Job ID = 10480736 sra ファイルのダウンロード中... Completed: 879346K bytes transferred in 22 seconds (315603K 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: SINGLE fastq に変換中... Written 36225931 spots for /home/okishinya/chipatlas/results/dm3/SRX3380795/SRR6278158.sra Written 36225931 spots total 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: 00:11:59 36225931 reads; of these: 36225931 (100.00%) were unpaired; of these: 1677750 (4.63%) aligned 0 times 29251258 (80.75%) aligned exactly 1 time 5296923 (14.62%) aligned >1 times 95.37% overall alignment rate Time searching: 00:11:59 Overall time: 00:11:59 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 5575410 / 34548181 = 0.1614 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, 16 Mar 2018 08:06:51: # Command line: callpeak -t SRX3380795.bam -f BAM -g dm -n SRX3380795.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3380795.10 # format = BAM # ChIP-seq file = ['SRX3380795.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Mar 2018 08:06:51: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:06:51: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:06:51: # Command line: callpeak -t SRX3380795.bam -f BAM -g dm -n SRX3380795.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3380795.20 # format = BAM # ChIP-seq file = ['SRX3380795.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Mar 2018 08:06:51: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:06:51: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:06:51: # Command line: callpeak -t SRX3380795.bam -f BAM -g dm -n SRX3380795.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3380795.05 # format = BAM # ChIP-seq file = ['SRX3380795.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Mar 2018 08:06:51: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:06:51: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:06:57: 1000000 INFO @ Fri, 16 Mar 2018 08:06:57: 1000000 INFO @ Fri, 16 Mar 2018 08:06:57: 1000000 INFO @ Fri, 16 Mar 2018 08:07:03: 2000000 INFO @ Fri, 16 Mar 2018 08:07:03: 2000000 INFO @ Fri, 16 Mar 2018 08:07:04: 2000000 INFO @ Fri, 16 Mar 2018 08:07:09: 3000000 INFO @ Fri, 16 Mar 2018 08:07:10: 3000000 INFO @ Fri, 16 Mar 2018 08:07:10: 3000000 INFO @ Fri, 16 Mar 2018 08:07:15: 4000000 INFO @ Fri, 16 Mar 2018 08:07:16: 4000000 INFO @ Fri, 16 Mar 2018 08:07:17: 4000000 INFO @ Fri, 16 Mar 2018 08:07:21: 5000000 INFO @ Fri, 16 Mar 2018 08:07:22: 5000000 INFO @ Fri, 16 Mar 2018 08:07:24: 5000000 INFO @ Fri, 16 Mar 2018 08:07:27: 6000000 INFO @ Fri, 16 Mar 2018 08:07:29: 6000000 INFO @ Fri, 16 Mar 2018 08:07:30: 6000000 INFO @ Fri, 16 Mar 2018 08:07:33: 7000000 INFO @ Fri, 16 Mar 2018 08:07:35: 7000000 INFO @ Fri, 16 Mar 2018 08:07:37: 7000000 INFO @ Fri, 16 Mar 2018 08:07:39: 8000000 INFO @ Fri, 16 Mar 2018 08:07:41: 8000000 INFO @ Fri, 16 Mar 2018 08:07:44: 8000000 INFO @ Fri, 16 Mar 2018 08:07:45: 9000000 INFO @ Fri, 16 Mar 2018 08:07:48: 9000000 INFO @ Fri, 16 Mar 2018 08:07:50: 9000000 INFO @ Fri, 16 Mar 2018 08:07:51: 10000000 INFO @ Fri, 16 Mar 2018 08:07:54: 10000000 INFO @ Fri, 16 Mar 2018 08:07:57: 11000000 INFO @ Fri, 16 Mar 2018 08:07:57: 10000000 INFO @ Fri, 16 Mar 2018 08:08:00: 11000000 INFO @ Fri, 16 Mar 2018 08:08:03: 12000000 INFO @ Fri, 16 Mar 2018 08:08:04: 11000000 INFO @ Fri, 16 Mar 2018 08:08:07: 12000000 INFO @ Fri, 16 Mar 2018 08:08:09: 13000000 INFO @ Fri, 16 Mar 2018 08:08:10: 12000000 INFO @ Fri, 16 Mar 2018 08:08:13: 13000000 INFO @ Fri, 16 Mar 2018 08:08:15: 14000000 INFO @ Fri, 16 Mar 2018 08:08:17: 13000000 INFO @ Fri, 16 Mar 2018 08:08:20: 14000000 INFO @ Fri, 16 Mar 2018 08:08:20: 15000000 INFO @ Fri, 16 Mar 2018 08:08:23: 14000000 INFO @ Fri, 16 Mar 2018 08:08:26: 15000000 INFO @ Fri, 16 Mar 2018 08:08:26: 16000000 INFO @ Fri, 16 Mar 2018 08:08:30: 15000000 INFO @ Fri, 16 Mar 2018 08:08:32: 17000000 INFO @ Fri, 16 Mar 2018 08:08:32: 16000000 INFO @ Fri, 16 Mar 2018 08:08:37: 16000000 INFO @ Fri, 16 Mar 2018 08:08:38: 18000000 INFO @ Fri, 16 Mar 2018 08:08:39: 17000000 INFO @ Fri, 16 Mar 2018 08:08:43: 17000000 INFO @ Fri, 16 Mar 2018 08:08:44: 19000000 INFO @ Fri, 16 Mar 2018 08:08:45: 18000000 INFO @ Fri, 16 Mar 2018 08:08:50: 18000000 INFO @ Fri, 16 Mar 2018 08:08:50: 20000000 INFO @ Fri, 16 Mar 2018 08:08:51: 19000000 INFO @ Fri, 16 Mar 2018 08:08:56: 21000000 INFO @ Fri, 16 Mar 2018 08:08:56: 19000000 INFO @ Fri, 16 Mar 2018 08:08:58: 20000000 INFO @ Fri, 16 Mar 2018 08:09:02: 22000000 INFO @ Fri, 16 Mar 2018 08:09:03: 20000000 INFO @ Fri, 16 Mar 2018 08:09:04: 21000000 INFO @ Fri, 16 Mar 2018 08:09:08: 23000000 INFO @ Fri, 16 Mar 2018 08:09:10: 21000000 INFO @ Fri, 16 Mar 2018 08:09:10: 22000000 INFO @ Fri, 16 Mar 2018 08:09:14: 24000000 INFO @ Fri, 16 Mar 2018 08:09:16: 22000000 INFO @ Fri, 16 Mar 2018 08:09:17: 23000000 INFO @ Fri, 16 Mar 2018 08:09:20: 25000000 INFO @ Fri, 16 Mar 2018 08:09:23: 23000000 INFO @ Fri, 16 Mar 2018 08:09:23: 24000000 INFO @ Fri, 16 Mar 2018 08:09:26: 26000000 INFO @ Fri, 16 Mar 2018 08:09:30: 25000000 INFO @ Fri, 16 Mar 2018 08:09:30: 24000000 INFO @ Fri, 16 Mar 2018 08:09:32: 27000000 INFO @ Fri, 16 Mar 2018 08:09:36: 26000000 INFO @ Fri, 16 Mar 2018 08:09:36: 25000000 INFO @ Fri, 16 Mar 2018 08:09:38: 28000000 INFO @ Fri, 16 Mar 2018 08:09:42: 27000000 INFO @ Fri, 16 Mar 2018 08:09:43: 26000000 INFO @ Fri, 16 Mar 2018 08:09:44: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 08:09:44: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 08:09:44: #1 total tags in treatment: 28972771 INFO @ Fri, 16 Mar 2018 08:09:44: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:09:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 08:09:44: #1 tags after filtering in treatment: 28972771 INFO @ Fri, 16 Mar 2018 08:09:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 08:09:44: #1 finished! INFO @ Fri, 16 Mar 2018 08:09:44: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:09:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:09:46: #2 number of paired peaks: 153 WARNING @ Fri, 16 Mar 2018 08:09:46: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Fri, 16 Mar 2018 08:09:46: start model_add_line... INFO @ Fri, 16 Mar 2018 08:09:47: start X-correlation... INFO @ Fri, 16 Mar 2018 08:09:47: end of X-cor INFO @ Fri, 16 Mar 2018 08:09:47: #2 finished! INFO @ Fri, 16 Mar 2018 08:09:47: #2 predicted fragment length is 167 bps INFO @ Fri, 16 Mar 2018 08:09:47: #2 alternative fragment length(s) may be 3,83,143,167,208 bps INFO @ Fri, 16 Mar 2018 08:09:47: #2.2 Generate R script for model : SRX3380795.20_model.r INFO @ Fri, 16 Mar 2018 08:09:47: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:09:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:09:48: 28000000 INFO @ Fri, 16 Mar 2018 08:09:49: 27000000 INFO @ Fri, 16 Mar 2018 08:09:55: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 08:09:55: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 08:09:55: #1 total tags in treatment: 28972771 INFO @ Fri, 16 Mar 2018 08:09:55: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:09:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 08:09:55: #1 tags after filtering in treatment: 28972771 INFO @ Fri, 16 Mar 2018 08:09:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 08:09:55: #1 finished! INFO @ Fri, 16 Mar 2018 08:09:55: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:09:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:09:56: 28000000 INFO @ Fri, 16 Mar 2018 08:09:57: #2 number of paired peaks: 153 WARNING @ Fri, 16 Mar 2018 08:09:57: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Fri, 16 Mar 2018 08:09:57: start model_add_line... INFO @ Fri, 16 Mar 2018 08:09:57: start X-correlation... INFO @ Fri, 16 Mar 2018 08:09:57: end of X-cor INFO @ Fri, 16 Mar 2018 08:09:57: #2 finished! INFO @ Fri, 16 Mar 2018 08:09:57: #2 predicted fragment length is 167 bps INFO @ Fri, 16 Mar 2018 08:09:57: #2 alternative fragment length(s) may be 3,83,143,167,208 bps INFO @ Fri, 16 Mar 2018 08:09:57: #2.2 Generate R script for model : SRX3380795.05_model.r INFO @ Fri, 16 Mar 2018 08:09:57: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:09:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:10:02: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 08:10:02: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 08:10:02: #1 total tags in treatment: 28972771 INFO @ Fri, 16 Mar 2018 08:10:02: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:10:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 08:10:03: #1 tags after filtering in treatment: 28972771 INFO @ Fri, 16 Mar 2018 08:10:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 08:10:03: #1 finished! INFO @ Fri, 16 Mar 2018 08:10:03: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:10:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:10:04: #2 number of paired peaks: 153 WARNING @ Fri, 16 Mar 2018 08:10:04: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Fri, 16 Mar 2018 08:10:04: start model_add_line... INFO @ Fri, 16 Mar 2018 08:10:05: start X-correlation... INFO @ Fri, 16 Mar 2018 08:10:05: end of X-cor INFO @ Fri, 16 Mar 2018 08:10:05: #2 finished! INFO @ Fri, 16 Mar 2018 08:10:05: #2 predicted fragment length is 167 bps INFO @ Fri, 16 Mar 2018 08:10:05: #2 alternative fragment length(s) may be 3,83,143,167,208 bps INFO @ Fri, 16 Mar 2018 08:10:05: #2.2 Generate R script for model : SRX3380795.10_model.r INFO @ Fri, 16 Mar 2018 08:10:05: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:10:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:10:46: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:11:03: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:11:07: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:11:18: #4 Write output xls file... SRX3380795.20_peaks.xls INFO @ Fri, 16 Mar 2018 08:11:18: #4 Write peak in narrowPeak format file... SRX3380795.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:11:18: #4 Write summits bed file... SRX3380795.20_summits.bed INFO @ Fri, 16 Mar 2018 08:11:18: Done! pass1 - making usageList (14 chroms): 13 millis pass2 - checking and writing primary data (2367 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 08:11:40: #4 Write output xls file... SRX3380795.10_peaks.xls INFO @ Fri, 16 Mar 2018 08:11:40: #4 Write peak in narrowPeak format file... SRX3380795.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:11:40: #4 Write summits bed file... SRX3380795.10_summits.bed INFO @ Fri, 16 Mar 2018 08:11:40: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4913 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 08:11:41: #4 Write output xls file... SRX3380795.05_peaks.xls INFO @ Fri, 16 Mar 2018 08:11:41: #4 Write peak in narrowPeak format file... SRX3380795.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:11:41: #4 Write summits bed file... SRX3380795.05_summits.bed INFO @ Fri, 16 Mar 2018 08:11:41: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7537 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。