Job ID = 10194899 sra ファイルのダウンロード中... Completed: 121830K bytes transferred in 13 seconds (72436K bits/sec), in 1 file. Completed: 122385K bytes transferred in 13 seconds (75789K bits/sec), in 1 file. Completed: 115742K bytes transferred in 8 seconds (106102K bits/sec), in 1 file. Completed: 114196K bytes transferred in 12 seconds (77176K bits/sec), in 1 file. Completed: 138826K bytes transferred in 11 seconds (97814K bits/sec), in 1 file. Completed: 140914K bytes transferred in 13 seconds (83844K 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 2593881 spots for /home/okishinya/chipatlas/results/rn6/SRX2202894/SRR4319911.sra Written 2593881 spots total Written 2622542 spots for /home/okishinya/chipatlas/results/rn6/SRX2202894/SRR4319910.sra Written 2622542 spots total Written 2750266 spots for /home/okishinya/chipatlas/results/rn6/SRX2202894/SRR4319909.sra Written 2750266 spots total Written 2747164 spots for /home/okishinya/chipatlas/results/rn6/SRX2202894/SRR4319908.sra Written 2747164 spots total Written 3091656 spots for /home/okishinya/chipatlas/results/rn6/SRX2202894/SRR4319913.sra Written 3091656 spots total Written 3057261 spots for /home/okishinya/chipatlas/results/rn6/SRX2202894/SRR4319912.sra Written 3057261 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 fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:27:05 16862770 reads; of these: 16862770 (100.00%) were unpaired; of these: 472857 (2.80%) aligned 0 times 11711175 (69.45%) aligned exactly 1 time 4678738 (27.75%) aligned >1 times 97.20% overall alignment rate Time searching: 00:27:09 Overall time: 00:27:09 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 691282 / 16389913 = 0.0422 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, 10 Nov 2017 22:31:46: # Command line: callpeak -t SRX2202894.bam -f BAM -g 2.15e9 -n SRX2202894.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202894.10 # format = BAM # ChIP-seq file = ['SRX2202894.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 10 Nov 2017 22:31:46: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:31:46: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:31:46: # Command line: callpeak -t SRX2202894.bam -f BAM -g 2.15e9 -n SRX2202894.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202894.20 # format = BAM # ChIP-seq file = ['SRX2202894.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 10 Nov 2017 22:31:46: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:31:46: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:31:46: # Command line: callpeak -t SRX2202894.bam -f BAM -g 2.15e9 -n SRX2202894.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202894.05 # format = BAM # ChIP-seq file = ['SRX2202894.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 10 Nov 2017 22:31:46: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:31:46: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:32:02: 1000000 INFO @ Fri, 10 Nov 2017 22:32:04: 1000000 INFO @ Fri, 10 Nov 2017 22:32:07: 1000000 INFO @ Fri, 10 Nov 2017 22:32:17: 2000000 INFO @ Fri, 10 Nov 2017 22:32:27: 2000000 INFO @ Fri, 10 Nov 2017 22:32:28: 2000000 INFO @ Fri, 10 Nov 2017 22:32:32: 3000000 INFO @ Fri, 10 Nov 2017 22:32:49: 3000000 INFO @ Fri, 10 Nov 2017 22:32:50: 4000000 INFO @ Fri, 10 Nov 2017 22:32:52: 3000000 INFO @ Fri, 10 Nov 2017 22:33:06: 4000000 INFO @ Fri, 10 Nov 2017 22:33:07: 5000000 INFO @ Fri, 10 Nov 2017 22:33:15: 4000000 INFO @ Fri, 10 Nov 2017 22:33:23: 6000000 INFO @ Fri, 10 Nov 2017 22:33:26: 5000000 INFO @ Fri, 10 Nov 2017 22:33:35: 5000000 INFO @ Fri, 10 Nov 2017 22:33:38: 7000000 INFO @ Fri, 10 Nov 2017 22:33:47: 6000000 INFO @ Fri, 10 Nov 2017 22:33:51: 8000000 INFO @ Fri, 10 Nov 2017 22:33:55: 6000000 INFO @ Fri, 10 Nov 2017 22:34:04: 9000000 INFO @ Fri, 10 Nov 2017 22:34:09: 7000000 INFO @ Fri, 10 Nov 2017 22:34:16: 10000000 INFO @ Fri, 10 Nov 2017 22:34:18: 7000000 INFO @ Fri, 10 Nov 2017 22:34:28: 11000000 INFO @ Fri, 10 Nov 2017 22:34:32: 8000000 INFO @ Fri, 10 Nov 2017 22:34:41: 12000000 INFO @ Fri, 10 Nov 2017 22:34:42: 8000000 INFO @ Fri, 10 Nov 2017 22:34:53: 9000000 INFO @ Fri, 10 Nov 2017 22:34:58: 13000000 INFO @ Fri, 10 Nov 2017 22:35:02: 9000000 INFO @ Fri, 10 Nov 2017 22:35:14: 10000000 INFO @ Fri, 10 Nov 2017 22:35:16: 14000000 INFO @ Fri, 10 Nov 2017 22:35:22: 10000000 INFO @ Fri, 10 Nov 2017 22:35:31: 15000000 INFO @ Fri, 10 Nov 2017 22:35:36: 11000000 INFO @ Fri, 10 Nov 2017 22:35:41: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 22:35:41: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 22:35:41: #1 total tags in treatment: 15698631 INFO @ Fri, 10 Nov 2017 22:35:41: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:35:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 22:35:42: #1 tags after filtering in treatment: 15698456 INFO @ Fri, 10 Nov 2017 22:35:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:35:42: #1 finished! INFO @ Fri, 10 Nov 2017 22:35:42: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:35:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:35:44: #2 number of paired peaks: 5288 INFO @ Fri, 10 Nov 2017 22:35:44: start model_add_line... INFO @ Fri, 10 Nov 2017 22:35:44: 11000000 INFO @ Fri, 10 Nov 2017 22:35:44: start X-correlation... INFO @ Fri, 10 Nov 2017 22:35:44: end of X-cor INFO @ Fri, 10 Nov 2017 22:35:44: #2 finished! INFO @ Fri, 10 Nov 2017 22:35:44: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Nov 2017 22:35:44: #2 alternative fragment length(s) may be 50,129,229,406,506 bps INFO @ Fri, 10 Nov 2017 22:35:44: #2.2 Generate R script for model : SRX2202894.10_model.r WARNING @ Fri, 10 Nov 2017 22:35:44: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 22:35:44: #2 You may need to consider one of the other alternative d(s): 50,129,229,406,506 WARNING @ Fri, 10 Nov 2017 22:35:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 22:35:44: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:35:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:35:57: 12000000 INFO @ Fri, 10 Nov 2017 22:36:04: 12000000 INFO @ Fri, 10 Nov 2017 22:36:18: 13000000 INFO @ Fri, 10 Nov 2017 22:36:25: 13000000 INFO @ Fri, 10 Nov 2017 22:36:36: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:36:40: 14000000 INFO @ Fri, 10 Nov 2017 22:36:45: 14000000 INFO @ Fri, 10 Nov 2017 22:37:01: 15000000 INFO @ Fri, 10 Nov 2017 22:37:05: #4 Write output xls file... SRX2202894.10_peaks.xls INFO @ Fri, 10 Nov 2017 22:37:05: #4 Write peak in narrowPeak format file... SRX2202894.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:37:05: #4 Write summits bed file... SRX2202894.10_summits.bed INFO @ Fri, 10 Nov 2017 22:37:05: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (765 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 22:37:06: 15000000 INFO @ Fri, 10 Nov 2017 22:37:16: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 22:37:16: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 22:37:16: #1 total tags in treatment: 15698631 INFO @ Fri, 10 Nov 2017 22:37:16: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:37:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 22:37:16: #1 tags after filtering in treatment: 15698456 INFO @ Fri, 10 Nov 2017 22:37:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:37:16: #1 finished! INFO @ Fri, 10 Nov 2017 22:37:16: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:37:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:37:19: #2 number of paired peaks: 5288 INFO @ Fri, 10 Nov 2017 22:37:19: start model_add_line... INFO @ Fri, 10 Nov 2017 22:37:19: start X-correlation... INFO @ Fri, 10 Nov 2017 22:37:19: end of X-cor INFO @ Fri, 10 Nov 2017 22:37:19: #2 finished! INFO @ Fri, 10 Nov 2017 22:37:19: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Nov 2017 22:37:19: #2 alternative fragment length(s) may be 50,129,229,406,506 bps INFO @ Fri, 10 Nov 2017 22:37:19: #2.2 Generate R script for model : SRX2202894.20_model.r WARNING @ Fri, 10 Nov 2017 22:37:19: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 22:37:19: #2 You may need to consider one of the other alternative d(s): 50,129,229,406,506 WARNING @ Fri, 10 Nov 2017 22:37:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 22:37:19: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:37:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:37:20: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 22:37:20: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 22:37:20: #1 total tags in treatment: 15698631 INFO @ Fri, 10 Nov 2017 22:37:20: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:37:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 22:37:21: #1 tags after filtering in treatment: 15698456 INFO @ Fri, 10 Nov 2017 22:37:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:37:21: #1 finished! INFO @ Fri, 10 Nov 2017 22:37:21: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:37:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:37:23: #2 number of paired peaks: 5288 INFO @ Fri, 10 Nov 2017 22:37:23: start model_add_line... INFO @ Fri, 10 Nov 2017 22:37:23: start X-correlation... INFO @ Fri, 10 Nov 2017 22:37:23: end of X-cor INFO @ Fri, 10 Nov 2017 22:37:23: #2 finished! INFO @ Fri, 10 Nov 2017 22:37:23: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Nov 2017 22:37:23: #2 alternative fragment length(s) may be 50,129,229,406,506 bps INFO @ Fri, 10 Nov 2017 22:37:23: #2.2 Generate R script for model : SRX2202894.05_model.r WARNING @ Fri, 10 Nov 2017 22:37:23: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 22:37:23: #2 You may need to consider one of the other alternative d(s): 50,129,229,406,506 WARNING @ Fri, 10 Nov 2017 22:37:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 22:37:23: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:37:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:38:09: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:38:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:38:37: #4 Write output xls file... SRX2202894.20_peaks.xls INFO @ Fri, 10 Nov 2017 22:38:37: #4 Write peak in narrowPeak format file... SRX2202894.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:38:37: #4 Write summits bed file... SRX2202894.20_summits.bed INFO @ Fri, 10 Nov 2017 22:38:37: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (380 records, 4 fields): 173 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 22:38:39: #4 Write output xls file... SRX2202894.05_peaks.xls INFO @ Fri, 10 Nov 2017 22:38:39: #4 Write peak in narrowPeak format file... SRX2202894.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:38:39: #4 Write summits bed file... SRX2202894.05_summits.bed INFO @ Fri, 10 Nov 2017 22:38:39: Done! pass1 - making usageList (44 chroms): 2 millis pass2 - checking and writing primary data (1278 records, 4 fields): 23 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。