Job ID = 11388945 sra ファイルのダウンロード中... Completed: 532760K bytes transferred in 10 seconds (398559K 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 6526508 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017463/SRR8198086.sra Written 6526508 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017463/SRR8198086.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: 00:15:57 6526508 reads; of these: 6526508 (100.00%) were paired; of these: 1791856 (27.46%) aligned concordantly 0 times 4013092 (61.49%) aligned concordantly exactly 1 time 721560 (11.06%) aligned concordantly >1 times ---- 1791856 pairs aligned concordantly 0 times; of these: 149148 (8.32%) aligned discordantly 1 time ---- 1642708 pairs aligned 0 times concordantly or discordantly; of these: 3285416 mates make up the pairs; of these: 2751808 (83.76%) aligned 0 times 356627 (10.85%) aligned exactly 1 time 176981 (5.39%) aligned >1 times 78.92% overall alignment rate Time searching: 00:15:57 Overall time: 00:15:58 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] 69911 / 4881002 = 0.0143 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 00:42:25: # Command line: callpeak -t SRX5017463.bam -f BAM -g 12100000 -n SRX5017463.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5017463.20 # format = BAM # ChIP-seq file = ['SRX5017463.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 00:42:25: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:42:25: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:42:25: # Command line: callpeak -t SRX5017463.bam -f BAM -g 12100000 -n SRX5017463.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5017463.10 # format = BAM # ChIP-seq file = ['SRX5017463.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 00:42:25: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:42:25: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:42:25: # Command line: callpeak -t SRX5017463.bam -f BAM -g 12100000 -n SRX5017463.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5017463.05 # format = BAM # ChIP-seq file = ['SRX5017463.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 00:42:25: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:42:25: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:42:41: 1000000 INFO @ Thu, 13 Dec 2018 00:42:41: 1000000 INFO @ Thu, 13 Dec 2018 00:42:44: 1000000 INFO @ Thu, 13 Dec 2018 00:42:59: 2000000 INFO @ Thu, 13 Dec 2018 00:43:00: 2000000 INFO @ Thu, 13 Dec 2018 00:43:05: 2000000 INFO @ Thu, 13 Dec 2018 00:43:17: 3000000 INFO @ Thu, 13 Dec 2018 00:43:18: 3000000 INFO @ Thu, 13 Dec 2018 00:43:25: 3000000 INFO @ Thu, 13 Dec 2018 00:43:29: 4000000 INFO @ Thu, 13 Dec 2018 00:43:32: 4000000 INFO @ Thu, 13 Dec 2018 00:43:38: 4000000 INFO @ Thu, 13 Dec 2018 00:43:40: 5000000 INFO @ Thu, 13 Dec 2018 00:43:47: 5000000 INFO @ Thu, 13 Dec 2018 00:43:50: 5000000 INFO @ Thu, 13 Dec 2018 00:43:53: 6000000 INFO @ Thu, 13 Dec 2018 00:44:00: 6000000 INFO @ Thu, 13 Dec 2018 00:44:02: 6000000 INFO @ Thu, 13 Dec 2018 00:44:06: 7000000 INFO @ Thu, 13 Dec 2018 00:44:12: 7000000 INFO @ Thu, 13 Dec 2018 00:44:15: 7000000 INFO @ Thu, 13 Dec 2018 00:44:19: 8000000 INFO @ Thu, 13 Dec 2018 00:44:27: 8000000 INFO @ Thu, 13 Dec 2018 00:44:29: 8000000 INFO @ Thu, 13 Dec 2018 00:44:34: 9000000 INFO @ Thu, 13 Dec 2018 00:44:40: 9000000 INFO @ Thu, 13 Dec 2018 00:44:42: 9000000 INFO @ Thu, 13 Dec 2018 00:44:47: 10000000 INFO @ Thu, 13 Dec 2018 00:44:49: #1 tag size is determined as 100 bps INFO @ Thu, 13 Dec 2018 00:44:49: #1 tag size = 100 INFO @ Thu, 13 Dec 2018 00:44:49: #1 total tags in treatment: 4665285 INFO @ Thu, 13 Dec 2018 00:44:49: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:44:49: #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 00:44:49: #1 tags after filtering in treatment: 3790980 INFO @ Thu, 13 Dec 2018 00:44:49: #1 Redundant rate of treatment: 0.19 INFO @ Thu, 13 Dec 2018 00:44:49: #1 finished! INFO @ Thu, 13 Dec 2018 00:44:49: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:44:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:44:49: #2 number of paired peaks: 28 WARNING @ Thu, 13 Dec 2018 00:44:49: 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 @ Thu, 13 Dec 2018 00:44:49: Process for pairing-model is terminated! cat: SRX5017463.10_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 `SRX5017463.10_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 `SRX5017463.10_*.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 `SRX5017463.10_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 00:44:52: 10000000 INFO @ Thu, 13 Dec 2018 00:44:54: #1 tag size is determined as 100 bps INFO @ Thu, 13 Dec 2018 00:44:54: #1 tag size = 100 INFO @ Thu, 13 Dec 2018 00:44:54: #1 total tags in treatment: 4665285 INFO @ Thu, 13 Dec 2018 00:44:54: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:44:54: #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 00:44:54: #1 tags after filtering in treatment: 3790980 INFO @ Thu, 13 Dec 2018 00:44:54: #1 Redundant rate of treatment: 0.19 INFO @ Thu, 13 Dec 2018 00:44:54: #1 finished! INFO @ Thu, 13 Dec 2018 00:44:54: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:44:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:44:54: #2 number of paired peaks: 28 WARNING @ Thu, 13 Dec 2018 00:44:54: 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 @ Thu, 13 Dec 2018 00:44:54: Process for pairing-model is terminated! cat: SRX5017463.05_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): 5 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017463.05_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 `SRX5017463.05_*.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 `SRX5017463.05_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 @ Thu, 13 Dec 2018 00:44:55: 10000000 INFO @ Thu, 13 Dec 2018 00:44:57: #1 tag size is determined as 100 bps INFO @ Thu, 13 Dec 2018 00:44:57: #1 tag size = 100 INFO @ Thu, 13 Dec 2018 00:44:57: #1 total tags in treatment: 4665285 INFO @ Thu, 13 Dec 2018 00:44:57: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:44:57: #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 00:44:57: #1 tags after filtering in treatment: 3790980 INFO @ Thu, 13 Dec 2018 00:44:57: #1 Redundant rate of treatment: 0.19 INFO @ Thu, 13 Dec 2018 00:44:57: #1 finished! INFO @ Thu, 13 Dec 2018 00:44:57: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:44:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:44:58: #2 number of paired peaks: 28 WARNING @ Thu, 13 Dec 2018 00:44:58: 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 @ Thu, 13 Dec 2018 00:44:58: Process for pairing-model is terminated! cat: SRX5017463.20_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): 5 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017463.20_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 `SRX5017463.20_*.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 `SRX5017463.20_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。