Job ID = 10480756 sra ファイルのダウンロード中... Completed: 2220968K bytes transferred in 46 seconds (392442K 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... Written 37255042 spots for /home/okishinya/chipatlas/results/dm3/SRX3733813/SRR6761591.sra Written 37255042 spots total 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: 00:00:01 Multiseed full-index search: 00:44:03 37255042 reads; of these: 37255042 (100.00%) were paired; of these: 25355967 (68.06%) aligned concordantly 0 times 9359884 (25.12%) aligned concordantly exactly 1 time 2539191 (6.82%) aligned concordantly >1 times ---- 25355967 pairs aligned concordantly 0 times; of these: 2116207 (8.35%) aligned discordantly 1 time ---- 23239760 pairs aligned 0 times concordantly or discordantly; of these: 46479520 mates make up the pairs; of these: 42835473 (92.16%) aligned 0 times 1942920 (4.18%) aligned exactly 1 time 1701127 (3.66%) aligned >1 times 42.51% overall alignment rate Time searching: 00:44:04 Overall time: 00:44:04 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 4799822 / 13980854 = 0.3433 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, 16 Mar 2018 08:47:46: # Command line: callpeak -t SRX3733813.bam -f BAM -g dm -n SRX3733813.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3733813.20 # format = BAM # ChIP-seq file = ['SRX3733813.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Mar 2018 08:47:46: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:47:46: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:47:46: # Command line: callpeak -t SRX3733813.bam -f BAM -g dm -n SRX3733813.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3733813.05 # format = BAM # ChIP-seq file = ['SRX3733813.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Mar 2018 08:47:46: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:47:46: # Command line: callpeak -t SRX3733813.bam -f BAM -g dm -n SRX3733813.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3733813.10 # format = BAM # ChIP-seq file = ['SRX3733813.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Mar 2018 08:47:46: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:47:46: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:47:46: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:47:52: 1000000 INFO @ Fri, 16 Mar 2018 08:47:52: 1000000 INFO @ Fri, 16 Mar 2018 08:47:52: 1000000 INFO @ Fri, 16 Mar 2018 08:47:58: 2000000 INFO @ Fri, 16 Mar 2018 08:47:58: 2000000 INFO @ Fri, 16 Mar 2018 08:47:58: 2000000 INFO @ Fri, 16 Mar 2018 08:48:04: 3000000 INFO @ Fri, 16 Mar 2018 08:48:05: 3000000 INFO @ Fri, 16 Mar 2018 08:48:06: 3000000 INFO @ Fri, 16 Mar 2018 08:48:11: 4000000 INFO @ Fri, 16 Mar 2018 08:48:13: 4000000 INFO @ Fri, 16 Mar 2018 08:48:16: 4000000 INFO @ Fri, 16 Mar 2018 08:48:17: 5000000 INFO @ Fri, 16 Mar 2018 08:48:20: 5000000 INFO @ Fri, 16 Mar 2018 08:48:23: 6000000 INFO @ Fri, 16 Mar 2018 08:48:25: 5000000 INFO @ Fri, 16 Mar 2018 08:48:28: 6000000 INFO @ Fri, 16 Mar 2018 08:48:29: 7000000 INFO @ Fri, 16 Mar 2018 08:48:34: 6000000 INFO @ Fri, 16 Mar 2018 08:48:35: 8000000 INFO @ Fri, 16 Mar 2018 08:48:35: 7000000 INFO @ Fri, 16 Mar 2018 08:48:41: 9000000 INFO @ Fri, 16 Mar 2018 08:48:43: 8000000 INFO @ Fri, 16 Mar 2018 08:48:43: 7000000 INFO @ Fri, 16 Mar 2018 08:48:48: 10000000 INFO @ Fri, 16 Mar 2018 08:48:50: 9000000 INFO @ Fri, 16 Mar 2018 08:48:52: 8000000 INFO @ Fri, 16 Mar 2018 08:48:55: 11000000 INFO @ Fri, 16 Mar 2018 08:48:58: 10000000 INFO @ Fri, 16 Mar 2018 08:49:01: 9000000 INFO @ Fri, 16 Mar 2018 08:49:03: 12000000 INFO @ Fri, 16 Mar 2018 08:49:05: 11000000 INFO @ Fri, 16 Mar 2018 08:49:10: 13000000 INFO @ Fri, 16 Mar 2018 08:49:10: 10000000 INFO @ Fri, 16 Mar 2018 08:49:12: 12000000 INFO @ Fri, 16 Mar 2018 08:49:17: 14000000 INFO @ Fri, 16 Mar 2018 08:49:19: 11000000 INFO @ Fri, 16 Mar 2018 08:49:20: 13000000 INFO @ Fri, 16 Mar 2018 08:49:23: 15000000 INFO @ Fri, 16 Mar 2018 08:49:27: 14000000 INFO @ Fri, 16 Mar 2018 08:49:28: 12000000 INFO @ Fri, 16 Mar 2018 08:49:29: 16000000 INFO @ Fri, 16 Mar 2018 08:49:35: 15000000 INFO @ Fri, 16 Mar 2018 08:49:35: 17000000 INFO @ Fri, 16 Mar 2018 08:49:37: 13000000 INFO @ Fri, 16 Mar 2018 08:49:41: 18000000 INFO @ Fri, 16 Mar 2018 08:49:43: 16000000 INFO @ Fri, 16 Mar 2018 08:49:46: 14000000 INFO @ Fri, 16 Mar 2018 08:49:48: 19000000 INFO @ Fri, 16 Mar 2018 08:49:50: 17000000 INFO @ Fri, 16 Mar 2018 08:49:54: 20000000 INFO @ Fri, 16 Mar 2018 08:49:55: 15000000 INFO @ Fri, 16 Mar 2018 08:49:58: 18000000 INFO @ Fri, 16 Mar 2018 08:50:00: 21000000 INFO @ Fri, 16 Mar 2018 08:50:04: 16000000 INFO @ Fri, 16 Mar 2018 08:50:06: 19000000 INFO @ Fri, 16 Mar 2018 08:50:06: 22000000 INFO @ Fri, 16 Mar 2018 08:50:07: #1 tag size is determined as 75 bps INFO @ Fri, 16 Mar 2018 08:50:07: #1 tag size = 75 INFO @ Fri, 16 Mar 2018 08:50:07: #1 total tags in treatment: 7533948 INFO @ Fri, 16 Mar 2018 08:50:07: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:50:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 08:50:07: #1 tags after filtering in treatment: 4991911 INFO @ Fri, 16 Mar 2018 08:50:07: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 16 Mar 2018 08:50:07: #1 finished! INFO @ Fri, 16 Mar 2018 08:50:07: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:50:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:50:07: #2 number of paired peaks: 2 WARNING @ Fri, 16 Mar 2018 08:50:07: Too few paired peaks (2) 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, 16 Mar 2018 08:50:07: Process for pairing-model is terminated! cat: SRX3733813.10_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): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3733813.10_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 `SRX3733813.10_*.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 `SRX3733813.10_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 @ Fri, 16 Mar 2018 08:50:13: 20000000 INFO @ Fri, 16 Mar 2018 08:50:13: 17000000 INFO @ Fri, 16 Mar 2018 08:50:21: 21000000 INFO @ Fri, 16 Mar 2018 08:50:23: 18000000 INFO @ Fri, 16 Mar 2018 08:50:28: 22000000 INFO @ Fri, 16 Mar 2018 08:50:29: #1 tag size is determined as 75 bps INFO @ Fri, 16 Mar 2018 08:50:29: #1 tag size = 75 INFO @ Fri, 16 Mar 2018 08:50:29: #1 total tags in treatment: 7533948 INFO @ Fri, 16 Mar 2018 08:50:29: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:50:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 08:50:29: #1 tags after filtering in treatment: 4991911 INFO @ Fri, 16 Mar 2018 08:50:29: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 16 Mar 2018 08:50:29: #1 finished! INFO @ Fri, 16 Mar 2018 08:50:29: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:50:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:50:30: #2 number of paired peaks: 2 WARNING @ Fri, 16 Mar 2018 08:50:30: Too few paired peaks (2) 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, 16 Mar 2018 08:50:30: Process for pairing-model is terminated! cat: SRX3733813.05_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): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3733813.05_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 `SRX3733813.05_*.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 `SRX3733813.05_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, 16 Mar 2018 08:50:32: 19000000 INFO @ Fri, 16 Mar 2018 08:50:41: 20000000 INFO @ Fri, 16 Mar 2018 08:50:50: 21000000 INFO @ Fri, 16 Mar 2018 08:50:59: 22000000 INFO @ Fri, 16 Mar 2018 08:50:59: #1 tag size is determined as 75 bps INFO @ Fri, 16 Mar 2018 08:50:59: #1 tag size = 75 INFO @ Fri, 16 Mar 2018 08:50:59: #1 total tags in treatment: 7533948 INFO @ Fri, 16 Mar 2018 08:50:59: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:50:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 08:51:00: #1 tags after filtering in treatment: 4991911 INFO @ Fri, 16 Mar 2018 08:51:00: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 16 Mar 2018 08:51:00: #1 finished! INFO @ Fri, 16 Mar 2018 08:51:00: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:51:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:51:00: #2 number of paired peaks: 2 WARNING @ Fri, 16 Mar 2018 08:51:00: Too few paired peaks (2) 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, 16 Mar 2018 08:51:00: Process for pairing-model is terminated! cat: SRX3733813.20_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): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3733813.20_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 `SRX3733813.20_*.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 `SRX3733813.20_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。