Job ID = 11158469 sra ファイルのダウンロード中... Completed: 1815016K bytes transferred in 17 seconds (835850K 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 28701701 spots for /home/okishinya/chipatlas/results/ce10/SRX4029335/SRR7100995.sra Written 28701701 spots for /home/okishinya/chipatlas/results/ce10/SRX4029335/SRR7100995.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: 00:50:00 28701701 reads; of these: 28701701 (100.00%) were paired; of these: 3554257 (12.38%) aligned concordantly 0 times 22122263 (77.08%) aligned concordantly exactly 1 time 3025181 (10.54%) aligned concordantly >1 times ---- 3554257 pairs aligned concordantly 0 times; of these: 1696976 (47.74%) aligned discordantly 1 time ---- 1857281 pairs aligned 0 times concordantly or discordantly; of these: 3714562 mates make up the pairs; of these: 2387147 (64.26%) aligned 0 times 790734 (21.29%) aligned exactly 1 time 536681 (14.45%) aligned >1 times 95.84% overall alignment rate Time searching: 00:50:00 Overall time: 00:50:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 24 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 chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 6598733 / 26817075 = 0.2461 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, 04 Sep 2018 10:47:29: # Command line: callpeak -t SRX4029335.bam -f BAM -g ce -n SRX4029335.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4029335.10 # format = BAM # ChIP-seq file = ['SRX4029335.bam'] # control file = None # effective genome size = 9.00e+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, 04 Sep 2018 10:47:29: #1 read tag files... INFO @ Tue, 04 Sep 2018 10:47:29: # Command line: callpeak -t SRX4029335.bam -f BAM -g ce -n SRX4029335.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4029335.05 # format = BAM # ChIP-seq file = ['SRX4029335.bam'] # control file = None # effective genome size = 9.00e+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, 04 Sep 2018 10:47:29: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 10:47:29: #1 read tag files... INFO @ Tue, 04 Sep 2018 10:47:29: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 10:47:29: # Command line: callpeak -t SRX4029335.bam -f BAM -g ce -n SRX4029335.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4029335.20 # format = BAM # ChIP-seq file = ['SRX4029335.bam'] # control file = None # effective genome size = 9.00e+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, 04 Sep 2018 10:47:29: #1 read tag files... INFO @ Tue, 04 Sep 2018 10:47:29: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 10:47:38: 1000000 INFO @ Tue, 04 Sep 2018 10:47:38: 1000000 INFO @ Tue, 04 Sep 2018 10:47:38: 1000000 INFO @ Tue, 04 Sep 2018 10:47:48: 2000000 INFO @ Tue, 04 Sep 2018 10:47:48: 2000000 INFO @ Tue, 04 Sep 2018 10:47:48: 2000000 INFO @ Tue, 04 Sep 2018 10:47:57: 3000000 INFO @ Tue, 04 Sep 2018 10:47:57: 3000000 INFO @ Tue, 04 Sep 2018 10:47:57: 3000000 INFO @ Tue, 04 Sep 2018 10:48:06: 4000000 INFO @ Tue, 04 Sep 2018 10:48:06: 4000000 INFO @ Tue, 04 Sep 2018 10:48:06: 4000000 INFO @ Tue, 04 Sep 2018 10:48:15: 5000000 INFO @ Tue, 04 Sep 2018 10:48:15: 5000000 INFO @ Tue, 04 Sep 2018 10:48:15: 5000000 INFO @ Tue, 04 Sep 2018 10:48:24: 6000000 INFO @ Tue, 04 Sep 2018 10:48:24: 6000000 INFO @ Tue, 04 Sep 2018 10:48:24: 6000000 INFO @ Tue, 04 Sep 2018 10:48:32: 7000000 INFO @ Tue, 04 Sep 2018 10:48:32: 7000000 INFO @ Tue, 04 Sep 2018 10:48:32: 7000000 INFO @ Tue, 04 Sep 2018 10:48:42: 8000000 INFO @ Tue, 04 Sep 2018 10:48:42: 8000000 INFO @ Tue, 04 Sep 2018 10:48:42: 8000000 INFO @ Tue, 04 Sep 2018 10:48:51: 9000000 INFO @ Tue, 04 Sep 2018 10:48:51: 9000000 INFO @ Tue, 04 Sep 2018 10:48:51: 9000000 INFO @ Tue, 04 Sep 2018 10:49:00: 10000000 INFO @ Tue, 04 Sep 2018 10:49:00: 10000000 INFO @ Tue, 04 Sep 2018 10:49:00: 10000000 INFO @ Tue, 04 Sep 2018 10:49:09: 11000000 INFO @ Tue, 04 Sep 2018 10:49:09: 11000000 INFO @ Tue, 04 Sep 2018 10:49:09: 11000000 INFO @ Tue, 04 Sep 2018 10:49:18: 12000000 INFO @ Tue, 04 Sep 2018 10:49:18: 12000000 INFO @ Tue, 04 Sep 2018 10:49:18: 12000000 INFO @ Tue, 04 Sep 2018 10:49:26: 13000000 INFO @ Tue, 04 Sep 2018 10:49:26: 13000000 INFO @ Tue, 04 Sep 2018 10:49:26: 13000000 INFO @ Tue, 04 Sep 2018 10:49:35: 14000000 INFO @ Tue, 04 Sep 2018 10:49:35: 14000000 INFO @ Tue, 04 Sep 2018 10:49:35: 14000000 INFO @ Tue, 04 Sep 2018 10:49:44: 15000000 INFO @ Tue, 04 Sep 2018 10:49:44: 15000000 INFO @ Tue, 04 Sep 2018 10:49:44: 15000000 INFO @ Tue, 04 Sep 2018 10:49:54: 16000000 INFO @ Tue, 04 Sep 2018 10:49:54: 16000000 INFO @ Tue, 04 Sep 2018 10:49:54: 16000000 INFO @ Tue, 04 Sep 2018 10:50:03: 17000000 INFO @ Tue, 04 Sep 2018 10:50:03: 17000000 INFO @ Tue, 04 Sep 2018 10:50:03: 17000000 INFO @ Tue, 04 Sep 2018 10:50:12: 18000000 INFO @ Tue, 04 Sep 2018 10:50:12: 18000000 INFO @ Tue, 04 Sep 2018 10:50:12: 18000000 INFO @ Tue, 04 Sep 2018 10:50:21: 19000000 INFO @ Tue, 04 Sep 2018 10:50:21: 19000000 INFO @ Tue, 04 Sep 2018 10:50:21: 19000000 INFO @ Tue, 04 Sep 2018 10:50:30: 20000000 INFO @ Tue, 04 Sep 2018 10:50:30: 20000000 INFO @ Tue, 04 Sep 2018 10:50:30: 20000000 INFO @ Tue, 04 Sep 2018 10:50:39: 21000000 INFO @ Tue, 04 Sep 2018 10:50:39: 21000000 INFO @ Tue, 04 Sep 2018 10:50:39: 21000000 INFO @ Tue, 04 Sep 2018 10:50:47: 22000000 INFO @ Tue, 04 Sep 2018 10:50:47: 22000000 INFO @ Tue, 04 Sep 2018 10:50:47: 22000000 INFO @ Tue, 04 Sep 2018 10:50:56: 23000000 INFO @ Tue, 04 Sep 2018 10:50:56: 23000000 INFO @ Tue, 04 Sep 2018 10:50:56: 23000000 INFO @ Tue, 04 Sep 2018 10:51:04: 24000000 INFO @ Tue, 04 Sep 2018 10:51:04: 24000000 INFO @ Tue, 04 Sep 2018 10:51:04: 24000000 INFO @ Tue, 04 Sep 2018 10:51:12: 25000000 INFO @ Tue, 04 Sep 2018 10:51:12: 25000000 INFO @ Tue, 04 Sep 2018 10:51:12: 25000000 INFO @ Tue, 04 Sep 2018 10:51:20: 26000000 INFO @ Tue, 04 Sep 2018 10:51:20: 26000000 INFO @ Tue, 04 Sep 2018 10:51:20: 26000000 INFO @ Tue, 04 Sep 2018 10:51:28: 27000000 INFO @ Tue, 04 Sep 2018 10:51:28: 27000000 INFO @ Tue, 04 Sep 2018 10:51:28: 27000000 INFO @ Tue, 04 Sep 2018 10:51:37: 28000000 INFO @ Tue, 04 Sep 2018 10:51:37: 28000000 INFO @ Tue, 04 Sep 2018 10:51:37: 28000000 INFO @ Tue, 04 Sep 2018 10:51:46: 29000000 INFO @ Tue, 04 Sep 2018 10:51:46: 29000000 INFO @ Tue, 04 Sep 2018 10:51:46: 29000000 INFO @ Tue, 04 Sep 2018 10:51:55: 30000000 INFO @ Tue, 04 Sep 2018 10:51:55: 30000000 INFO @ Tue, 04 Sep 2018 10:51:55: 30000000 INFO @ Tue, 04 Sep 2018 10:52:04: 31000000 INFO @ Tue, 04 Sep 2018 10:52:04: 31000000 INFO @ Tue, 04 Sep 2018 10:52:04: 31000000 INFO @ Tue, 04 Sep 2018 10:52:14: 32000000 INFO @ Tue, 04 Sep 2018 10:52:14: 32000000 INFO @ Tue, 04 Sep 2018 10:52:14: 32000000 INFO @ Tue, 04 Sep 2018 10:52:23: 33000000 INFO @ Tue, 04 Sep 2018 10:52:23: 33000000 INFO @ Tue, 04 Sep 2018 10:52:23: 33000000 INFO @ Tue, 04 Sep 2018 10:52:31: 34000000 INFO @ Tue, 04 Sep 2018 10:52:31: 34000000 INFO @ Tue, 04 Sep 2018 10:52:31: 34000000 INFO @ Tue, 04 Sep 2018 10:52:40: 35000000 INFO @ Tue, 04 Sep 2018 10:52:40: 35000000 INFO @ Tue, 04 Sep 2018 10:52:40: 35000000 INFO @ Tue, 04 Sep 2018 10:52:48: 36000000 INFO @ Tue, 04 Sep 2018 10:52:48: 36000000 INFO @ Tue, 04 Sep 2018 10:52:48: 36000000 INFO @ Tue, 04 Sep 2018 10:52:56: 37000000 INFO @ Tue, 04 Sep 2018 10:52:56: 37000000 INFO @ Tue, 04 Sep 2018 10:52:56: 37000000 INFO @ Tue, 04 Sep 2018 10:53:05: 38000000 INFO @ Tue, 04 Sep 2018 10:53:05: 38000000 INFO @ Tue, 04 Sep 2018 10:53:05: 38000000 INFO @ Tue, 04 Sep 2018 10:53:13: 39000000 INFO @ Tue, 04 Sep 2018 10:53:13: 39000000 INFO @ Tue, 04 Sep 2018 10:53:13: 39000000 INFO @ Tue, 04 Sep 2018 10:53:21: 40000000 INFO @ Tue, 04 Sep 2018 10:53:21: 40000000 INFO @ Tue, 04 Sep 2018 10:53:21: 40000000 INFO @ Tue, 04 Sep 2018 10:53:29: 41000000 INFO @ Tue, 04 Sep 2018 10:53:29: 41000000 INFO @ Tue, 04 Sep 2018 10:53:29: 41000000 INFO @ Tue, 04 Sep 2018 10:53:35: #1 tag size is determined as 76 bps INFO @ Tue, 04 Sep 2018 10:53:35: #1 tag size = 76 INFO @ Tue, 04 Sep 2018 10:53:35: #1 total tags in treatment: 18763445 INFO @ Tue, 04 Sep 2018 10:53:35: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 10:53:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 10:53:35: #1 tag size is determined as 76 bps INFO @ Tue, 04 Sep 2018 10:53:35: #1 tag size = 76 INFO @ Tue, 04 Sep 2018 10:53:35: #1 total tags in treatment: 18763445 INFO @ Tue, 04 Sep 2018 10:53:35: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 10:53:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 10:53:36: #1 tag size is determined as 76 bps INFO @ Tue, 04 Sep 2018 10:53:36: #1 tag size = 76 INFO @ Tue, 04 Sep 2018 10:53:36: #1 total tags in treatment: 18763445 INFO @ Tue, 04 Sep 2018 10:53:36: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 10:53:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 10:53:36: #1 tags after filtering in treatment: 15884961 INFO @ Tue, 04 Sep 2018 10:53:36: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 04 Sep 2018 10:53:36: #1 finished! INFO @ Tue, 04 Sep 2018 10:53:36: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 10:53:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 10:53:36: #1 tags after filtering in treatment: 15884961 INFO @ Tue, 04 Sep 2018 10:53:36: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 04 Sep 2018 10:53:36: #1 finished! INFO @ Tue, 04 Sep 2018 10:53:36: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 10:53:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 10:53:36: #1 tags after filtering in treatment: 15884961 INFO @ Tue, 04 Sep 2018 10:53:36: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 04 Sep 2018 10:53:36: #1 finished! INFO @ Tue, 04 Sep 2018 10:53:36: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 10:53:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 10:53:37: #2 number of paired peaks: 633 WARNING @ Tue, 04 Sep 2018 10:53:37: Fewer paired peaks (633) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 633 pairs to build model! INFO @ Tue, 04 Sep 2018 10:53:37: start model_add_line... INFO @ Tue, 04 Sep 2018 10:53:37: #2 number of paired peaks: 633 WARNING @ Tue, 04 Sep 2018 10:53:37: Fewer paired peaks (633) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 633 pairs to build model! INFO @ Tue, 04 Sep 2018 10:53:37: start model_add_line... INFO @ Tue, 04 Sep 2018 10:53:37: start X-correlation... INFO @ Tue, 04 Sep 2018 10:53:37: #2 number of paired peaks: 633 WARNING @ Tue, 04 Sep 2018 10:53:37: Fewer paired peaks (633) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 633 pairs to build model! INFO @ Tue, 04 Sep 2018 10:53:37: start model_add_line... INFO @ Tue, 04 Sep 2018 10:53:37: start X-correlation... INFO @ Tue, 04 Sep 2018 10:53:37: end of X-cor INFO @ Tue, 04 Sep 2018 10:53:37: end of X-cor INFO @ Tue, 04 Sep 2018 10:53:37: #2 finished! INFO @ Tue, 04 Sep 2018 10:53:37: #2 finished! INFO @ Tue, 04 Sep 2018 10:53:37: #2 predicted fragment length is 226 bps INFO @ Tue, 04 Sep 2018 10:53:37: #2 predicted fragment length is 226 bps INFO @ Tue, 04 Sep 2018 10:53:37: #2 alternative fragment length(s) may be 226 bps INFO @ Tue, 04 Sep 2018 10:53:37: #2 alternative fragment length(s) may be 226 bps INFO @ Tue, 04 Sep 2018 10:53:37: #2.2 Generate R script for model : SRX4029335.10_model.r INFO @ Tue, 04 Sep 2018 10:53:37: #2.2 Generate R script for model : SRX4029335.20_model.r INFO @ Tue, 04 Sep 2018 10:53:37: start X-correlation... INFO @ Tue, 04 Sep 2018 10:53:37: #3 Call peaks... INFO @ Tue, 04 Sep 2018 10:53:37: end of X-cor INFO @ Tue, 04 Sep 2018 10:53:37: #2 finished! INFO @ Tue, 04 Sep 2018 10:53:37: #2 predicted fragment length is 226 bps INFO @ Tue, 04 Sep 2018 10:53:37: #2 alternative fragment length(s) may be 226 bps INFO @ Tue, 04 Sep 2018 10:53:37: #2.2 Generate R script for model : SRX4029335.05_model.r INFO @ Tue, 04 Sep 2018 10:53:37: #3 Call peaks... INFO @ Tue, 04 Sep 2018 10:53:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 10:53:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 10:53:37: #3 Call peaks... INFO @ Tue, 04 Sep 2018 10:53:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 10:54:18: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 10:54:20: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 10:54:21: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 10:54:38: #4 Write output xls file... SRX4029335.20_peaks.xls INFO @ Tue, 04 Sep 2018 10:54:38: #4 Write peak in narrowPeak format file... SRX4029335.20_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 10:54:38: #4 Write summits bed file... SRX4029335.20_summits.bed INFO @ Tue, 04 Sep 2018 10:54:38: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (2192 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 10:54:41: #4 Write output xls file... SRX4029335.05_peaks.xls INFO @ Tue, 04 Sep 2018 10:54:41: #4 Write peak in narrowPeak format file... SRX4029335.05_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 10:54:41: #4 Write summits bed file... SRX4029335.05_summits.bed INFO @ Tue, 04 Sep 2018 10:54:41: Done! pass1 - making usageList (7 chroms): 5 millis pass2 - checking and writing primary data (5550 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 10:54:43: #4 Write output xls file... SRX4029335.10_peaks.xls INFO @ Tue, 04 Sep 2018 10:54:43: #4 Write peak in narrowPeak format file... SRX4029335.10_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 10:54:43: #4 Write summits bed file... SRX4029335.10_summits.bed INFO @ Tue, 04 Sep 2018 10:54:43: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (3844 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。