Job ID = 10714502 sra ファイルのダウンロード中... Completed: 1217341K bytes transferred in 17 seconds (581000K 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 19006442 spots for /home/okishinya/chipatlas/results/ce10/SRX4085419/SRR7167448.sra Written 19006442 spots for /home/okishinya/chipatlas/results/ce10/SRX4085419/SRR7167448.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: 00:15:15 19006442 reads; of these: 19006442 (100.00%) were paired; of these: 9009236 (47.40%) aligned concordantly 0 times 8483331 (44.63%) aligned concordantly exactly 1 time 1513875 (7.97%) aligned concordantly >1 times ---- 9009236 pairs aligned concordantly 0 times; of these: 374949 (4.16%) aligned discordantly 1 time ---- 8634287 pairs aligned 0 times concordantly or discordantly; of these: 17268574 mates make up the pairs; of these: 13060625 (75.63%) aligned 0 times 3626574 (21.00%) aligned exactly 1 time 581375 (3.37%) aligned >1 times 65.64% overall alignment rate Time searching: 00:15:15 Overall time: 00:15:15 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 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 chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 687746 / 10244553 = 0.0671 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 @ Sun, 03 Jun 2018 13:25:25: # Command line: callpeak -t SRX4085419.bam -f BAM -g ce -n SRX4085419.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085419.20 # format = BAM # ChIP-seq file = ['SRX4085419.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 @ Sun, 03 Jun 2018 13:25:25: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:25:25: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:25:25: # Command line: callpeak -t SRX4085419.bam -f BAM -g ce -n SRX4085419.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085419.05 # format = BAM # ChIP-seq file = ['SRX4085419.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 @ Sun, 03 Jun 2018 13:25:25: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:25:25: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:25:25: # Command line: callpeak -t SRX4085419.bam -f BAM -g ce -n SRX4085419.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085419.10 # format = BAM # ChIP-seq file = ['SRX4085419.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 @ Sun, 03 Jun 2018 13:25:25: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:25:25: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:25:31: 1000000 INFO @ Sun, 03 Jun 2018 13:25:31: 1000000 INFO @ Sun, 03 Jun 2018 13:25:31: 1000000 INFO @ Sun, 03 Jun 2018 13:25:37: 2000000 INFO @ Sun, 03 Jun 2018 13:25:37: 2000000 INFO @ Sun, 03 Jun 2018 13:25:37: 2000000 INFO @ Sun, 03 Jun 2018 13:25:42: 3000000 INFO @ Sun, 03 Jun 2018 13:25:42: 3000000 INFO @ Sun, 03 Jun 2018 13:25:42: 3000000 INFO @ Sun, 03 Jun 2018 13:25:48: 4000000 INFO @ Sun, 03 Jun 2018 13:25:48: 4000000 INFO @ Sun, 03 Jun 2018 13:25:48: 4000000 INFO @ Sun, 03 Jun 2018 13:25:54: 5000000 INFO @ Sun, 03 Jun 2018 13:25:54: 5000000 INFO @ Sun, 03 Jun 2018 13:25:54: 5000000 INFO @ Sun, 03 Jun 2018 13:26:00: 6000000 INFO @ Sun, 03 Jun 2018 13:26:00: 6000000 INFO @ Sun, 03 Jun 2018 13:26:00: 6000000 INFO @ Sun, 03 Jun 2018 13:26:06: 7000000 INFO @ Sun, 03 Jun 2018 13:26:06: 7000000 INFO @ Sun, 03 Jun 2018 13:26:07: 7000000 INFO @ Sun, 03 Jun 2018 13:26:12: 8000000 INFO @ Sun, 03 Jun 2018 13:26:12: 8000000 INFO @ Sun, 03 Jun 2018 13:26:13: 8000000 INFO @ Sun, 03 Jun 2018 13:26:18: 9000000 INFO @ Sun, 03 Jun 2018 13:26:18: 9000000 INFO @ Sun, 03 Jun 2018 13:26:19: 9000000 INFO @ Sun, 03 Jun 2018 13:26:24: 10000000 INFO @ Sun, 03 Jun 2018 13:26:24: 10000000 INFO @ Sun, 03 Jun 2018 13:26:25: 10000000 INFO @ Sun, 03 Jun 2018 13:26:30: 11000000 INFO @ Sun, 03 Jun 2018 13:26:30: 11000000 INFO @ Sun, 03 Jun 2018 13:26:32: 11000000 INFO @ Sun, 03 Jun 2018 13:26:36: 12000000 INFO @ Sun, 03 Jun 2018 13:26:36: 12000000 INFO @ Sun, 03 Jun 2018 13:26:38: 12000000 INFO @ Sun, 03 Jun 2018 13:26:42: 13000000 INFO @ Sun, 03 Jun 2018 13:26:43: 13000000 INFO @ Sun, 03 Jun 2018 13:26:44: 13000000 INFO @ Sun, 03 Jun 2018 13:26:48: 14000000 INFO @ Sun, 03 Jun 2018 13:26:49: 14000000 INFO @ Sun, 03 Jun 2018 13:26:51: 14000000 INFO @ Sun, 03 Jun 2018 13:26:55: 15000000 INFO @ Sun, 03 Jun 2018 13:26:55: 15000000 INFO @ Sun, 03 Jun 2018 13:26:57: 15000000 INFO @ Sun, 03 Jun 2018 13:27:01: 16000000 INFO @ Sun, 03 Jun 2018 13:27:02: 16000000 INFO @ Sun, 03 Jun 2018 13:27:03: 16000000 INFO @ Sun, 03 Jun 2018 13:27:07: 17000000 INFO @ Sun, 03 Jun 2018 13:27:08: 17000000 INFO @ Sun, 03 Jun 2018 13:27:10: 17000000 INFO @ Sun, 03 Jun 2018 13:27:14: 18000000 INFO @ Sun, 03 Jun 2018 13:27:15: 18000000 INFO @ Sun, 03 Jun 2018 13:27:16: 18000000 INFO @ Sun, 03 Jun 2018 13:27:20: 19000000 INFO @ Sun, 03 Jun 2018 13:27:21: 19000000 INFO @ Sun, 03 Jun 2018 13:27:23: 19000000 INFO @ Sun, 03 Jun 2018 13:27:26: 20000000 INFO @ Sun, 03 Jun 2018 13:27:27: 20000000 INFO @ Sun, 03 Jun 2018 13:27:29: 20000000 INFO @ Sun, 03 Jun 2018 13:27:33: 21000000 INFO @ Sun, 03 Jun 2018 13:27:34: 21000000 INFO @ Sun, 03 Jun 2018 13:27:35: 21000000 INFO @ Sun, 03 Jun 2018 13:27:39: 22000000 INFO @ Sun, 03 Jun 2018 13:27:40: 22000000 INFO @ Sun, 03 Jun 2018 13:27:42: 22000000 INFO @ Sun, 03 Jun 2018 13:27:45: 23000000 INFO @ Sun, 03 Jun 2018 13:27:47: 23000000 INFO @ Sun, 03 Jun 2018 13:27:48: 23000000 INFO @ Sun, 03 Jun 2018 13:27:49: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:27:49: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:27:49: #1 total tags in treatment: 9327983 INFO @ Sun, 03 Jun 2018 13:27:49: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:27:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:27:49: #1 tags after filtering in treatment: 8426910 INFO @ Sun, 03 Jun 2018 13:27:49: #1 Redundant rate of treatment: 0.10 INFO @ Sun, 03 Jun 2018 13:27:49: #1 finished! INFO @ Sun, 03 Jun 2018 13:27:49: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:27:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:27:50: #2 number of paired peaks: 373 WARNING @ Sun, 03 Jun 2018 13:27:50: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Sun, 03 Jun 2018 13:27:50: start model_add_line... INFO @ Sun, 03 Jun 2018 13:27:50: start X-correlation... INFO @ Sun, 03 Jun 2018 13:27:50: end of X-cor INFO @ Sun, 03 Jun 2018 13:27:50: #2 finished! INFO @ Sun, 03 Jun 2018 13:27:50: #2 predicted fragment length is 112 bps INFO @ Sun, 03 Jun 2018 13:27:50: #2 alternative fragment length(s) may be 112,594 bps INFO @ Sun, 03 Jun 2018 13:27:50: #2.2 Generate R script for model : SRX4085419.10_model.r INFO @ Sun, 03 Jun 2018 13:27:50: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:27:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:27:50: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:27:50: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:27:50: #1 total tags in treatment: 9327983 INFO @ Sun, 03 Jun 2018 13:27:50: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:27:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:27:50: #1 tags after filtering in treatment: 8426910 INFO @ Sun, 03 Jun 2018 13:27:50: #1 Redundant rate of treatment: 0.10 INFO @ Sun, 03 Jun 2018 13:27:50: #1 finished! INFO @ Sun, 03 Jun 2018 13:27:50: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:27:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:27:51: #2 number of paired peaks: 373 WARNING @ Sun, 03 Jun 2018 13:27:51: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Sun, 03 Jun 2018 13:27:51: start model_add_line... INFO @ Sun, 03 Jun 2018 13:27:51: start X-correlation... INFO @ Sun, 03 Jun 2018 13:27:51: end of X-cor INFO @ Sun, 03 Jun 2018 13:27:51: #2 finished! INFO @ Sun, 03 Jun 2018 13:27:51: #2 predicted fragment length is 112 bps INFO @ Sun, 03 Jun 2018 13:27:51: #2 alternative fragment length(s) may be 112,594 bps INFO @ Sun, 03 Jun 2018 13:27:51: #2.2 Generate R script for model : SRX4085419.05_model.r INFO @ Sun, 03 Jun 2018 13:27:51: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:27:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:27:51: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:27:51: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:27:51: #1 total tags in treatment: 9327983 INFO @ Sun, 03 Jun 2018 13:27:51: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:27:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:27:52: #1 tags after filtering in treatment: 8426910 INFO @ Sun, 03 Jun 2018 13:27:52: #1 Redundant rate of treatment: 0.10 INFO @ Sun, 03 Jun 2018 13:27:52: #1 finished! INFO @ Sun, 03 Jun 2018 13:27:52: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:27:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:27:52: #2 number of paired peaks: 373 WARNING @ Sun, 03 Jun 2018 13:27:52: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Sun, 03 Jun 2018 13:27:52: start model_add_line... INFO @ Sun, 03 Jun 2018 13:27:52: start X-correlation... INFO @ Sun, 03 Jun 2018 13:27:52: end of X-cor INFO @ Sun, 03 Jun 2018 13:27:52: #2 finished! INFO @ Sun, 03 Jun 2018 13:27:52: #2 predicted fragment length is 112 bps INFO @ Sun, 03 Jun 2018 13:27:52: #2 alternative fragment length(s) may be 112,594 bps INFO @ Sun, 03 Jun 2018 13:27:52: #2.2 Generate R script for model : SRX4085419.20_model.r INFO @ Sun, 03 Jun 2018 13:27:52: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:27:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:28:09: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:28:10: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:28:13: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:28:19: #4 Write output xls file... SRX4085419.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:28:19: #4 Write peak in narrowPeak format file... SRX4085419.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:28:19: #4 Write summits bed file... SRX4085419.10_summits.bed INFO @ Sun, 03 Jun 2018 13:28:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1079 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:28:20: #4 Write output xls file... SRX4085419.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:28:20: #4 Write peak in narrowPeak format file... SRX4085419.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:28:20: #4 Write summits bed file... SRX4085419.05_summits.bed INFO @ Sun, 03 Jun 2018 13:28:20: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1888 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:28:24: #4 Write output xls file... SRX4085419.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:28:24: #4 Write peak in narrowPeak format file... SRX4085419.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:28:24: #4 Write summits bed file... SRX4085419.20_summits.bed INFO @ Sun, 03 Jun 2018 13:28:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (509 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。