Job ID = 9029537 sra ファイルのダウンロード中... Completed: 1309953K bytes transferred in 14 seconds (755684K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 30318 0 30318 0 0 3811 0 --:--:-- 0:00:07 --:--:-- 20025 100 71421 0 71421 0 0 8285 0 --:--:-- 0:00:08 --:--:-- 32807 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 20437980 spots for /home/okishinya/chipatlas/results/dm3/SRX1837977/SRR3658918.sra Written 20437980 spots total 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: 00:17:11 20437980 reads; of these: 20437980 (100.00%) were unpaired; of these: 495280 (2.42%) aligned 0 times 17295218 (84.62%) aligned exactly 1 time 2647482 (12.95%) aligned >1 times 97.58% overall alignment rate Time searching: 00:17:11 Overall time: 00:17:11 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] 4602118 / 19942700 = 0.2308 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 @ Sat, 03 Jun 2017 14:31:38: # Command line: callpeak -t SRX1837977.bam -f BAM -g dm -n SRX1837977.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1837977.20 # format = BAM # ChIP-seq file = ['SRX1837977.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 INFO @ Sat, 03 Jun 2017 14:31:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:31:38: # Command line: callpeak -t SRX1837977.bam -f BAM -g dm -n SRX1837977.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1837977.05 # format = BAM # ChIP-seq file = ['SRX1837977.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 INFO @ Sat, 03 Jun 2017 14:31:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:31:38: # Command line: callpeak -t SRX1837977.bam -f BAM -g dm -n SRX1837977.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1837977.10 # format = BAM # ChIP-seq file = ['SRX1837977.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 INFO @ Sat, 03 Jun 2017 14:31:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:31:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:31:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:31:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:31:47: 1000000 INFO @ Sat, 03 Jun 2017 14:31:49: 1000000 INFO @ Sat, 03 Jun 2017 14:31:49: 1000000 INFO @ Sat, 03 Jun 2017 14:31:57: 2000000 INFO @ Sat, 03 Jun 2017 14:32:00: 2000000 INFO @ Sat, 03 Jun 2017 14:32:00: 2000000 INFO @ Sat, 03 Jun 2017 14:32:06: 3000000 INFO @ Sat, 03 Jun 2017 14:32:11: 3000000 INFO @ Sat, 03 Jun 2017 14:32:11: 3000000 INFO @ Sat, 03 Jun 2017 14:32:15: 4000000 INFO @ Sat, 03 Jun 2017 14:32:22: 4000000 INFO @ Sat, 03 Jun 2017 14:32:22: 4000000 INFO @ Sat, 03 Jun 2017 14:32:24: 5000000 INFO @ Sat, 03 Jun 2017 14:32:33: 5000000 INFO @ Sat, 03 Jun 2017 14:32:33: 5000000 INFO @ Sat, 03 Jun 2017 14:32:33: 6000000 INFO @ Sat, 03 Jun 2017 14:32:43: 7000000 INFO @ Sat, 03 Jun 2017 14:32:44: 6000000 INFO @ Sat, 03 Jun 2017 14:32:44: 6000000 INFO @ Sat, 03 Jun 2017 14:32:52: 8000000 INFO @ Sat, 03 Jun 2017 14:32:55: 7000000 INFO @ Sat, 03 Jun 2017 14:32:55: 7000000 INFO @ Sat, 03 Jun 2017 14:33:01: 9000000 INFO @ Sat, 03 Jun 2017 14:33:07: 8000000 INFO @ Sat, 03 Jun 2017 14:33:07: 8000000 INFO @ Sat, 03 Jun 2017 14:33:10: 10000000 INFO @ Sat, 03 Jun 2017 14:33:18: 9000000 INFO @ Sat, 03 Jun 2017 14:33:18: 9000000 INFO @ Sat, 03 Jun 2017 14:33:19: 11000000 INFO @ Sat, 03 Jun 2017 14:33:29: 12000000 INFO @ Sat, 03 Jun 2017 14:33:29: 10000000 INFO @ Sat, 03 Jun 2017 14:33:29: 10000000 INFO @ Sat, 03 Jun 2017 14:33:38: 13000000 INFO @ Sat, 03 Jun 2017 14:33:40: 11000000 INFO @ Sat, 03 Jun 2017 14:33:40: 11000000 INFO @ Sat, 03 Jun 2017 14:33:47: 14000000 INFO @ Sat, 03 Jun 2017 14:33:51: 12000000 INFO @ Sat, 03 Jun 2017 14:33:51: 12000000 INFO @ Sat, 03 Jun 2017 14:33:56: 15000000 INFO @ Sat, 03 Jun 2017 14:34:00: #1 tag size is determined as 148 bps INFO @ Sat, 03 Jun 2017 14:34:00: #1 tag size = 148 INFO @ Sat, 03 Jun 2017 14:34:00: #1 total tags in treatment: 15340582 INFO @ Sat, 03 Jun 2017 14:34:00: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:34:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 14:34:02: 13000000 INFO @ Sat, 03 Jun 2017 14:34:02: 13000000 INFO @ Sat, 03 Jun 2017 14:34:03: #1 tags after filtering in treatment: 15299525 INFO @ Sat, 03 Jun 2017 14:34:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:34:03: #1 finished! INFO @ Sat, 03 Jun 2017 14:34:03: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:34:06: #2 number of paired peaks: 3460 INFO @ Sat, 03 Jun 2017 14:34:06: start model_add_line... INFO @ Sat, 03 Jun 2017 14:34:13: 14000000 INFO @ Sat, 03 Jun 2017 14:34:13: 14000000 INFO @ Sat, 03 Jun 2017 14:34:26: 15000000 INFO @ Sat, 03 Jun 2017 14:34:26: 15000000 INFO @ Sat, 03 Jun 2017 14:34:31: #1 tag size is determined as 148 bps INFO @ Sat, 03 Jun 2017 14:34:31: #1 tag size is determined as 148 bps INFO @ Sat, 03 Jun 2017 14:34:31: #1 tag size = 148 INFO @ Sat, 03 Jun 2017 14:34:31: #1 tag size = 148 INFO @ Sat, 03 Jun 2017 14:34:31: #1 total tags in treatment: 15340582 INFO @ Sat, 03 Jun 2017 14:34:31: #1 total tags in treatment: 15340582 INFO @ Sat, 03 Jun 2017 14:34:31: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:34:31: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:34:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 14:34:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 14:34:34: #1 tags after filtering in treatment: 15299525 INFO @ Sat, 03 Jun 2017 14:34:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:34:34: #1 finished! INFO @ Sat, 03 Jun 2017 14:34:34: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:34:35: #1 tags after filtering in treatment: 15299525 INFO @ Sat, 03 Jun 2017 14:34:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:34:35: #1 finished! INFO @ Sat, 03 Jun 2017 14:34:35: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:34:38: #2 number of paired peaks: 3460 INFO @ Sat, 03 Jun 2017 14:34:38: start model_add_line... INFO @ Sat, 03 Jun 2017 14:34:38: #2 number of paired peaks: 3460 INFO @ Sat, 03 Jun 2017 14:34:38: start model_add_line... INFO @ Sat, 03 Jun 2017 14:34:43: start X-correlation... INFO @ Sat, 03 Jun 2017 14:34:43: end of X-cor INFO @ Sat, 03 Jun 2017 14:34:43: #2 finished! INFO @ Sat, 03 Jun 2017 14:34:43: #2 predicted fragment length is 162 bps INFO @ Sat, 03 Jun 2017 14:34:43: #2 alternative fragment length(s) may be 162 bps INFO @ Sat, 03 Jun 2017 14:34:43: #2.2 Generate R script for model : SRX1837977.20_model.r WARNING @ Sat, 03 Jun 2017 14:34:43: #2 Since the d (162) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:34:43: #2 You may need to consider one of the other alternative d(s): 162 WARNING @ Sat, 03 Jun 2017 14:34:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 14:34:43: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:34:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:35:18: start X-correlation... INFO @ Sat, 03 Jun 2017 14:35:18: end of X-cor INFO @ Sat, 03 Jun 2017 14:35:18: #2 finished! INFO @ Sat, 03 Jun 2017 14:35:18: #2 predicted fragment length is 162 bps INFO @ Sat, 03 Jun 2017 14:35:18: #2 alternative fragment length(s) may be 162 bps INFO @ Sat, 03 Jun 2017 14:35:18: #2.2 Generate R script for model : SRX1837977.10_model.r WARNING @ Sat, 03 Jun 2017 14:35:18: #2 Since the d (162) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:35:18: #2 You may need to consider one of the other alternative d(s): 162 WARNING @ Sat, 03 Jun 2017 14:35:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 14:35:18: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:35:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:35:18: start X-correlation... INFO @ Sat, 03 Jun 2017 14:35:18: end of X-cor INFO @ Sat, 03 Jun 2017 14:35:18: #2 finished! INFO @ Sat, 03 Jun 2017 14:35:18: #2 predicted fragment length is 162 bps INFO @ Sat, 03 Jun 2017 14:35:18: #2 alternative fragment length(s) may be 162 bps INFO @ Sat, 03 Jun 2017 14:35:18: #2.2 Generate R script for model : SRX1837977.05_model.r WARNING @ Sat, 03 Jun 2017 14:35:18: #2 Since the d (162) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:35:18: #2 You may need to consider one of the other alternative d(s): 162 WARNING @ Sat, 03 Jun 2017 14:35:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 14:35:18: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:35:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:36:16: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:36:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:36:53: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:37:18: #4 Write output xls file... SRX1837977.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:37:18: #4 Write peak in narrowPeak format file... SRX1837977.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:37:18: #4 Write summits bed file... SRX1837977.20_summits.bed INFO @ Sat, 03 Jun 2017 14:37:18: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4236 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 14:38:03: #4 Write output xls file... SRX1837977.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:38:04: #4 Write peak in narrowPeak format file... SRX1837977.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:38:04: #4 Write summits bed file... SRX1837977.10_summits.bed INFO @ Sat, 03 Jun 2017 14:38:04: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7685 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:38:09: #4 Write output xls file... SRX1837977.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:38:09: #4 Write peak in narrowPeak format file... SRX1837977.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:38:09: #4 Write summits bed file... SRX1837977.05_summits.bed INFO @ Sat, 03 Jun 2017 14:38:09: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11464 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。