Job ID = 11293677 sra ファイルのダウンロード中... Completed: 774345K bytes transferred in 31 seconds (199686K 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... Read 23677165 spots for /home/okishinya/chipatlas/results/dm3/SRX4375839/SRR7506493.sra Written 23677165 spots for /home/okishinya/chipatlas/results/dm3/SRX4375839/SRR7506493.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: 00:08:06 23677165 reads; of these: 23677165 (100.00%) were unpaired; of these: 3687752 (15.58%) aligned 0 times 14647753 (61.86%) aligned exactly 1 time 5341660 (22.56%) aligned >1 times 84.42% overall alignment rate Time searching: 00:08:06 Overall time: 00:08:06 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 12 files... [bam_rmdupse_core] 6351143 / 19989413 = 0.3177 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, 04 Nov 2018 18:01:56: # Command line: callpeak -t SRX4375839.bam -f BAM -g dm -n SRX4375839.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4375839.05 # format = BAM # ChIP-seq file = ['SRX4375839.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 @ Sun, 04 Nov 2018 18:01:56: # Command line: callpeak -t SRX4375839.bam -f BAM -g dm -n SRX4375839.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4375839.10 # format = BAM # ChIP-seq file = ['SRX4375839.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 @ Sun, 04 Nov 2018 18:01:56: # Command line: callpeak -t SRX4375839.bam -f BAM -g dm -n SRX4375839.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4375839.20 # format = BAM # ChIP-seq file = ['SRX4375839.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 @ Sun, 04 Nov 2018 18:01:56: #1 read tag files... INFO @ Sun, 04 Nov 2018 18:01:56: #1 read tag files... INFO @ Sun, 04 Nov 2018 18:01:56: #1 read tag files... INFO @ Sun, 04 Nov 2018 18:01:56: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 18:01:56: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 18:01:56: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 18:02:03: 1000000 INFO @ Sun, 04 Nov 2018 18:02:03: 1000000 INFO @ Sun, 04 Nov 2018 18:02:03: 1000000 INFO @ Sun, 04 Nov 2018 18:02:09: 2000000 INFO @ Sun, 04 Nov 2018 18:02:09: 2000000 INFO @ Sun, 04 Nov 2018 18:02:10: 2000000 INFO @ Sun, 04 Nov 2018 18:02:16: 3000000 INFO @ Sun, 04 Nov 2018 18:02:16: 3000000 INFO @ Sun, 04 Nov 2018 18:02:16: 3000000 INFO @ Sun, 04 Nov 2018 18:02:22: 4000000 INFO @ Sun, 04 Nov 2018 18:02:23: 4000000 INFO @ Sun, 04 Nov 2018 18:02:23: 4000000 INFO @ Sun, 04 Nov 2018 18:02:28: 5000000 INFO @ Sun, 04 Nov 2018 18:02:29: 5000000 INFO @ Sun, 04 Nov 2018 18:02:29: 5000000 INFO @ Sun, 04 Nov 2018 18:02:35: 6000000 INFO @ Sun, 04 Nov 2018 18:02:36: 6000000 INFO @ Sun, 04 Nov 2018 18:02:36: 6000000 INFO @ Sun, 04 Nov 2018 18:02:41: 7000000 INFO @ Sun, 04 Nov 2018 18:02:42: 7000000 INFO @ Sun, 04 Nov 2018 18:02:43: 7000000 INFO @ Sun, 04 Nov 2018 18:02:47: 8000000 INFO @ Sun, 04 Nov 2018 18:02:49: 8000000 INFO @ Sun, 04 Nov 2018 18:02:49: 8000000 INFO @ Sun, 04 Nov 2018 18:02:53: 9000000 INFO @ Sun, 04 Nov 2018 18:02:56: 9000000 INFO @ Sun, 04 Nov 2018 18:02:56: 9000000 INFO @ Sun, 04 Nov 2018 18:03:00: 10000000 INFO @ Sun, 04 Nov 2018 18:03:02: 10000000 INFO @ Sun, 04 Nov 2018 18:03:02: 10000000 INFO @ Sun, 04 Nov 2018 18:03:06: 11000000 INFO @ Sun, 04 Nov 2018 18:03:09: 11000000 INFO @ Sun, 04 Nov 2018 18:03:09: 11000000 INFO @ Sun, 04 Nov 2018 18:03:12: 12000000 INFO @ Sun, 04 Nov 2018 18:03:16: 12000000 INFO @ Sun, 04 Nov 2018 18:03:16: 12000000 INFO @ Sun, 04 Nov 2018 18:03:19: 13000000 INFO @ Sun, 04 Nov 2018 18:03:22: 13000000 INFO @ Sun, 04 Nov 2018 18:03:22: 13000000 INFO @ Sun, 04 Nov 2018 18:03:23: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 18:03:23: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 18:03:23: #1 total tags in treatment: 13638270 INFO @ Sun, 04 Nov 2018 18:03:23: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 18:03:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 18:03:23: #1 tags after filtering in treatment: 13638270 INFO @ Sun, 04 Nov 2018 18:03:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 18:03:23: #1 finished! INFO @ Sun, 04 Nov 2018 18:03:23: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 18:03:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 18:03:24: #2 number of paired peaks: 716 WARNING @ Sun, 04 Nov 2018 18:03:24: Fewer paired peaks (716) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 716 pairs to build model! INFO @ Sun, 04 Nov 2018 18:03:24: start model_add_line... INFO @ Sun, 04 Nov 2018 18:03:24: start X-correlation... INFO @ Sun, 04 Nov 2018 18:03:25: end of X-cor INFO @ Sun, 04 Nov 2018 18:03:25: #2 finished! INFO @ Sun, 04 Nov 2018 18:03:25: #2 predicted fragment length is 60 bps INFO @ Sun, 04 Nov 2018 18:03:25: #2 alternative fragment length(s) may be 60 bps INFO @ Sun, 04 Nov 2018 18:03:25: #2.2 Generate R script for model : SRX4375839.10_model.r WARNING @ Sun, 04 Nov 2018 18:03:25: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 18:03:25: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Sun, 04 Nov 2018 18:03:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Nov 2018 18:03:25: #3 Call peaks... INFO @ Sun, 04 Nov 2018 18:03:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 18:03:26: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 18:03:26: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 18:03:26: #1 total tags in treatment: 13638270 INFO @ Sun, 04 Nov 2018 18:03:26: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 18:03:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 18:03:27: #1 tags after filtering in treatment: 13638270 INFO @ Sun, 04 Nov 2018 18:03:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 18:03:27: #1 finished! INFO @ Sun, 04 Nov 2018 18:03:27: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 18:03:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 18:03:27: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 18:03:27: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 18:03:27: #1 total tags in treatment: 13638270 INFO @ Sun, 04 Nov 2018 18:03:27: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 18:03:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 18:03:27: #1 tags after filtering in treatment: 13638270 INFO @ Sun, 04 Nov 2018 18:03:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 18:03:27: #1 finished! INFO @ Sun, 04 Nov 2018 18:03:27: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 18:03:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 18:03:28: #2 number of paired peaks: 716 WARNING @ Sun, 04 Nov 2018 18:03:28: Fewer paired peaks (716) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 716 pairs to build model! INFO @ Sun, 04 Nov 2018 18:03:28: start model_add_line... INFO @ Sun, 04 Nov 2018 18:03:28: start X-correlation... INFO @ Sun, 04 Nov 2018 18:03:28: end of X-cor INFO @ Sun, 04 Nov 2018 18:03:28: #2 finished! INFO @ Sun, 04 Nov 2018 18:03:28: #2 predicted fragment length is 60 bps INFO @ Sun, 04 Nov 2018 18:03:28: #2 alternative fragment length(s) may be 60 bps INFO @ Sun, 04 Nov 2018 18:03:28: #2.2 Generate R script for model : SRX4375839.20_model.r WARNING @ Sun, 04 Nov 2018 18:03:28: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 18:03:28: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Sun, 04 Nov 2018 18:03:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Nov 2018 18:03:28: #3 Call peaks... INFO @ Sun, 04 Nov 2018 18:03:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 18:03:28: #2 number of paired peaks: 716 WARNING @ Sun, 04 Nov 2018 18:03:28: Fewer paired peaks (716) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 716 pairs to build model! INFO @ Sun, 04 Nov 2018 18:03:28: start model_add_line... INFO @ Sun, 04 Nov 2018 18:03:28: start X-correlation... INFO @ Sun, 04 Nov 2018 18:03:28: end of X-cor INFO @ Sun, 04 Nov 2018 18:03:28: #2 finished! INFO @ Sun, 04 Nov 2018 18:03:28: #2 predicted fragment length is 60 bps INFO @ Sun, 04 Nov 2018 18:03:28: #2 alternative fragment length(s) may be 60 bps INFO @ Sun, 04 Nov 2018 18:03:28: #2.2 Generate R script for model : SRX4375839.05_model.r WARNING @ Sun, 04 Nov 2018 18:03:28: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 18:03:28: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Sun, 04 Nov 2018 18:03:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Nov 2018 18:03:28: #3 Call peaks... INFO @ Sun, 04 Nov 2018 18:03:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 18:03:54: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 18:03:56: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 18:03:58: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 18:04:09: #4 Write output xls file... SRX4375839.10_peaks.xls INFO @ Sun, 04 Nov 2018 18:04:09: #4 Write peak in narrowPeak format file... SRX4375839.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 18:04:09: #4 Write summits bed file... SRX4375839.10_summits.bed INFO @ Sun, 04 Nov 2018 18:04:09: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1490 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 18:04:11: #4 Write output xls file... SRX4375839.20_peaks.xls INFO @ Sun, 04 Nov 2018 18:04:11: #4 Write peak in narrowPeak format file... SRX4375839.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 18:04:11: #4 Write summits bed file... SRX4375839.20_summits.bed INFO @ Sun, 04 Nov 2018 18:04:11: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (914 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 18:04:17: #4 Write output xls file... SRX4375839.05_peaks.xls INFO @ Sun, 04 Nov 2018 18:04:17: #4 Write peak in narrowPeak format file... SRX4375839.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 18:04:17: #4 Write summits bed file... SRX4375839.05_summits.bed INFO @ Sun, 04 Nov 2018 18:04:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2284 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。