Job ID = 11192638 sra ファイルのダウンロード中... Completed: 840559K bytes transferred in 10 seconds (677447K 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 25880216 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1743199/SRR3476613.sra Written 25880216 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1743199/SRR3476613.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: 00:12:23 25880216 reads; of these: 25880216 (100.00%) were paired; of these: 13758818 (53.16%) aligned concordantly 0 times 10743901 (41.51%) aligned concordantly exactly 1 time 1377497 (5.32%) aligned concordantly >1 times ---- 13758818 pairs aligned concordantly 0 times; of these: 362879 (2.64%) aligned discordantly 1 time ---- 13395939 pairs aligned 0 times concordantly or discordantly; of these: 26791878 mates make up the pairs; of these: 21933899 (81.87%) aligned 0 times 4194740 (15.66%) aligned exactly 1 time 663239 (2.48%) aligned >1 times 57.62% overall alignment rate Time searching: 00:12:23 Overall time: 00:12:23 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 8 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] 3548393 / 12390881 = 0.2864 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, 15 Sep 2018 10:00:49: # Command line: callpeak -t SRX1743199.bam -f BAM -g 12100000 -n SRX1743199.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1743199.20 # format = BAM # ChIP-seq file = ['SRX1743199.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 @ Sat, 15 Sep 2018 10:00:49: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:00:49: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:00:49: # Command line: callpeak -t SRX1743199.bam -f BAM -g 12100000 -n SRX1743199.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1743199.05 # format = BAM # ChIP-seq file = ['SRX1743199.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 @ Sat, 15 Sep 2018 10:00:49: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:00:49: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:00:49: # Command line: callpeak -t SRX1743199.bam -f BAM -g 12100000 -n SRX1743199.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1743199.10 # format = BAM # ChIP-seq file = ['SRX1743199.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 @ Sat, 15 Sep 2018 10:00:49: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:00:49: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:00:55: 1000000 INFO @ Sat, 15 Sep 2018 10:00:55: 1000000 INFO @ Sat, 15 Sep 2018 10:00:55: 1000000 INFO @ Sat, 15 Sep 2018 10:01:00: 2000000 INFO @ Sat, 15 Sep 2018 10:01:00: 2000000 INFO @ Sat, 15 Sep 2018 10:01:00: 2000000 INFO @ Sat, 15 Sep 2018 10:01:06: 3000000 INFO @ Sat, 15 Sep 2018 10:01:06: 3000000 INFO @ Sat, 15 Sep 2018 10:01:06: 3000000 INFO @ Sat, 15 Sep 2018 10:01:11: 4000000 INFO @ Sat, 15 Sep 2018 10:01:11: 4000000 INFO @ Sat, 15 Sep 2018 10:01:11: 4000000 INFO @ Sat, 15 Sep 2018 10:01:16: 5000000 INFO @ Sat, 15 Sep 2018 10:01:16: 5000000 INFO @ Sat, 15 Sep 2018 10:01:16: 5000000 INFO @ Sat, 15 Sep 2018 10:01:22: 6000000 INFO @ Sat, 15 Sep 2018 10:01:22: 6000000 INFO @ Sat, 15 Sep 2018 10:01:22: 6000000 INFO @ Sat, 15 Sep 2018 10:01:27: 7000000 INFO @ Sat, 15 Sep 2018 10:01:27: 7000000 INFO @ Sat, 15 Sep 2018 10:01:27: 7000000 INFO @ Sat, 15 Sep 2018 10:01:32: 8000000 INFO @ Sat, 15 Sep 2018 10:01:32: 8000000 INFO @ Sat, 15 Sep 2018 10:01:32: 8000000 INFO @ Sat, 15 Sep 2018 10:01:37: 9000000 INFO @ Sat, 15 Sep 2018 10:01:38: 9000000 INFO @ Sat, 15 Sep 2018 10:01:38: 9000000 INFO @ Sat, 15 Sep 2018 10:01:43: 10000000 INFO @ Sat, 15 Sep 2018 10:01:43: 10000000 INFO @ Sat, 15 Sep 2018 10:01:43: 10000000 INFO @ Sat, 15 Sep 2018 10:01:48: 11000000 INFO @ Sat, 15 Sep 2018 10:01:48: 11000000 INFO @ Sat, 15 Sep 2018 10:01:48: 11000000 INFO @ Sat, 15 Sep 2018 10:01:53: 12000000 INFO @ Sat, 15 Sep 2018 10:01:54: 12000000 INFO @ Sat, 15 Sep 2018 10:01:54: 12000000 INFO @ Sat, 15 Sep 2018 10:01:59: 13000000 INFO @ Sat, 15 Sep 2018 10:01:59: 13000000 INFO @ Sat, 15 Sep 2018 10:01:59: 13000000 INFO @ Sat, 15 Sep 2018 10:02:04: 14000000 INFO @ Sat, 15 Sep 2018 10:02:04: 14000000 INFO @ Sat, 15 Sep 2018 10:02:04: 14000000 INFO @ Sat, 15 Sep 2018 10:02:09: 15000000 INFO @ Sat, 15 Sep 2018 10:02:10: 15000000 INFO @ Sat, 15 Sep 2018 10:02:10: 15000000 INFO @ Sat, 15 Sep 2018 10:02:14: 16000000 INFO @ Sat, 15 Sep 2018 10:02:15: 16000000 INFO @ Sat, 15 Sep 2018 10:02:15: 16000000 INFO @ Sat, 15 Sep 2018 10:02:20: 17000000 INFO @ Sat, 15 Sep 2018 10:02:20: 17000000 INFO @ Sat, 15 Sep 2018 10:02:20: 17000000 INFO @ Sat, 15 Sep 2018 10:02:25: 18000000 INFO @ Sat, 15 Sep 2018 10:02:25: 18000000 INFO @ Sat, 15 Sep 2018 10:02:26: 18000000 INFO @ Sat, 15 Sep 2018 10:02:30: 19000000 INFO @ Sat, 15 Sep 2018 10:02:31: 19000000 INFO @ Sat, 15 Sep 2018 10:02:31: 19000000 INFO @ Sat, 15 Sep 2018 10:02:36: 20000000 INFO @ Sat, 15 Sep 2018 10:02:36: 20000000 INFO @ Sat, 15 Sep 2018 10:02:36: 20000000 INFO @ Sat, 15 Sep 2018 10:02:41: 21000000 INFO @ Sat, 15 Sep 2018 10:02:42: 21000000 INFO @ Sat, 15 Sep 2018 10:02:42: 21000000 INFO @ Sat, 15 Sep 2018 10:02:46: 22000000 INFO @ Sat, 15 Sep 2018 10:02:47: 22000000 INFO @ Sat, 15 Sep 2018 10:02:47: 22000000 INFO @ Sat, 15 Sep 2018 10:02:50: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 10:02:50: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 10:02:50: #1 total tags in treatment: 8659195 INFO @ Sat, 15 Sep 2018 10:02:50: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:02:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:02:50: #1 tags after filtering in treatment: 6520686 INFO @ Sat, 15 Sep 2018 10:02:50: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Sep 2018 10:02:50: #1 finished! INFO @ Sat, 15 Sep 2018 10:02:50: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:02:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:02:51: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 10:02:51: 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 @ Sat, 15 Sep 2018 10:02:51: Process for pairing-model is terminated! cat: SRX1743199.20_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Sat, 15 Sep 2018 10:02:51: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 10:02:51: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 10:02:51: #1 total tags in treatment: 8659195 INFO @ Sat, 15 Sep 2018 10:02:51: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:02:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) rm: cannot remove `SRX1743199.20_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 `SRX1743199.20_*.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 `SRX1743199.20_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, 15 Sep 2018 10:02:51: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 10:02:51: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 10:02:51: #1 total tags in treatment: 8659195 INFO @ Sat, 15 Sep 2018 10:02:51: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:02:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:02:51: #1 tags after filtering in treatment: 6520686 INFO @ Sat, 15 Sep 2018 10:02:51: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Sep 2018 10:02:51: #1 finished! INFO @ Sat, 15 Sep 2018 10:02:51: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:02:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:02:51: #1 tags after filtering in treatment: 6520686 INFO @ Sat, 15 Sep 2018 10:02:51: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Sep 2018 10:02:51: #1 finished! INFO @ Sat, 15 Sep 2018 10:02:51: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:02:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:02:51: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 10:02:51: 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 @ Sat, 15 Sep 2018 10:02:51: Process for pairing-model is terminated! cat: SRX1743199.05_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 `SRX1743199.05_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 `SRX1743199.05_*.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 `SRX1743199.05_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, 15 Sep 2018 10:02:51: #2 number of paired peaks: 0 WARNING @ Sat, 15 Sep 2018 10:02:51: 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 @ Sat, 15 Sep 2018 10:02:51: Process for pairing-model is terminated! cat: SRX1743199.10_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1743199.10_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 `SRX1743199.10_*.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 `SRX1743199.10_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。