Job ID = 10045042 sra ファイルのダウンロード中... Completed: 727431K bytes transferred in 29 seconds (205383K bits/sec), in 2 files, 3 directories. 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 14875219 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2704970/SRR5413018.sra Written 14875219 spots total Written 15382447 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2704970/SRR5413017.sra Written 15382447 spots total 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: 00:12:47 30257666 reads; of these: 30257666 (100.00%) were paired; of these: 7952161 (26.28%) aligned concordantly 0 times 19146778 (63.28%) aligned concordantly exactly 1 time 3158727 (10.44%) aligned concordantly >1 times ---- 7952161 pairs aligned concordantly 0 times; of these: 1178060 (14.81%) aligned discordantly 1 time ---- 6774101 pairs aligned 0 times concordantly or discordantly; of these: 13548202 mates make up the pairs; of these: 11117415 (82.06%) aligned 0 times 1718866 (12.69%) aligned exactly 1 time 711921 (5.25%) aligned >1 times 81.63% overall alignment rate Time searching: 00:12:47 Overall time: 00:12:47 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 16 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] 9590464 / 22522901 = 0.4258 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 @ Mon, 02 Oct 2017 15:01:52: # Command line: callpeak -t SRX2704970.bam -f BAM -g 12100000 -n SRX2704970.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2704970.05 # format = BAM # ChIP-seq file = ['SRX2704970.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 @ Mon, 02 Oct 2017 15:01:52: #1 read tag files... INFO @ Mon, 02 Oct 2017 15:01:52: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 15:01:52: # Command line: callpeak -t SRX2704970.bam -f BAM -g 12100000 -n SRX2704970.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2704970.10 # format = BAM # ChIP-seq file = ['SRX2704970.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 @ Mon, 02 Oct 2017 15:01:52: #1 read tag files... INFO @ Mon, 02 Oct 2017 15:01:52: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 15:01:52: # Command line: callpeak -t SRX2704970.bam -f BAM -g 12100000 -n SRX2704970.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2704970.20 # format = BAM # ChIP-seq file = ['SRX2704970.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 @ Mon, 02 Oct 2017 15:01:52: #1 read tag files... INFO @ Mon, 02 Oct 2017 15:01:52: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 15:01:57: 1000000 INFO @ Mon, 02 Oct 2017 15:01:57: 1000000 INFO @ Mon, 02 Oct 2017 15:01:57: 1000000 INFO @ Mon, 02 Oct 2017 15:02:02: 2000000 INFO @ Mon, 02 Oct 2017 15:02:02: 2000000 INFO @ Mon, 02 Oct 2017 15:02:02: 2000000 INFO @ Mon, 02 Oct 2017 15:02:06: 3000000 INFO @ Mon, 02 Oct 2017 15:02:06: 3000000 INFO @ Mon, 02 Oct 2017 15:02:07: 3000000 INFO @ Mon, 02 Oct 2017 15:02:11: 4000000 INFO @ Mon, 02 Oct 2017 15:02:11: 4000000 INFO @ Mon, 02 Oct 2017 15:02:12: 4000000 INFO @ Mon, 02 Oct 2017 15:02:16: 5000000 INFO @ Mon, 02 Oct 2017 15:02:16: 5000000 INFO @ Mon, 02 Oct 2017 15:02:17: 5000000 INFO @ Mon, 02 Oct 2017 15:02:21: 6000000 INFO @ Mon, 02 Oct 2017 15:02:21: 6000000 INFO @ Mon, 02 Oct 2017 15:02:22: 6000000 INFO @ Mon, 02 Oct 2017 15:02:26: 7000000 INFO @ Mon, 02 Oct 2017 15:02:26: 7000000 INFO @ Mon, 02 Oct 2017 15:02:27: 7000000 INFO @ Mon, 02 Oct 2017 15:02:31: 8000000 INFO @ Mon, 02 Oct 2017 15:02:31: 8000000 INFO @ Mon, 02 Oct 2017 15:02:33: 8000000 INFO @ Mon, 02 Oct 2017 15:02:35: 9000000 INFO @ Mon, 02 Oct 2017 15:02:36: 9000000 INFO @ Mon, 02 Oct 2017 15:02:38: 9000000 INFO @ Mon, 02 Oct 2017 15:02:40: 10000000 INFO @ Mon, 02 Oct 2017 15:02:40: 10000000 INFO @ Mon, 02 Oct 2017 15:02:43: 10000000 INFO @ Mon, 02 Oct 2017 15:02:45: 11000000 INFO @ Mon, 02 Oct 2017 15:02:45: 11000000 INFO @ Mon, 02 Oct 2017 15:02:48: 11000000 INFO @ Mon, 02 Oct 2017 15:02:50: 12000000 INFO @ Mon, 02 Oct 2017 15:02:50: 12000000 INFO @ Mon, 02 Oct 2017 15:02:53: 12000000 INFO @ Mon, 02 Oct 2017 15:02:55: 13000000 INFO @ Mon, 02 Oct 2017 15:02:55: 13000000 INFO @ Mon, 02 Oct 2017 15:02:58: 13000000 INFO @ Mon, 02 Oct 2017 15:03:00: 14000000 INFO @ Mon, 02 Oct 2017 15:03:00: 14000000 INFO @ Mon, 02 Oct 2017 15:03:04: 14000000 INFO @ Mon, 02 Oct 2017 15:03:05: 15000000 INFO @ Mon, 02 Oct 2017 15:03:05: 15000000 INFO @ Mon, 02 Oct 2017 15:03:09: 15000000 INFO @ Mon, 02 Oct 2017 15:03:10: 16000000 INFO @ Mon, 02 Oct 2017 15:03:10: 16000000 INFO @ Mon, 02 Oct 2017 15:03:14: 16000000 INFO @ Mon, 02 Oct 2017 15:03:15: 17000000 INFO @ Mon, 02 Oct 2017 15:03:15: 17000000 INFO @ Mon, 02 Oct 2017 15:03:19: 17000000 INFO @ Mon, 02 Oct 2017 15:03:19: 18000000 INFO @ Mon, 02 Oct 2017 15:03:20: 18000000 INFO @ Mon, 02 Oct 2017 15:03:24: 19000000 INFO @ Mon, 02 Oct 2017 15:03:24: 18000000 INFO @ Mon, 02 Oct 2017 15:03:24: 19000000 INFO @ Mon, 02 Oct 2017 15:03:29: 20000000 INFO @ Mon, 02 Oct 2017 15:03:29: 19000000 INFO @ Mon, 02 Oct 2017 15:03:29: 20000000 INFO @ Mon, 02 Oct 2017 15:03:34: 21000000 INFO @ Mon, 02 Oct 2017 15:03:34: 21000000 INFO @ Mon, 02 Oct 2017 15:03:34: 20000000 INFO @ Mon, 02 Oct 2017 15:03:39: 22000000 INFO @ Mon, 02 Oct 2017 15:03:39: 22000000 INFO @ Mon, 02 Oct 2017 15:03:39: 21000000 INFO @ Mon, 02 Oct 2017 15:03:44: 23000000 INFO @ Mon, 02 Oct 2017 15:03:44: 23000000 INFO @ Mon, 02 Oct 2017 15:03:45: 22000000 INFO @ Mon, 02 Oct 2017 15:03:49: 24000000 INFO @ Mon, 02 Oct 2017 15:03:49: 24000000 INFO @ Mon, 02 Oct 2017 15:03:50: 23000000 INFO @ Mon, 02 Oct 2017 15:03:54: 25000000 INFO @ Mon, 02 Oct 2017 15:03:54: 25000000 INFO @ Mon, 02 Oct 2017 15:03:55: 24000000 INFO @ Mon, 02 Oct 2017 15:03:59: 26000000 INFO @ Mon, 02 Oct 2017 15:03:59: 26000000 INFO @ Mon, 02 Oct 2017 15:04:01: 25000000 INFO @ Mon, 02 Oct 2017 15:04:04: 27000000 INFO @ Mon, 02 Oct 2017 15:04:04: 27000000 INFO @ Mon, 02 Oct 2017 15:04:06: 26000000 INFO @ Mon, 02 Oct 2017 15:04:09: 28000000 INFO @ Mon, 02 Oct 2017 15:04:09: 28000000 INFO @ Mon, 02 Oct 2017 15:04:12: 27000000 INFO @ Mon, 02 Oct 2017 15:04:14: 29000000 INFO @ Mon, 02 Oct 2017 15:04:14: 29000000 INFO @ Mon, 02 Oct 2017 15:04:17: 28000000 INFO @ Mon, 02 Oct 2017 15:04:19: 30000000 INFO @ Mon, 02 Oct 2017 15:04:20: 30000000 INFO @ Mon, 02 Oct 2017 15:04:21: #1 tag size is determined as 25 bps INFO @ Mon, 02 Oct 2017 15:04:21: #1 tag size = 25 INFO @ Mon, 02 Oct 2017 15:04:21: #1 total tags in treatment: 12716955 INFO @ Mon, 02 Oct 2017 15:04:21: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 15:04:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 15:04:21: #1 tag size is determined as 25 bps INFO @ Mon, 02 Oct 2017 15:04:21: #1 tag size = 25 INFO @ Mon, 02 Oct 2017 15:04:21: #1 total tags in treatment: 12716955 INFO @ Mon, 02 Oct 2017 15:04:21: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 15:04:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 15:04:21: #1 tags after filtering in treatment: 4777220 INFO @ Mon, 02 Oct 2017 15:04:21: #1 Redundant rate of treatment: 0.62 INFO @ Mon, 02 Oct 2017 15:04:21: #1 finished! INFO @ Mon, 02 Oct 2017 15:04:21: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 15:04:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 15:04:21: #1 tags after filtering in treatment: 4777220 INFO @ Mon, 02 Oct 2017 15:04:21: #1 Redundant rate of treatment: 0.62 INFO @ Mon, 02 Oct 2017 15:04:21: #1 finished! INFO @ Mon, 02 Oct 2017 15:04:21: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 15:04:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 15:04:21: #2 number of paired peaks: 0 WARNING @ Mon, 02 Oct 2017 15:04:21: 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 @ Mon, 02 Oct 2017 15:04:21: Process for pairing-model is terminated! cat: SRX2704970.20_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 `SRX2704970.20_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 `SRX2704970.20_*.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 `SRX2704970.20_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 @ Mon, 02 Oct 2017 15:04:21: #2 number of paired peaks: 0 WARNING @ Mon, 02 Oct 2017 15:04:21: 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 @ Mon, 02 Oct 2017 15:04:21: Process for pairing-model is terminated! cat: SRX2704970.10_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 `SRX2704970.10_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 `SRX2704970.10_*.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 `SRX2704970.10_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 @ Mon, 02 Oct 2017 15:04:22: 29000000 INFO @ Mon, 02 Oct 2017 15:04:27: 30000000 INFO @ Mon, 02 Oct 2017 15:04:28: #1 tag size is determined as 25 bps INFO @ Mon, 02 Oct 2017 15:04:28: #1 tag size = 25 INFO @ Mon, 02 Oct 2017 15:04:28: #1 total tags in treatment: 12716955 INFO @ Mon, 02 Oct 2017 15:04:28: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 15:04:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 02 Oct 2017 15:04:28: #1 tags after filtering in treatment: 4777220 INFO @ Mon, 02 Oct 2017 15:04:28: #1 Redundant rate of treatment: 0.62 INFO @ Mon, 02 Oct 2017 15:04:28: #1 finished! INFO @ Mon, 02 Oct 2017 15:04:28: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 15:04:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 15:04:28: #2 number of paired peaks: 0 WARNING @ Mon, 02 Oct 2017 15:04:28: 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 @ Mon, 02 Oct 2017 15:04:28: Process for pairing-model is terminated! cat: SRX2704970.05_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2704970.05_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 `SRX2704970.05_*.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 `SRX2704970.05_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 BigWig に変換しました。