Job ID = 11388943 sra ファイルのダウンロード中... Completed: 471160K bytes transferred in 9 seconds (386570K 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 5758335 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017461/SRR8198084.sra Written 5758335 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017461/SRR8198084.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: 00:14:38 5758335 reads; of these: 5758335 (100.00%) were paired; of these: 1472219 (25.57%) aligned concordantly 0 times 3682774 (63.96%) aligned concordantly exactly 1 time 603342 (10.48%) aligned concordantly >1 times ---- 1472219 pairs aligned concordantly 0 times; of these: 159372 (10.83%) aligned discordantly 1 time ---- 1312847 pairs aligned 0 times concordantly or discordantly; of these: 2625694 mates make up the pairs; of these: 2142794 (81.61%) aligned 0 times 320089 (12.19%) aligned exactly 1 time 162811 (6.20%) aligned >1 times 81.39% overall alignment rate Time searching: 00:14:38 Overall time: 00:14:38 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_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] 38909 / 4442749 = 0.0088 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 00:39:28: # Command line: callpeak -t SRX5017461.bam -f BAM -g 12100000 -n SRX5017461.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5017461.10 # format = BAM # ChIP-seq file = ['SRX5017461.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 00:39:28: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:39:28: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:39:28: # Command line: callpeak -t SRX5017461.bam -f BAM -g 12100000 -n SRX5017461.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5017461.05 # format = BAM # ChIP-seq file = ['SRX5017461.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 00:39:28: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:39:28: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:39:28: # Command line: callpeak -t SRX5017461.bam -f BAM -g 12100000 -n SRX5017461.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5017461.20 # format = BAM # ChIP-seq file = ['SRX5017461.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 00:39:28: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:39:28: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:39:40: 1000000 INFO @ Thu, 13 Dec 2018 00:39:55: 2000000 INFO @ Thu, 13 Dec 2018 00:39:55: 1000000 INFO @ Thu, 13 Dec 2018 00:39:58: 1000000 INFO @ Thu, 13 Dec 2018 00:40:12: 3000000 INFO @ Thu, 13 Dec 2018 00:40:22: 2000000 INFO @ Thu, 13 Dec 2018 00:40:24: 2000000 INFO @ Thu, 13 Dec 2018 00:40:29: 4000000 INFO @ Thu, 13 Dec 2018 00:40:45: 5000000 INFO @ Thu, 13 Dec 2018 00:40:46: 3000000 INFO @ Thu, 13 Dec 2018 00:40:49: 3000000 INFO @ Thu, 13 Dec 2018 00:41:01: 6000000 INFO @ Thu, 13 Dec 2018 00:41:11: 4000000 INFO @ Thu, 13 Dec 2018 00:41:15: 4000000 INFO @ Thu, 13 Dec 2018 00:41:18: 7000000 INFO @ Thu, 13 Dec 2018 00:41:34: 8000000 INFO @ Thu, 13 Dec 2018 00:41:35: 5000000 INFO @ Thu, 13 Dec 2018 00:41:40: 5000000 INFO @ Thu, 13 Dec 2018 00:41:48: 9000000 INFO @ Thu, 13 Dec 2018 00:41:52: #1 tag size is determined as 100 bps INFO @ Thu, 13 Dec 2018 00:41:52: #1 tag size = 100 INFO @ Thu, 13 Dec 2018 00:41:52: #1 total tags in treatment: 4247602 INFO @ Thu, 13 Dec 2018 00:41:52: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:41:52: #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 00:41:52: #1 tags after filtering in treatment: 3533632 INFO @ Thu, 13 Dec 2018 00:41:52: #1 Redundant rate of treatment: 0.17 INFO @ Thu, 13 Dec 2018 00:41:52: #1 finished! INFO @ Thu, 13 Dec 2018 00:41:52: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:41:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:41:52: #2 number of paired peaks: 29 WARNING @ Thu, 13 Dec 2018 00:41:52: Too few paired peaks (29) 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 00:41:52: Process for pairing-model is terminated! cat: SRX5017461.05_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 `SRX5017461.05_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 `SRX5017461.05_*.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 `SRX5017461.05_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 00:41:59: 6000000 INFO @ Thu, 13 Dec 2018 00:42:02: 6000000 INFO @ Thu, 13 Dec 2018 00:42:16: 7000000 INFO @ Thu, 13 Dec 2018 00:42:23: 7000000 INFO @ Thu, 13 Dec 2018 00:42:34: 8000000 INFO @ Thu, 13 Dec 2018 00:42:45: 8000000 INFO @ Thu, 13 Dec 2018 00:42:49: 9000000 INFO @ Thu, 13 Dec 2018 00:42:53: #1 tag size is determined as 100 bps INFO @ Thu, 13 Dec 2018 00:42:53: #1 tag size = 100 INFO @ Thu, 13 Dec 2018 00:42:53: #1 total tags in treatment: 4247602 INFO @ Thu, 13 Dec 2018 00:42:53: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:42:53: #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 00:42:54: #1 tags after filtering in treatment: 3533632 INFO @ Thu, 13 Dec 2018 00:42:54: #1 Redundant rate of treatment: 0.17 INFO @ Thu, 13 Dec 2018 00:42:54: #1 finished! INFO @ Thu, 13 Dec 2018 00:42:54: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:42:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:42:54: #2 number of paired peaks: 29 WARNING @ Thu, 13 Dec 2018 00:42:54: Too few paired peaks (29) 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 00:42:54: Process for pairing-model is terminated! cat: SRX5017461.20_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): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017461.20_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 `SRX5017461.20_*.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 `SRX5017461.20_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... INFO @ Thu, 13 Dec 2018 00:43:10: 9000000 INFO @ Thu, 13 Dec 2018 00:43:16: #1 tag size is determined as 100 bps INFO @ Thu, 13 Dec 2018 00:43:16: #1 tag size = 100 INFO @ Thu, 13 Dec 2018 00:43:16: #1 total tags in treatment: 4247602 INFO @ Thu, 13 Dec 2018 00:43:16: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:43:16: #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 00:43:16: #1 tags after filtering in treatment: 3533632 INFO @ Thu, 13 Dec 2018 00:43:16: #1 Redundant rate of treatment: 0.17 INFO @ Thu, 13 Dec 2018 00:43:16: #1 finished! INFO @ Thu, 13 Dec 2018 00:43:16: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:43:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:43:17: #2 number of paired peaks: 29 WARNING @ Thu, 13 Dec 2018 00:43:17: Too few paired peaks (29) 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 00:43:17: Process for pairing-model is terminated! cat: SRX5017461.10_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 `SRX5017461.10_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 `SRX5017461.10_*.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 `SRX5017461.10_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 BigWig に変換しました。