Job ID = 11171340 sra ファイルのダウンロード中... Completed: 486129K bytes transferred in 19 seconds (199526K bits/sec), in 1 file. Completed: 217312K bytes transferred in 13 seconds (128820K bits/sec), in 1 file. Completed: 262445K bytes transferred in 16 seconds (134292K bits/sec), in 1 file. Completed: 115142K bytes transferred in 7 seconds (134085K 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 2042425 spots for /home/okishinya/chipatlas/results/dm3/SRX3632914/SRR6655563.sra Written 2042425 spots for /home/okishinya/chipatlas/results/dm3/SRX3632914/SRR6655563.sra Read 3945940 spots for /home/okishinya/chipatlas/results/dm3/SRX3632914/SRR6655561.sra Written 3945940 spots for /home/okishinya/chipatlas/results/dm3/SRX3632914/SRR6655561.sra Read 4666419 spots for /home/okishinya/chipatlas/results/dm3/SRX3632914/SRR6655562.sra Written 4666419 spots for /home/okishinya/chipatlas/results/dm3/SRX3632914/SRR6655562.sra Read 8812022 spots for /home/okishinya/chipatlas/results/dm3/SRX3632914/SRR6655560.sra Written 8812022 spots for /home/okishinya/chipatlas/results/dm3/SRX3632914/SRR6655560.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 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: 00:44:26 19466806 reads; of these: 19466806 (100.00%) were paired; of these: 4253416 (21.85%) aligned concordantly 0 times 13132186 (67.46%) aligned concordantly exactly 1 time 2081204 (10.69%) aligned concordantly >1 times ---- 4253416 pairs aligned concordantly 0 times; of these: 473487 (11.13%) aligned discordantly 1 time ---- 3779929 pairs aligned 0 times concordantly or discordantly; of these: 7559858 mates make up the pairs; of these: 6444023 (85.24%) aligned 0 times 554064 (7.33%) aligned exactly 1 time 561771 (7.43%) aligned >1 times 83.45% overall alignment rate Time searching: 00:44:26 Overall time: 00:44:26 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] 543296 / 15612921 = 0.0348 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 @ Sat, 08 Sep 2018 14:43:33: # Command line: callpeak -t SRX3632914.bam -f BAM -g dm -n SRX3632914.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3632914.05 # format = BAM # ChIP-seq file = ['SRX3632914.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 @ Sat, 08 Sep 2018 14:43:33: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:43:33: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:43:33: # Command line: callpeak -t SRX3632914.bam -f BAM -g dm -n SRX3632914.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3632914.20 # format = BAM # ChIP-seq file = ['SRX3632914.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 @ Sat, 08 Sep 2018 14:43:33: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:43:33: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:43:33: # Command line: callpeak -t SRX3632914.bam -f BAM -g dm -n SRX3632914.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3632914.10 # format = BAM # ChIP-seq file = ['SRX3632914.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 @ Sat, 08 Sep 2018 14:43:33: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:43:33: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:43:40: 1000000 INFO @ Sat, 08 Sep 2018 14:43:40: 1000000 INFO @ Sat, 08 Sep 2018 14:43:41: 1000000 INFO @ Sat, 08 Sep 2018 14:43:47: 2000000 INFO @ Sat, 08 Sep 2018 14:43:48: 2000000 INFO @ Sat, 08 Sep 2018 14:43:49: 2000000 INFO @ Sat, 08 Sep 2018 14:43:55: 3000000 INFO @ Sat, 08 Sep 2018 14:43:56: 3000000 INFO @ Sat, 08 Sep 2018 14:43:56: 3000000 INFO @ Sat, 08 Sep 2018 14:44:02: 4000000 INFO @ Sat, 08 Sep 2018 14:44:04: 4000000 INFO @ Sat, 08 Sep 2018 14:44:04: 4000000 INFO @ Sat, 08 Sep 2018 14:44:09: 5000000 INFO @ Sat, 08 Sep 2018 14:44:11: 5000000 INFO @ Sat, 08 Sep 2018 14:44:12: 5000000 INFO @ Sat, 08 Sep 2018 14:44:16: 6000000 INFO @ Sat, 08 Sep 2018 14:44:19: 6000000 INFO @ Sat, 08 Sep 2018 14:44:21: 6000000 INFO @ Sat, 08 Sep 2018 14:44:24: 7000000 INFO @ Sat, 08 Sep 2018 14:44:27: 7000000 INFO @ Sat, 08 Sep 2018 14:44:29: 7000000 INFO @ Sat, 08 Sep 2018 14:44:31: 8000000 INFO @ Sat, 08 Sep 2018 14:44:35: 8000000 INFO @ Sat, 08 Sep 2018 14:44:38: 8000000 INFO @ Sat, 08 Sep 2018 14:44:38: 9000000 INFO @ Sat, 08 Sep 2018 14:44:43: 9000000 INFO @ Sat, 08 Sep 2018 14:44:45: 10000000 INFO @ Sat, 08 Sep 2018 14:44:46: 9000000 INFO @ Sat, 08 Sep 2018 14:44:51: 10000000 INFO @ Sat, 08 Sep 2018 14:44:52: 11000000 INFO @ Sat, 08 Sep 2018 14:44:54: 10000000 INFO @ Sat, 08 Sep 2018 14:44:59: 11000000 INFO @ Sat, 08 Sep 2018 14:45:00: 12000000 INFO @ Sat, 08 Sep 2018 14:45:03: 11000000 INFO @ Sat, 08 Sep 2018 14:45:07: 12000000 INFO @ Sat, 08 Sep 2018 14:45:07: 13000000 INFO @ Sat, 08 Sep 2018 14:45:11: 12000000 INFO @ Sat, 08 Sep 2018 14:45:14: 14000000 INFO @ Sat, 08 Sep 2018 14:45:15: 13000000 INFO @ Sat, 08 Sep 2018 14:45:19: 13000000 INFO @ Sat, 08 Sep 2018 14:45:21: 15000000 INFO @ Sat, 08 Sep 2018 14:45:22: 14000000 INFO @ Sat, 08 Sep 2018 14:45:28: 14000000 INFO @ Sat, 08 Sep 2018 14:45:28: 16000000 INFO @ Sat, 08 Sep 2018 14:45:30: 15000000 INFO @ Sat, 08 Sep 2018 14:45:35: 17000000 INFO @ Sat, 08 Sep 2018 14:45:36: 15000000 INFO @ Sat, 08 Sep 2018 14:45:38: 16000000 INFO @ Sat, 08 Sep 2018 14:45:43: 18000000 INFO @ Sat, 08 Sep 2018 14:45:44: 16000000 INFO @ Sat, 08 Sep 2018 14:45:46: 17000000 INFO @ Sat, 08 Sep 2018 14:45:50: 19000000 INFO @ Sat, 08 Sep 2018 14:45:52: 17000000 INFO @ Sat, 08 Sep 2018 14:45:54: 18000000 INFO @ Sat, 08 Sep 2018 14:45:57: 20000000 INFO @ Sat, 08 Sep 2018 14:46:00: 18000000 INFO @ Sat, 08 Sep 2018 14:46:02: 19000000 INFO @ Sat, 08 Sep 2018 14:46:04: 21000000 INFO @ Sat, 08 Sep 2018 14:46:08: 19000000 INFO @ Sat, 08 Sep 2018 14:46:09: 20000000 INFO @ Sat, 08 Sep 2018 14:46:11: 22000000 INFO @ Sat, 08 Sep 2018 14:46:16: 20000000 INFO @ Sat, 08 Sep 2018 14:46:17: 21000000 INFO @ Sat, 08 Sep 2018 14:46:18: 23000000 INFO @ Sat, 08 Sep 2018 14:46:24: 21000000 INFO @ Sat, 08 Sep 2018 14:46:25: 22000000 INFO @ Sat, 08 Sep 2018 14:46:26: 24000000 INFO @ Sat, 08 Sep 2018 14:46:31: 22000000 INFO @ Sat, 08 Sep 2018 14:46:33: 23000000 INFO @ Sat, 08 Sep 2018 14:46:33: 25000000 INFO @ Sat, 08 Sep 2018 14:46:39: 23000000 INFO @ Sat, 08 Sep 2018 14:46:40: 26000000 INFO @ Sat, 08 Sep 2018 14:46:41: 24000000 INFO @ Sat, 08 Sep 2018 14:46:47: 24000000 INFO @ Sat, 08 Sep 2018 14:46:48: 27000000 INFO @ Sat, 08 Sep 2018 14:46:49: 25000000 INFO @ Sat, 08 Sep 2018 14:46:55: 28000000 INFO @ Sat, 08 Sep 2018 14:46:55: 25000000 INFO @ Sat, 08 Sep 2018 14:46:57: 26000000 INFO @ Sat, 08 Sep 2018 14:47:02: 29000000 INFO @ Sat, 08 Sep 2018 14:47:03: 26000000 INFO @ Sat, 08 Sep 2018 14:47:05: 27000000 INFO @ Sat, 08 Sep 2018 14:47:09: 30000000 INFO @ Sat, 08 Sep 2018 14:47:11: 27000000 INFO @ Sat, 08 Sep 2018 14:47:12: 28000000 INFO @ Sat, 08 Sep 2018 14:47:16: 31000000 INFO @ Sat, 08 Sep 2018 14:47:19: 28000000 INFO @ Sat, 08 Sep 2018 14:47:19: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 14:47:19: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 14:47:19: #1 total tags in treatment: 14683587 INFO @ Sat, 08 Sep 2018 14:47:19: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:47:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:47:20: #1 tags after filtering in treatment: 12854775 INFO @ Sat, 08 Sep 2018 14:47:20: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 08 Sep 2018 14:47:20: #1 finished! INFO @ Sat, 08 Sep 2018 14:47:20: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:47:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:47:20: 29000000 INFO @ Sat, 08 Sep 2018 14:47:20: #2 number of paired peaks: 8 WARNING @ Sat, 08 Sep 2018 14:47:20: Too few paired peaks (8) 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 @ Sat, 08 Sep 2018 14:47:20: Process for pairing-model is terminated! cat: SRX3632914.05_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 `SRX3632914.05_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 `SRX3632914.05_*.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 `SRX3632914.05_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 @ Sat, 08 Sep 2018 14:47:26: 29000000 INFO @ Sat, 08 Sep 2018 14:47:28: 30000000 INFO @ Sat, 08 Sep 2018 14:47:34: 30000000 INFO @ Sat, 08 Sep 2018 14:47:36: 31000000 INFO @ Sat, 08 Sep 2018 14:47:39: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 14:47:39: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 14:47:39: #1 total tags in treatment: 14683587 INFO @ Sat, 08 Sep 2018 14:47:39: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:47:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:47:39: #1 tags after filtering in treatment: 12854775 INFO @ Sat, 08 Sep 2018 14:47:39: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 08 Sep 2018 14:47:39: #1 finished! INFO @ Sat, 08 Sep 2018 14:47:39: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:47:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:47:40: #2 number of paired peaks: 8 WARNING @ Sat, 08 Sep 2018 14:47:40: Too few paired peaks (8) 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 @ Sat, 08 Sep 2018 14:47:40: Process for pairing-model is terminated! cat: SRX3632914.20_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 `SRX3632914.20_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 `SRX3632914.20_*.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 `SRX3632914.20_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 @ Sat, 08 Sep 2018 14:47:41: 31000000 INFO @ Sat, 08 Sep 2018 14:47:44: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 14:47:44: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 14:47:44: #1 total tags in treatment: 14683587 INFO @ Sat, 08 Sep 2018 14:47:44: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:47:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:47:45: #1 tags after filtering in treatment: 12854775 INFO @ Sat, 08 Sep 2018 14:47:45: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 08 Sep 2018 14:47:45: #1 finished! INFO @ Sat, 08 Sep 2018 14:47:45: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:47:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:47:45: #2 number of paired peaks: 8 WARNING @ Sat, 08 Sep 2018 14:47:45: Too few paired peaks (8) 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 @ Sat, 08 Sep 2018 14:47:45: Process for pairing-model is terminated! cat: SRX3632914.10_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 `SRX3632914.10_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 `SRX3632914.10_*.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 `SRX3632914.10_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。