Job ID = 11296965 sra ファイルのダウンロード中... Completed: 149167K bytes transferred in 5 seconds (238416K 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 5246115 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4212600/SRR7310232.sra Written 5246115 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4212600/SRR7310232.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: 00:03:41 5246115 reads; of these: 5246115 (100.00%) were paired; of these: 133719 (2.55%) aligned concordantly 0 times 4441340 (84.66%) aligned concordantly exactly 1 time 671056 (12.79%) aligned concordantly >1 times ---- 133719 pairs aligned concordantly 0 times; of these: 12925 (9.67%) aligned discordantly 1 time ---- 120794 pairs aligned 0 times concordantly or discordantly; of these: 241588 mates make up the pairs; of these: 213480 (88.37%) aligned 0 times 19490 (8.07%) aligned exactly 1 time 8618 (3.57%) aligned >1 times 97.97% overall alignment rate Time searching: 00:03:41 Overall time: 00:03:41 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] 160127 / 5122789 = 0.0313 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, 05 Nov 2018 18:08:19: # Command line: callpeak -t SRX4212600.bam -f BAM -g 12100000 -n SRX4212600.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4212600.10 # format = BAM # ChIP-seq file = ['SRX4212600.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, 05 Nov 2018 18:08:19: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:08:19: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:08:19: # Command line: callpeak -t SRX4212600.bam -f BAM -g 12100000 -n SRX4212600.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4212600.05 # format = BAM # ChIP-seq file = ['SRX4212600.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, 05 Nov 2018 18:08:19: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:08:19: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:08:19: # Command line: callpeak -t SRX4212600.bam -f BAM -g 12100000 -n SRX4212600.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4212600.20 # format = BAM # ChIP-seq file = ['SRX4212600.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, 05 Nov 2018 18:08:19: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:08:19: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:08:25: 1000000 INFO @ Mon, 05 Nov 2018 18:08:26: 1000000 INFO @ Mon, 05 Nov 2018 18:08:26: 1000000 INFO @ Mon, 05 Nov 2018 18:08:32: 2000000 INFO @ Mon, 05 Nov 2018 18:08:32: 2000000 INFO @ Mon, 05 Nov 2018 18:08:33: 2000000 INFO @ Mon, 05 Nov 2018 18:08:39: 3000000 INFO @ Mon, 05 Nov 2018 18:08:39: 3000000 INFO @ Mon, 05 Nov 2018 18:08:40: 3000000 INFO @ Mon, 05 Nov 2018 18:08:45: 4000000 INFO @ Mon, 05 Nov 2018 18:08:46: 4000000 INFO @ Mon, 05 Nov 2018 18:08:47: 4000000 INFO @ Mon, 05 Nov 2018 18:08:52: 5000000 INFO @ Mon, 05 Nov 2018 18:08:53: 5000000 INFO @ Mon, 05 Nov 2018 18:08:53: 5000000 INFO @ Mon, 05 Nov 2018 18:08:59: 6000000 INFO @ Mon, 05 Nov 2018 18:09:00: 6000000 INFO @ Mon, 05 Nov 2018 18:09:00: 6000000 INFO @ Mon, 05 Nov 2018 18:09:05: 7000000 INFO @ Mon, 05 Nov 2018 18:09:07: 7000000 INFO @ Mon, 05 Nov 2018 18:09:07: 7000000 INFO @ Mon, 05 Nov 2018 18:09:12: 8000000 INFO @ Mon, 05 Nov 2018 18:09:14: 8000000 INFO @ Mon, 05 Nov 2018 18:09:14: 8000000 INFO @ Mon, 05 Nov 2018 18:09:19: 9000000 INFO @ Mon, 05 Nov 2018 18:09:21: 9000000 INFO @ Mon, 05 Nov 2018 18:09:21: 9000000 INFO @ Mon, 05 Nov 2018 18:09:25: #1 tag size is determined as 38 bps INFO @ Mon, 05 Nov 2018 18:09:25: #1 tag size = 38 INFO @ Mon, 05 Nov 2018 18:09:25: #1 total tags in treatment: 4952433 INFO @ Mon, 05 Nov 2018 18:09:25: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:09:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 18:09:25: #1 tags after filtering in treatment: 4082193 INFO @ Mon, 05 Nov 2018 18:09:25: #1 Redundant rate of treatment: 0.18 INFO @ Mon, 05 Nov 2018 18:09:25: #1 finished! INFO @ Mon, 05 Nov 2018 18:09:25: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:09:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:09:26: #2 number of paired peaks: 28 WARNING @ Mon, 05 Nov 2018 18:09:26: Too few paired peaks (28) 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, 05 Nov 2018 18:09:26: Process for pairing-model is terminated! cat: SRX4212600.05_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 `SRX4212600.05_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 `SRX4212600.05_*.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 `SRX4212600.05_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 @ Mon, 05 Nov 2018 18:09:27: #1 tag size is determined as 38 bps INFO @ Mon, 05 Nov 2018 18:09:27: #1 tag size = 38 INFO @ Mon, 05 Nov 2018 18:09:27: #1 total tags in treatment: 4952433 INFO @ Mon, 05 Nov 2018 18:09:27: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:09:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 18:09:27: #1 tags after filtering in treatment: 4082193 INFO @ Mon, 05 Nov 2018 18:09:27: #1 Redundant rate of treatment: 0.18 INFO @ Mon, 05 Nov 2018 18:09:27: #1 finished! INFO @ Mon, 05 Nov 2018 18:09:27: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:09:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:09:27: #2 number of paired peaks: 28 WARNING @ Mon, 05 Nov 2018 18:09:27: Too few paired peaks (28) 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, 05 Nov 2018 18:09:27: Process for pairing-model is terminated! cat: SRX4212600.10_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 `SRX4212600.10_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 `SRX4212600.10_*.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 `SRX4212600.10_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, 05 Nov 2018 18:09:28: #1 tag size is determined as 38 bps INFO @ Mon, 05 Nov 2018 18:09:28: #1 tag size = 38 INFO @ Mon, 05 Nov 2018 18:09:28: #1 total tags in treatment: 4952433 INFO @ Mon, 05 Nov 2018 18:09:28: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:09:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 18:09:28: #1 tags after filtering in treatment: 4082193 INFO @ Mon, 05 Nov 2018 18:09:28: #1 Redundant rate of treatment: 0.18 INFO @ Mon, 05 Nov 2018 18:09:28: #1 finished! INFO @ Mon, 05 Nov 2018 18:09:28: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:09:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:09:28: #2 number of paired peaks: 28 WARNING @ Mon, 05 Nov 2018 18:09:28: Too few paired peaks (28) 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, 05 Nov 2018 18:09:28: Process for pairing-model is terminated! cat: SRX4212600.20_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 `SRX4212600.20_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 `SRX4212600.20_*.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 `SRX4212600.20_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。