Job ID = 11388947 sra ファイルのダウンロード中... Completed: 470817K bytes transferred in 10 seconds (359402K 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 5721275 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017465/SRR8198088.sra Written 5721275 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017465/SRR8198088.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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:13:54 5721275 reads; of these: 5721275 (100.00%) were paired; of these: 1693308 (29.60%) aligned concordantly 0 times 3365886 (58.83%) aligned concordantly exactly 1 time 662081 (11.57%) aligned concordantly >1 times ---- 1693308 pairs aligned concordantly 0 times; of these: 141805 (8.37%) aligned discordantly 1 time ---- 1551503 pairs aligned 0 times concordantly or discordantly; of these: 3103006 mates make up the pairs; of these: 2625194 (84.60%) aligned 0 times 305430 (9.84%) aligned exactly 1 time 172382 (5.56%) aligned >1 times 77.06% overall alignment rate Time searching: 00:13:55 Overall time: 00:13:55 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] 53467 / 4167311 = 0.0128 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 00:39:13: # Command line: callpeak -t SRX5017465.bam -f BAM -g 12100000 -n SRX5017465.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5017465.20 # format = BAM # ChIP-seq file = ['SRX5017465.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 00:39:13: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:39:13: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:39:13: # Command line: callpeak -t SRX5017465.bam -f BAM -g 12100000 -n SRX5017465.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5017465.10 # format = BAM # ChIP-seq file = ['SRX5017465.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 00:39:13: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:39:13: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:39:13: # Command line: callpeak -t SRX5017465.bam -f BAM -g 12100000 -n SRX5017465.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5017465.05 # format = BAM # ChIP-seq file = ['SRX5017465.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 00:39:13: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:39:13: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:39:24: 1000000 INFO @ Thu, 13 Dec 2018 00:39:26: 1000000 INFO @ Thu, 13 Dec 2018 00:39:26: 1000000 INFO @ Thu, 13 Dec 2018 00:39:37: 2000000 INFO @ Thu, 13 Dec 2018 00:39:40: 2000000 INFO @ Thu, 13 Dec 2018 00:39:40: 2000000 INFO @ Thu, 13 Dec 2018 00:39:48: 3000000 INFO @ Thu, 13 Dec 2018 00:39:51: 3000000 INFO @ Thu, 13 Dec 2018 00:39:56: 3000000 INFO @ Thu, 13 Dec 2018 00:39:59: 4000000 INFO @ Thu, 13 Dec 2018 00:40:02: 4000000 INFO @ Thu, 13 Dec 2018 00:40:10: 5000000 INFO @ Thu, 13 Dec 2018 00:40:15: 5000000 INFO @ Thu, 13 Dec 2018 00:40:15: 4000000 INFO @ Thu, 13 Dec 2018 00:40:21: 6000000 INFO @ Thu, 13 Dec 2018 00:40:29: 6000000 INFO @ Thu, 13 Dec 2018 00:40:33: 7000000 INFO @ Thu, 13 Dec 2018 00:40:34: 5000000 INFO @ Thu, 13 Dec 2018 00:40:42: 7000000 INFO @ Thu, 13 Dec 2018 00:40:44: 8000000 INFO @ Thu, 13 Dec 2018 00:40:51: #1 tag size is determined as 100 bps INFO @ Thu, 13 Dec 2018 00:40:51: #1 tag size = 100 INFO @ Thu, 13 Dec 2018 00:40:51: #1 total tags in treatment: 3974943 INFO @ Thu, 13 Dec 2018 00:40:51: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:40:51: #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 00:40:51: #1 tags after filtering in treatment: 3266603 INFO @ Thu, 13 Dec 2018 00:40:51: #1 Redundant rate of treatment: 0.18 INFO @ Thu, 13 Dec 2018 00:40:51: #1 finished! INFO @ Thu, 13 Dec 2018 00:40:51: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:40:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:40:52: #2 number of paired peaks: 28 WARNING @ Thu, 13 Dec 2018 00:40:52: 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 00:40:52: Process for pairing-model is terminated! cat: SRX5017465.20_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 `SRX5017465.20_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 `SRX5017465.20_*.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 `SRX5017465.20_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 @ Thu, 13 Dec 2018 00:40:52: 6000000 INFO @ Thu, 13 Dec 2018 00:40:55: 8000000 INFO @ Thu, 13 Dec 2018 00:41:05: #1 tag size is determined as 100 bps INFO @ Thu, 13 Dec 2018 00:41:05: #1 tag size = 100 INFO @ Thu, 13 Dec 2018 00:41:05: #1 total tags in treatment: 3974943 INFO @ Thu, 13 Dec 2018 00:41:05: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:41:05: #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 00:41:05: #1 tags after filtering in treatment: 3266603 INFO @ Thu, 13 Dec 2018 00:41:05: #1 Redundant rate of treatment: 0.18 INFO @ Thu, 13 Dec 2018 00:41:05: #1 finished! INFO @ Thu, 13 Dec 2018 00:41:05: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:41:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:41:06: #2 number of paired peaks: 28 WARNING @ Thu, 13 Dec 2018 00:41:06: 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 00:41:06: Process for pairing-model is terminated! cat: SRX5017465.10_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): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017465.10_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 `SRX5017465.10_*.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 `SRX5017465.10_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 00:41:10: 7000000 INFO @ Thu, 13 Dec 2018 00:41:28: 8000000 INFO @ Thu, 13 Dec 2018 00:41:41: #1 tag size is determined as 100 bps INFO @ Thu, 13 Dec 2018 00:41:41: #1 tag size = 100 INFO @ Thu, 13 Dec 2018 00:41:41: #1 total tags in treatment: 3974943 INFO @ Thu, 13 Dec 2018 00:41:41: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:41:41: #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 00:41:41: #1 tags after filtering in treatment: 3266603 INFO @ Thu, 13 Dec 2018 00:41:41: #1 Redundant rate of treatment: 0.18 INFO @ Thu, 13 Dec 2018 00:41:41: #1 finished! INFO @ Thu, 13 Dec 2018 00:41:41: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:41:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:41:41: #2 number of paired peaks: 28 WARNING @ Thu, 13 Dec 2018 00:41:41: 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 00:41:41: Process for pairing-model is terminated! cat: SRX5017465.05_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 `SRX5017465.05_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 `SRX5017465.05_*.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 `SRX5017465.05_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... BigWig に変換しました。