aligned concordantly 0 times 6298667 (59.90%) aligned concordantly exactly 1 time 1174053 (11.17%) aligned concordantly >1 times ---- 3041949 pairs aligned concordantly 0 times; of these: 135747 (4.46%) aligned discordantly 1 time ---- 2906202 pairs aligned 0 times concordantly or discordantly; of these: 5812404 mates make up the pairs; of these: 5029390 (86.53%) aligned 0 times 557143 (9.59%) aligned exactly 1 time 225871 (3.89%) aligned >1 times 76.08% overall alignment rate Time searching: 00:24:33 Overall time: 00:24:33 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] 236266 / 7604557 = 0.0311 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 @ Thu, 13 Dec 2018 00:54:45: # Command line: callpeak -t SRX5017462.bam -f BAM -g 12100000 -n SRX5017462.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5017462.10 # format = BAM # ChIP-seq file = ['SRX5017462.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 @ Thu, 13 Dec 2018 00:54:45: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:54:45: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:54:45: # Command line: callpeak -t SRX5017462.bam -f BAM -g 12100000 -n SRX5017462.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5017462.20 # format = BAM # ChIP-seq file = ['SRX5017462.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 @ Thu, 13 Dec 2018 00:54:45: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:54:45: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:54:45: # Command line: callpeak -t SRX5017462.bam -f BAM -g 12100000 -n SRX5017462.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5017462.05 # format = BAM # ChIP-seq file = ['SRX5017462.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 @ Thu, 13 Dec 2018 00:54:45: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:54:45: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:54:59: 1000000 INFO @ Thu, 13 Dec 2018 00:54:59: 1000000 INFO @ Thu, 13 Dec 2018 00:55:09: 1000000 INFO @ Thu, 13 Dec 2018 00:55:15: 2000000 INFO @ Thu, 13 Dec 2018 00:55:20: 2000000 INFO @ Thu, 13 Dec 2018 00:55:33: 2000000 INFO @ Thu, 13 Dec 2018 00:55:35: 3000000 INFO @ Thu, 13 Dec 2018 00:55:41: 3000000 INFO @ Thu, 13 Dec 2018 00:55:52: 3000000 INFO @ Thu, 13 Dec 2018 00:55:58: 4000000 INFO @ Thu, 13 Dec 2018 00:56:06: 4000000 INFO @ Thu, 13 Dec 2018 00:56:12: 4000000 INFO @ Thu, 13 Dec 2018 00:56:16: 5000000 INFO @ Thu, 13 Dec 2018 00:56:28: 5000000 INFO @ Thu, 13 Dec 2018 00:56:32: 6000000 INFO @ Thu, 13 Dec 2018 00:56:34: 5000000 INFO @ Thu, 13 Dec 2018 00:56:43: 6000000 INFO @ Thu, 13 Dec 2018 00:56:54: 7000000 INFO @ Thu, 13 Dec 2018 00:56:56: 6000000 INFO @ Thu, 13 Dec 2018 00:57:08: 7000000 INFO @ Thu, 13 Dec 2018 00:57:09: 7000000 INFO @ Thu, 13 Dec 2018 00:57:26: 8000000 INFO @ Thu, 13 Dec 2018 00:57:34: 8000000 INFO @ Thu, 13 Dec 2018 00:57:38: 8000000 INFO @ Thu, 13 Dec 2018 00:57:49: 9000000 INFO @ Thu, 13 Dec 2018 00:57:51: 9000000 INFO @ Thu, 13 Dec 2018 00:58:00: 9000000 INFO @ Thu, 13 Dec 2018 00:58:03: 10000000 INFO @ Thu, 13 Dec 2018 00:58:06: 10000000 INFO @ Thu, 13 Dec 2018 00:58:15: 10000000 INFO @ Thu, 13 Dec 2018 00:58:16: 11000000 INFO @ Thu, 13 Dec 2018 00:58:26: 11000000 INFO @ Thu, 13 Dec 2018 00:58:27: 12000000 INFO @ Thu, 13 Dec 2018 00:58:35: 11000000 INFO @ Thu, 13 Dec 2018 00:58:38: 13000000 INFO @ Thu, 13 Dec 2018 00:58:48: 14000000 INFO @ Thu, 13 Dec 2018 00:58:51: 12000000 INFO @ Thu, 13 Dec 2018 00:59:00: 15000000 INFO @ Thu, 13 Dec 2018 00:59:00: 12000000 INFO @ Thu, 13 Dec 2018 00:59:07: #1 tag size is determined as 100 bps INFO @ Thu, 13 Dec 2018 00:59:07: #1 tag size = 100 INFO @ Thu, 13 Dec 2018 00:59:07: #1 total tags in treatment: 7238073 INFO @ Thu, 13 Dec 2018 00:59:07: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:59:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 00:59:07: #1 tags after filtering in treatment: 5524685 INFO @ Thu, 13 Dec 2018 00:59:07: #1 Redundant rate of treatment: 0.24 INFO @ Thu, 13 Dec 2018 00:59:07: #1 finished! INFO @ Thu, 13 Dec 2018 00:59:07: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:59:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:59:07: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 00:59:07: 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 @ Thu, 13 Dec 2018 00:59:07: Process for pairing-model is terminated! cat: SRX5017462.05_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): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017462.05_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 `SRX5017462.05_*.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 `SRX5017462.05_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 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 13 Dec 2018 00:59:15: 13000000 INFO @ Thu, 13 Dec 2018 00:59:23: 13000000 BigWig に変換しました。 INFO @ Thu, 13 Dec 2018 00:59:39: 14000000 INFO @ Thu, 13 Dec 2018 00:59:51: 14000000 INFO @ Thu, 13 Dec 2018 01:00:06: 15000000 INFO @ Thu, 13 Dec 2018 01:00:14: 15000000 INFO @ Thu, 13 Dec 2018 01:00:16: #1 tag size is determined as 100 bps INFO @ Thu, 13 Dec 2018 01:00:16: #1 tag size = 100 INFO @ Thu, 13 Dec 2018 01:00:16: #1 total tags in treatment: 7238073 INFO @ Thu, 13 Dec 2018 01:00:16: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:00:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 01:00:17: #1 tags after filtering in treatment: 5524685 INFO @ Thu, 13 Dec 2018 01:00:17: #1 Redundant rate of treatment: 0.24 INFO @ Thu, 13 Dec 2018 01:00:17: #1 finished! INFO @ Thu, 13 Dec 2018 01:00:17: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:00:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:00:17: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 01:00:17: 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 @ Thu, 13 Dec 2018 01:00:17: Process for pairing-model is terminated! cat: SRX5017462.10_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): 9 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017462.10_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 `SRX5017462.10_*.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 `SRX5017462.10_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 @ Thu, 13 Dec 2018 01:00:22: #1 tag size is determined as 100 bps INFO @ Thu, 13 Dec 2018 01:00:22: #1 tag size = 100 INFO @ Thu, 13 Dec 2018 01:00:22: #1 total tags in treatment: 7238073 INFO @ Thu, 13 Dec 2018 01:00:22: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:00:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 01:00:22: #1 tags after filtering in treatment: 5524685 INFO @ Thu, 13 Dec 2018 01:00:22: #1 Redundant rate of treatment: 0.24 INFO @ Thu, 13 Dec 2018 01:00:22: #1 finished! INFO @ Thu, 13 Dec 2018 01:00:22: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:00:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:00:22: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 01:00:22: 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 @ Thu, 13 Dec 2018 01:00:22: Process for pairing-model is terminated! cat: SRX5017462.20_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): 8 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017462.20_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 `SRX5017462.20_*.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 `SRX5017462.20_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