Job ID = 11245220 sra ファイルのダウンロード中... Completed: 410512K bytes transferred in 7 seconds (469524K bits/sec), in 1 file. Completed: 413518K bytes transferred in 7 seconds (480019K bits/sec), in 1 file. Completed: 417886K bytes transferred in 7 seconds (488722K bits/sec), in 1 file. Completed: 222173K bytes transferred in 5 seconds (320768K 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 2138169 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669669/SRR7818322.sra Written 2138169 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669669/SRR7818322.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669669/SRR7818320.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669669/SRR7818320.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669669/SRR7818321.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669669/SRR7818321.sra Read 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669669/SRR7818319.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669669/SRR7818319.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: 00:14:03 14138169 reads; of these: 14138169 (100.00%) were paired; of these: 1982067 (14.02%) aligned concordantly 0 times 10613862 (75.07%) aligned concordantly exactly 1 time 1542240 (10.91%) aligned concordantly >1 times ---- 1982067 pairs aligned concordantly 0 times; of these: 209491 (10.57%) aligned discordantly 1 time ---- 1772576 pairs aligned 0 times concordantly or discordantly; of these: 3545152 mates make up the pairs; of these: 2975534 (83.93%) aligned 0 times 404529 (11.41%) aligned exactly 1 time 165089 (4.66%) aligned >1 times 89.48% overall alignment rate Time searching: 00:14:03 Overall time: 00:14:03 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 12 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] 262081 / 12321416 = 0.0213 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 @ Wed, 10 Oct 2018 00:15:59: # Command line: callpeak -t SRX4669669.bam -f BAM -g 12100000 -n SRX4669669.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669669.05 # format = BAM # ChIP-seq file = ['SRX4669669.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 @ Wed, 10 Oct 2018 00:15:59: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:15:59: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:15:59: # Command line: callpeak -t SRX4669669.bam -f BAM -g 12100000 -n SRX4669669.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669669.10 # format = BAM # ChIP-seq file = ['SRX4669669.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 @ Wed, 10 Oct 2018 00:15:59: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:15:59: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:15:59: # Command line: callpeak -t SRX4669669.bam -f BAM -g 12100000 -n SRX4669669.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669669.20 # format = BAM # ChIP-seq file = ['SRX4669669.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 @ Wed, 10 Oct 2018 00:15:59: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:15:59: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:16:07: 1000000 INFO @ Wed, 10 Oct 2018 00:16:07: 1000000 INFO @ Wed, 10 Oct 2018 00:16:07: 1000000 INFO @ Wed, 10 Oct 2018 00:16:14: 2000000 INFO @ Wed, 10 Oct 2018 00:16:14: 2000000 INFO @ Wed, 10 Oct 2018 00:16:14: 2000000 INFO @ Wed, 10 Oct 2018 00:16:22: 3000000 INFO @ Wed, 10 Oct 2018 00:16:22: 3000000 INFO @ Wed, 10 Oct 2018 00:16:22: 3000000 INFO @ Wed, 10 Oct 2018 00:16:29: 4000000 INFO @ Wed, 10 Oct 2018 00:16:30: 4000000 INFO @ Wed, 10 Oct 2018 00:16:30: 4000000 INFO @ Wed, 10 Oct 2018 00:16:37: 5000000 INFO @ Wed, 10 Oct 2018 00:16:37: 5000000 INFO @ Wed, 10 Oct 2018 00:16:37: 5000000 INFO @ Wed, 10 Oct 2018 00:16:44: 6000000 INFO @ Wed, 10 Oct 2018 00:16:45: 6000000 INFO @ Wed, 10 Oct 2018 00:16:45: 6000000 INFO @ Wed, 10 Oct 2018 00:16:52: 7000000 INFO @ Wed, 10 Oct 2018 00:16:53: 7000000 INFO @ Wed, 10 Oct 2018 00:16:53: 7000000 INFO @ Wed, 10 Oct 2018 00:16:59: 8000000 INFO @ Wed, 10 Oct 2018 00:17:00: 8000000 INFO @ Wed, 10 Oct 2018 00:17:00: 8000000 INFO @ Wed, 10 Oct 2018 00:17:08: 9000000 INFO @ Wed, 10 Oct 2018 00:17:08: 9000000 INFO @ Wed, 10 Oct 2018 00:17:09: 9000000 INFO @ Wed, 10 Oct 2018 00:17:16: 10000000 INFO @ Wed, 10 Oct 2018 00:17:16: 10000000 INFO @ Wed, 10 Oct 2018 00:17:17: 10000000 INFO @ Wed, 10 Oct 2018 00:17:24: 11000000 INFO @ Wed, 10 Oct 2018 00:17:24: 11000000 INFO @ Wed, 10 Oct 2018 00:17:25: 11000000 INFO @ Wed, 10 Oct 2018 00:17:31: 12000000 INFO @ Wed, 10 Oct 2018 00:17:32: 12000000 INFO @ Wed, 10 Oct 2018 00:17:33: 12000000 INFO @ Wed, 10 Oct 2018 00:17:40: 13000000 INFO @ Wed, 10 Oct 2018 00:17:41: 13000000 INFO @ Wed, 10 Oct 2018 00:17:41: 13000000 INFO @ Wed, 10 Oct 2018 00:17:49: 14000000 INFO @ Wed, 10 Oct 2018 00:17:49: 14000000 INFO @ Wed, 10 Oct 2018 00:17:50: 14000000 INFO @ Wed, 10 Oct 2018 00:17:57: 15000000 INFO @ Wed, 10 Oct 2018 00:17:57: 15000000 INFO @ Wed, 10 Oct 2018 00:17:58: 15000000 INFO @ Wed, 10 Oct 2018 00:18:04: 16000000 INFO @ Wed, 10 Oct 2018 00:18:05: 16000000 INFO @ Wed, 10 Oct 2018 00:18:05: 16000000 INFO @ Wed, 10 Oct 2018 00:18:11: 17000000 INFO @ Wed, 10 Oct 2018 00:18:13: 17000000 INFO @ Wed, 10 Oct 2018 00:18:13: 17000000 INFO @ Wed, 10 Oct 2018 00:18:18: 18000000 INFO @ Wed, 10 Oct 2018 00:18:20: 18000000 INFO @ Wed, 10 Oct 2018 00:18:20: 18000000 INFO @ Wed, 10 Oct 2018 00:18:26: 19000000 INFO @ Wed, 10 Oct 2018 00:18:28: 19000000 INFO @ Wed, 10 Oct 2018 00:18:28: 19000000 INFO @ Wed, 10 Oct 2018 00:18:33: 20000000 INFO @ Wed, 10 Oct 2018 00:18:35: 20000000 INFO @ Wed, 10 Oct 2018 00:18:35: 20000000 INFO @ Wed, 10 Oct 2018 00:18:40: 21000000 INFO @ Wed, 10 Oct 2018 00:18:43: 21000000 INFO @ Wed, 10 Oct 2018 00:18:43: 21000000 INFO @ Wed, 10 Oct 2018 00:18:47: 22000000 INFO @ Wed, 10 Oct 2018 00:18:50: 22000000 INFO @ Wed, 10 Oct 2018 00:18:50: 22000000 INFO @ Wed, 10 Oct 2018 00:18:54: 23000000 INFO @ Wed, 10 Oct 2018 00:18:58: 23000000 INFO @ Wed, 10 Oct 2018 00:18:58: 23000000 INFO @ Wed, 10 Oct 2018 00:19:01: 24000000 INFO @ Wed, 10 Oct 2018 00:19:05: 24000000 INFO @ Wed, 10 Oct 2018 00:19:05: 24000000 INFO @ Wed, 10 Oct 2018 00:19:07: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:19:07: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:19:07: #1 total tags in treatment: 11895844 INFO @ Wed, 10 Oct 2018 00:19:07: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:19:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:19:07: #1 tags after filtering in treatment: 8664546 INFO @ Wed, 10 Oct 2018 00:19:07: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 10 Oct 2018 00:19:07: #1 finished! INFO @ Wed, 10 Oct 2018 00:19:07: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:19:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:19:08: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:19:08: Too few paired peaks (0) 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 @ Wed, 10 Oct 2018 00:19:08: Process for pairing-model is terminated! cat: SRX4669669.05_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 `SRX4669669.05_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 `SRX4669669.05_*.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 `SRX4669669.05_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 @ Wed, 10 Oct 2018 00:19:11: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:19:11: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:19:11: #1 total tags in treatment: 11895844 INFO @ Wed, 10 Oct 2018 00:19:11: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:19:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:19:11: #1 tag size is determined as 75 bps INFO @ Wed, 10 Oct 2018 00:19:11: #1 tag size = 75 INFO @ Wed, 10 Oct 2018 00:19:11: #1 total tags in treatment: 11895844 INFO @ Wed, 10 Oct 2018 00:19:11: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:19:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:19:12: #1 tags after filtering in treatment: 8664546 INFO @ Wed, 10 Oct 2018 00:19:12: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 10 Oct 2018 00:19:12: #1 finished! INFO @ Wed, 10 Oct 2018 00:19:12: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:19:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:19:12: #1 tags after filtering in treatment: 8664546 INFO @ Wed, 10 Oct 2018 00:19:12: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 10 Oct 2018 00:19:12: #1 finished! INFO @ Wed, 10 Oct 2018 00:19:12: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:19:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:19:12: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:19:12: Too few paired peaks (0) 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 @ Wed, 10 Oct 2018 00:19:12: Process for pairing-model is terminated! cat: SRX4669669.10_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 `SRX4669669.10_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 `SRX4669669.10_*.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 `SRX4669669.10_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 @ Wed, 10 Oct 2018 00:19:12: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:19:12: Too few paired peaks (0) 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 @ Wed, 10 Oct 2018 00:19:12: Process for pairing-model is terminated! cat: SRX4669669.20_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 `SRX4669669.20_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 `SRX4669669.20_*.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 `SRX4669669.20_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。