Job ID = 11244892 sra ファイルのダウンロード中... Completed: 627174K bytes transferred in 11 seconds (459810K bits/sec), in 1 file. Completed: 666150K bytes transferred in 10 seconds (535664K 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 14324255 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4065338/SRR7145395.sra Written 14324255 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4065338/SRR7145395.sra Read 15247617 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4065338/SRR7145396.sra Written 15247617 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4065338/SRR7145396.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: 00:14:16 29571872 reads; of these: 29571872 (100.00%) were paired; of these: 18257459 (61.74%) aligned concordantly 0 times 9997727 (33.81%) aligned concordantly exactly 1 time 1316686 (4.45%) aligned concordantly >1 times ---- 18257459 pairs aligned concordantly 0 times; of these: 293605 (1.61%) aligned discordantly 1 time ---- 17963854 pairs aligned 0 times concordantly or discordantly; of these: 35927708 mates make up the pairs; of these: 35489448 (98.78%) aligned 0 times 298992 (0.83%) aligned exactly 1 time 139268 (0.39%) aligned >1 times 39.99% overall alignment rate Time searching: 00:14:16 Overall time: 00:14:16 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] 387476 / 11557727 = 0.0335 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 22:59:52: # Command line: callpeak -t SRX4065338.bam -f BAM -g 12100000 -n SRX4065338.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4065338.05 # format = BAM # ChIP-seq file = ['SRX4065338.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 22:59:52: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:59:52: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:59:52: # Command line: callpeak -t SRX4065338.bam -f BAM -g 12100000 -n SRX4065338.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4065338.10 # format = BAM # ChIP-seq file = ['SRX4065338.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 22:59:52: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:59:52: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:59:52: # Command line: callpeak -t SRX4065338.bam -f BAM -g 12100000 -n SRX4065338.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4065338.20 # format = BAM # ChIP-seq file = ['SRX4065338.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 22:59:52: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:59:52: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:59:58: 1000000 INFO @ Tue, 09 Oct 2018 22:59:59: 1000000 INFO @ Tue, 09 Oct 2018 22:59:59: 1000000 INFO @ Tue, 09 Oct 2018 23:00:05: 2000000 INFO @ Tue, 09 Oct 2018 23:00:06: 2000000 INFO @ Tue, 09 Oct 2018 23:00:06: 2000000 INFO @ Tue, 09 Oct 2018 23:00:11: 3000000 INFO @ Tue, 09 Oct 2018 23:00:14: 3000000 INFO @ Tue, 09 Oct 2018 23:00:14: 3000000 INFO @ Tue, 09 Oct 2018 23:00:18: 4000000 INFO @ Tue, 09 Oct 2018 23:00:22: 4000000 INFO @ Tue, 09 Oct 2018 23:00:22: 4000000 INFO @ Tue, 09 Oct 2018 23:00:25: 5000000 INFO @ Tue, 09 Oct 2018 23:00:29: 5000000 INFO @ Tue, 09 Oct 2018 23:00:29: 5000000 INFO @ Tue, 09 Oct 2018 23:00:31: 6000000 INFO @ Tue, 09 Oct 2018 23:00:36: 6000000 INFO @ Tue, 09 Oct 2018 23:00:36: 6000000 INFO @ Tue, 09 Oct 2018 23:00:38: 7000000 INFO @ Tue, 09 Oct 2018 23:00:44: 7000000 INFO @ Tue, 09 Oct 2018 23:00:44: 7000000 INFO @ Tue, 09 Oct 2018 23:00:45: 8000000 INFO @ Tue, 09 Oct 2018 23:00:51: 8000000 INFO @ Tue, 09 Oct 2018 23:00:51: 8000000 INFO @ Tue, 09 Oct 2018 23:00:52: 9000000 INFO @ Tue, 09 Oct 2018 23:00:58: 9000000 INFO @ Tue, 09 Oct 2018 23:00:58: 9000000 INFO @ Tue, 09 Oct 2018 23:00:58: 10000000 INFO @ Tue, 09 Oct 2018 23:01:05: 10000000 INFO @ Tue, 09 Oct 2018 23:01:05: 10000000 INFO @ Tue, 09 Oct 2018 23:01:05: 11000000 INFO @ Tue, 09 Oct 2018 23:01:12: 12000000 INFO @ Tue, 09 Oct 2018 23:01:12: 11000000 INFO @ Tue, 09 Oct 2018 23:01:12: 11000000 INFO @ Tue, 09 Oct 2018 23:01:19: 13000000 INFO @ Tue, 09 Oct 2018 23:01:19: 12000000 INFO @ Tue, 09 Oct 2018 23:01:19: 12000000 INFO @ Tue, 09 Oct 2018 23:01:26: 14000000 INFO @ Tue, 09 Oct 2018 23:01:26: 13000000 INFO @ Tue, 09 Oct 2018 23:01:26: 13000000 INFO @ Tue, 09 Oct 2018 23:01:33: 15000000 INFO @ Tue, 09 Oct 2018 23:01:33: 14000000 INFO @ Tue, 09 Oct 2018 23:01:33: 14000000 INFO @ Tue, 09 Oct 2018 23:01:40: 16000000 INFO @ Tue, 09 Oct 2018 23:01:40: 15000000 INFO @ Tue, 09 Oct 2018 23:01:40: 15000000 INFO @ Tue, 09 Oct 2018 23:01:47: 17000000 INFO @ Tue, 09 Oct 2018 23:01:47: 16000000 INFO @ Tue, 09 Oct 2018 23:01:47: 16000000 INFO @ Tue, 09 Oct 2018 23:01:53: 18000000 INFO @ Tue, 09 Oct 2018 23:01:55: 17000000 INFO @ Tue, 09 Oct 2018 23:01:55: 17000000 INFO @ Tue, 09 Oct 2018 23:02:00: 19000000 INFO @ Tue, 09 Oct 2018 23:02:02: 18000000 INFO @ Tue, 09 Oct 2018 23:02:02: 18000000 INFO @ Tue, 09 Oct 2018 23:02:06: 20000000 INFO @ Tue, 09 Oct 2018 23:02:09: 19000000 INFO @ Tue, 09 Oct 2018 23:02:09: 19000000 INFO @ Tue, 09 Oct 2018 23:02:13: 21000000 INFO @ Tue, 09 Oct 2018 23:02:16: 20000000 INFO @ Tue, 09 Oct 2018 23:02:16: 20000000 INFO @ Tue, 09 Oct 2018 23:02:19: 22000000 INFO @ Tue, 09 Oct 2018 23:02:24: 21000000 INFO @ Tue, 09 Oct 2018 23:02:24: 21000000 INFO @ Tue, 09 Oct 2018 23:02:25: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:02:25: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:02:25: #1 total tags in treatment: 10932412 INFO @ Tue, 09 Oct 2018 23:02:25: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:02:25: #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 23:02:25: #1 tags after filtering in treatment: 8202581 INFO @ Tue, 09 Oct 2018 23:02:25: #1 Redundant rate of treatment: 0.25 INFO @ Tue, 09 Oct 2018 23:02:25: #1 finished! INFO @ Tue, 09 Oct 2018 23:02:25: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:02:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:02:26: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:02:26: 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 23:02:26: Process for pairing-model is terminated! cat: SRX4065338.20_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 `SRX4065338.20_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 `SRX4065338.20_*.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 `SRX4065338.20_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 @ Tue, 09 Oct 2018 23:02:31: 22000000 INFO @ Tue, 09 Oct 2018 23:02:31: 22000000 INFO @ Tue, 09 Oct 2018 23:02:37: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:02:37: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:02:37: #1 total tags in treatment: 10932412 INFO @ Tue, 09 Oct 2018 23:02:37: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:02:37: #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 23:02:37: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:02:37: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:02:37: #1 total tags in treatment: 10932412 INFO @ Tue, 09 Oct 2018 23:02:37: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:02:37: #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 23:02:37: #1 tags after filtering in treatment: 8202581 INFO @ Tue, 09 Oct 2018 23:02:37: #1 Redundant rate of treatment: 0.25 INFO @ Tue, 09 Oct 2018 23:02:37: #1 finished! INFO @ Tue, 09 Oct 2018 23:02:37: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:02:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:02:37: #1 tags after filtering in treatment: 8202581 INFO @ Tue, 09 Oct 2018 23:02:37: #1 Redundant rate of treatment: 0.25 INFO @ Tue, 09 Oct 2018 23:02:37: #1 finished! INFO @ Tue, 09 Oct 2018 23:02:37: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:02:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:02:38: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:02:38: 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 23:02:38: Process for pairing-model is terminated! INFO @ Tue, 09 Oct 2018 23:02:38: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:02:38: 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 23:02:38: Process for pairing-model is terminated! cat: SRX4065338.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX4065338.10_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4065338.05_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 `SRX4065338.05_*.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 `SRX4065338.05_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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4065338.10_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 `SRX4065338.10_*.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 `SRX4065338.10_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。