Job ID = 11244861 sra ファイルのダウンロード中... Completed: 885756K bytes transferred in 11 seconds (611048K 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 9152340 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3765654/SRR6807377.sra Written 9152340 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3765654/SRR6807377.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: 00:12:43 9152340 reads; of these: 9152340 (100.00%) were paired; of these: 254992 (2.79%) aligned concordantly 0 times 8036891 (87.81%) aligned concordantly exactly 1 time 860457 (9.40%) aligned concordantly >1 times ---- 254992 pairs aligned concordantly 0 times; of these: 45582 (17.88%) aligned discordantly 1 time ---- 209410 pairs aligned 0 times concordantly or discordantly; of these: 418820 mates make up the pairs; of these: 322975 (77.12%) aligned 0 times 75653 (18.06%) aligned exactly 1 time 20192 (4.82%) aligned >1 times 98.24% overall alignment rate Time searching: 00:12:43 Overall time: 00:12:43 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] 874611 / 8841795 = 0.0989 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 @ Tue, 09 Oct 2018 22:33:21: # Command line: callpeak -t SRX3765654.bam -f BAM -g 12100000 -n SRX3765654.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3765654.10 # format = BAM # ChIP-seq file = ['SRX3765654.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 @ Tue, 09 Oct 2018 22:33:21: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:33:21: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:33:21: # Command line: callpeak -t SRX3765654.bam -f BAM -g 12100000 -n SRX3765654.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3765654.05 # format = BAM # ChIP-seq file = ['SRX3765654.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 @ Tue, 09 Oct 2018 22:33:21: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:33:21: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:33:21: # Command line: callpeak -t SRX3765654.bam -f BAM -g 12100000 -n SRX3765654.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3765654.20 # format = BAM # ChIP-seq file = ['SRX3765654.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 @ Tue, 09 Oct 2018 22:33:21: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:33:21: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:33:30: 1000000 INFO @ Tue, 09 Oct 2018 22:33:30: 1000000 INFO @ Tue, 09 Oct 2018 22:33:30: 1000000 INFO @ Tue, 09 Oct 2018 22:33:38: 2000000 INFO @ Tue, 09 Oct 2018 22:33:38: 2000000 INFO @ Tue, 09 Oct 2018 22:33:39: 2000000 INFO @ Tue, 09 Oct 2018 22:33:46: 3000000 INFO @ Tue, 09 Oct 2018 22:33:46: 3000000 INFO @ Tue, 09 Oct 2018 22:33:48: 3000000 INFO @ Tue, 09 Oct 2018 22:33:56: 4000000 INFO @ Tue, 09 Oct 2018 22:33:56: 4000000 INFO @ Tue, 09 Oct 2018 22:33:57: 4000000 INFO @ Tue, 09 Oct 2018 22:34:06: 5000000 INFO @ Tue, 09 Oct 2018 22:34:06: 5000000 INFO @ Tue, 09 Oct 2018 22:34:08: 5000000 INFO @ Tue, 09 Oct 2018 22:34:16: 6000000 INFO @ Tue, 09 Oct 2018 22:34:16: 6000000 INFO @ Tue, 09 Oct 2018 22:34:18: 6000000 INFO @ Tue, 09 Oct 2018 22:34:27: 7000000 INFO @ Tue, 09 Oct 2018 22:34:27: 7000000 INFO @ Tue, 09 Oct 2018 22:34:28: 7000000 INFO @ Tue, 09 Oct 2018 22:34:37: 8000000 INFO @ Tue, 09 Oct 2018 22:34:37: 8000000 INFO @ Tue, 09 Oct 2018 22:34:39: 8000000 INFO @ Tue, 09 Oct 2018 22:34:48: 9000000 INFO @ Tue, 09 Oct 2018 22:34:48: 9000000 INFO @ Tue, 09 Oct 2018 22:34:49: 9000000 INFO @ Tue, 09 Oct 2018 22:34:58: 10000000 INFO @ Tue, 09 Oct 2018 22:34:58: 10000000 INFO @ Tue, 09 Oct 2018 22:35:00: 10000000 INFO @ Tue, 09 Oct 2018 22:35:09: 11000000 INFO @ Tue, 09 Oct 2018 22:35:09: 11000000 INFO @ Tue, 09 Oct 2018 22:35:11: 11000000 INFO @ Tue, 09 Oct 2018 22:35:20: 12000000 INFO @ Tue, 09 Oct 2018 22:35:20: 12000000 INFO @ Tue, 09 Oct 2018 22:35:21: 12000000 INFO @ Tue, 09 Oct 2018 22:35:30: 13000000 INFO @ Tue, 09 Oct 2018 22:35:31: 13000000 INFO @ Tue, 09 Oct 2018 22:35:32: 13000000 INFO @ Tue, 09 Oct 2018 22:35:41: 14000000 INFO @ Tue, 09 Oct 2018 22:35:41: 14000000 INFO @ Tue, 09 Oct 2018 22:35:42: 14000000 INFO @ Tue, 09 Oct 2018 22:35:51: 15000000 INFO @ Tue, 09 Oct 2018 22:35:51: 15000000 INFO @ Tue, 09 Oct 2018 22:35:52: 15000000 INFO @ Tue, 09 Oct 2018 22:36:00: 16000000 INFO @ Tue, 09 Oct 2018 22:36:00: 16000000 INFO @ Tue, 09 Oct 2018 22:36:01: 16000000 INFO @ Tue, 09 Oct 2018 22:36:02: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:36:02: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:36:02: #1 total tags in treatment: 8023481 INFO @ Tue, 09 Oct 2018 22:36:02: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:36:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:36:02: #1 tags after filtering in treatment: 5059622 INFO @ Tue, 09 Oct 2018 22:36:02: #1 Redundant rate of treatment: 0.37 INFO @ Tue, 09 Oct 2018 22:36:02: #1 finished! INFO @ Tue, 09 Oct 2018 22:36:02: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:36:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:36:02: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:36:02: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:36:02: #1 total tags in treatment: 8023481 INFO @ Tue, 09 Oct 2018 22:36:02: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:36:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:36:02: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:36:02: 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 @ Tue, 09 Oct 2018 22:36:02: Process for pairing-model is terminated! cat: SRX3765654.10_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 `SRX3765654.10_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 `SRX3765654.10_*.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 `SRX3765654.10_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 @ Tue, 09 Oct 2018 22:36:02: #1 tags after filtering in treatment: 5059622 INFO @ Tue, 09 Oct 2018 22:36:02: #1 Redundant rate of treatment: 0.37 INFO @ Tue, 09 Oct 2018 22:36:02: #1 finished! INFO @ Tue, 09 Oct 2018 22:36:02: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:36:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:36:03: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:36:03: 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 @ Tue, 09 Oct 2018 22:36:03: Process for pairing-model is terminated! cat: SRX3765654.05_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 `SRX3765654.05_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 `SRX3765654.05_*.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 `SRX3765654.05_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 @ Tue, 09 Oct 2018 22:36:04: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:36:04: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:36:04: #1 total tags in treatment: 8023481 INFO @ Tue, 09 Oct 2018 22:36:04: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:36:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:36:04: #1 tags after filtering in treatment: 5059622 INFO @ Tue, 09 Oct 2018 22:36:04: #1 Redundant rate of treatment: 0.37 INFO @ Tue, 09 Oct 2018 22:36:04: #1 finished! INFO @ Tue, 09 Oct 2018 22:36:04: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:36:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:36:04: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 22:36:04: 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 @ Tue, 09 Oct 2018 22:36:04: Process for pairing-model is terminated! cat: SRX3765654.20_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 `SRX3765654.20_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 `SRX3765654.20_*.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 `SRX3765654.20_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。