Job ID = 10937530 sra ファイルのダウンロード中... Completed: 497678K bytes transferred in 62 seconds (65334K 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 5128379 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010328/SRR5833327.sra Written 5128379 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010328/SRR5833327.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: 00:06:19 5128379 reads; of these: 5128379 (100.00%) were paired; of these: 302573 (5.90%) aligned concordantly 0 times 4238394 (82.65%) aligned concordantly exactly 1 time 587412 (11.45%) aligned concordantly >1 times ---- 302573 pairs aligned concordantly 0 times; of these: 26553 (8.78%) aligned discordantly 1 time ---- 276020 pairs aligned 0 times concordantly or discordantly; of these: 552040 mates make up the pairs; of these: 500077 (90.59%) aligned 0 times 34550 (6.26%) aligned exactly 1 time 17413 (3.15%) aligned >1 times 95.12% overall alignment rate Time searching: 00:06:19 Overall time: 00:06:19 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_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] 62838 / 4843283 = 0.0130 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 @ Fri, 10 Aug 2018 02:43:23: # Command line: callpeak -t SRX3010328.bam -f BAM -g 12100000 -n SRX3010328.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3010328.05 # format = BAM # ChIP-seq file = ['SRX3010328.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 @ Fri, 10 Aug 2018 02:43:23: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:43:23: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:43:23: # Command line: callpeak -t SRX3010328.bam -f BAM -g 12100000 -n SRX3010328.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3010328.20 # format = BAM # ChIP-seq file = ['SRX3010328.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 @ Fri, 10 Aug 2018 02:43:23: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:43:23: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:43:23: # Command line: callpeak -t SRX3010328.bam -f BAM -g 12100000 -n SRX3010328.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3010328.10 # format = BAM # ChIP-seq file = ['SRX3010328.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 @ Fri, 10 Aug 2018 02:43:23: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:43:23: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:43:30: 1000000 INFO @ Fri, 10 Aug 2018 02:43:30: 1000000 INFO @ Fri, 10 Aug 2018 02:43:30: 1000000 INFO @ Fri, 10 Aug 2018 02:43:37: 2000000 INFO @ Fri, 10 Aug 2018 02:43:37: 2000000 INFO @ Fri, 10 Aug 2018 02:43:38: 2000000 INFO @ Fri, 10 Aug 2018 02:43:44: 3000000 INFO @ Fri, 10 Aug 2018 02:43:44: 3000000 INFO @ Fri, 10 Aug 2018 02:43:46: 3000000 INFO @ Fri, 10 Aug 2018 02:43:52: 4000000 INFO @ Fri, 10 Aug 2018 02:43:52: 4000000 INFO @ Fri, 10 Aug 2018 02:43:54: 4000000 INFO @ Fri, 10 Aug 2018 02:44:00: 5000000 INFO @ Fri, 10 Aug 2018 02:44:00: 5000000 INFO @ Fri, 10 Aug 2018 02:44:03: 5000000 INFO @ Fri, 10 Aug 2018 02:44:07: 6000000 INFO @ Fri, 10 Aug 2018 02:44:07: 6000000 INFO @ Fri, 10 Aug 2018 02:44:11: 6000000 INFO @ Fri, 10 Aug 2018 02:44:14: 7000000 INFO @ Fri, 10 Aug 2018 02:44:14: 7000000 INFO @ Fri, 10 Aug 2018 02:44:19: 7000000 INFO @ Fri, 10 Aug 2018 02:44:21: 8000000 INFO @ Fri, 10 Aug 2018 02:44:21: 8000000 INFO @ Fri, 10 Aug 2018 02:44:27: 8000000 INFO @ Fri, 10 Aug 2018 02:44:29: 9000000 INFO @ Fri, 10 Aug 2018 02:44:30: 9000000 INFO @ Fri, 10 Aug 2018 02:44:34: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:44:34: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:44:34: #1 total tags in treatment: 4763037 INFO @ Fri, 10 Aug 2018 02:44:34: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:44:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:44:34: #1 tags after filtering in treatment: 3960331 INFO @ Fri, 10 Aug 2018 02:44:34: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 10 Aug 2018 02:44:34: #1 finished! INFO @ Fri, 10 Aug 2018 02:44:34: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:44:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:44:34: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:44:34: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:44:34: #1 total tags in treatment: 4763037 INFO @ Fri, 10 Aug 2018 02:44:34: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:44:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:44:34: #2 number of paired peaks: 38 WARNING @ Fri, 10 Aug 2018 02:44:34: Too few paired peaks (38) 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 @ Fri, 10 Aug 2018 02:44:34: Process for pairing-model is terminated! cat: SRX3010328.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Fri, 10 Aug 2018 02:44:34: #1 tags after filtering in treatment: 3960331 INFO @ Fri, 10 Aug 2018 02:44:34: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 10 Aug 2018 02:44:34: #1 finished! INFO @ Fri, 10 Aug 2018 02:44:34: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:44:34: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3010328.20_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 `SRX3010328.20_*.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 `SRX3010328.20_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 @ Fri, 10 Aug 2018 02:44:35: #2 number of paired peaks: 38 WARNING @ Fri, 10 Aug 2018 02:44:35: Too few paired peaks (38) 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 @ Fri, 10 Aug 2018 02:44:35: Process for pairing-model is terminated! cat: SRX3010328.05_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 `SRX3010328.05_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 `SRX3010328.05_*.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 `SRX3010328.05_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 @ Fri, 10 Aug 2018 02:44:35: 9000000 INFO @ Fri, 10 Aug 2018 02:44:39: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:44:39: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:44:39: #1 total tags in treatment: 4763037 INFO @ Fri, 10 Aug 2018 02:44:39: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:44:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:44:40: #1 tags after filtering in treatment: 3960331 INFO @ Fri, 10 Aug 2018 02:44:40: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 10 Aug 2018 02:44:40: #1 finished! INFO @ Fri, 10 Aug 2018 02:44:40: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:44:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:44:40: #2 number of paired peaks: 38 WARNING @ Fri, 10 Aug 2018 02:44:40: Too few paired peaks (38) 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 @ Fri, 10 Aug 2018 02:44:40: Process for pairing-model is terminated! cat: SRX3010328.10_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 `SRX3010328.10_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 `SRX3010328.10_*.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 `SRX3010328.10_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。