Job ID = 3805897 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 38,961,651 reads read : 77,923,302 reads written : 38,961,651 reads 0-length : 38,961,651 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:44:31 38961651 reads; of these: 38961651 (100.00%) were unpaired; of these: 2053403 (5.27%) aligned 0 times 28363024 (72.80%) aligned exactly 1 time 8545224 (21.93%) aligned >1 times 94.73% overall alignment rate Time searching: 00:44:36 Overall time: 00:44:36 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 16 files... [bam_rmdupse_core] 9668080 / 36908248 = 0.2619 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Mon, 04 Nov 2019 02:58:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4098374/SRX4098374.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4098374/SRX4098374.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4098374/SRX4098374.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4098374/SRX4098374.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 @ Mon, 04 Nov 2019 02:58:31: #1 read tag files... INFO @ Mon, 04 Nov 2019 02:58:31: #1 read treatment tags... INFO @ Mon, 04 Nov 2019 02:58:42: 1000000 INFO @ Mon, 04 Nov 2019 02:58:53: 2000000 INFO @ Mon, 04 Nov 2019 02:59:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4098374/SRX4098374.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4098374/SRX4098374.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4098374/SRX4098374.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4098374/SRX4098374.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 @ Mon, 04 Nov 2019 02:59:00: #1 read tag files... INFO @ Mon, 04 Nov 2019 02:59:00: #1 read treatment tags... INFO @ Mon, 04 Nov 2019 02:59:05: 3000000 INFO @ Mon, 04 Nov 2019 02:59:13: 1000000 INFO @ Mon, 04 Nov 2019 02:59:16: 4000000 INFO @ Mon, 04 Nov 2019 02:59:24: 2000000 INFO @ Mon, 04 Nov 2019 02:59:27: 5000000 BedGraph に変換中... INFO @ Mon, 04 Nov 2019 02:59:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4098374/SRX4098374.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4098374/SRX4098374.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4098374/SRX4098374.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4098374/SRX4098374.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 @ Mon, 04 Nov 2019 02:59:31: #1 read tag files... INFO @ Mon, 04 Nov 2019 02:59:31: #1 read treatment tags... INFO @ Mon, 04 Nov 2019 02:59:36: 3000000 INFO @ Mon, 04 Nov 2019 02:59:39: 6000000 INFO @ Mon, 04 Nov 2019 02:59:42: 1000000 INFO @ Mon, 04 Nov 2019 02:59:48: 4000000 INFO @ Mon, 04 Nov 2019 02:59:51: 7000000 INFO @ Mon, 04 Nov 2019 02:59:53: 2000000 INFO @ Mon, 04 Nov 2019 03:00:00: 5000000 INFO @ Mon, 04 Nov 2019 03:00:01: 8000000 INFO @ Mon, 04 Nov 2019 03:00:03: 3000000 INFO @ Mon, 04 Nov 2019 03:00:11: 6000000 INFO @ Mon, 04 Nov 2019 03:00:11: 9000000 INFO @ Mon, 04 Nov 2019 03:00:13: 4000000 INFO @ Mon, 04 Nov 2019 03:00:21: 10000000 INFO @ Mon, 04 Nov 2019 03:00:22: 7000000 INFO @ Mon, 04 Nov 2019 03:00:23: 5000000 INFO @ Mon, 04 Nov 2019 03:00:31: 11000000 INFO @ Mon, 04 Nov 2019 03:00:34: 8000000 INFO @ Mon, 04 Nov 2019 03:00:34: 6000000 INFO @ Mon, 04 Nov 2019 03:00:41: 12000000 INFO @ Mon, 04 Nov 2019 03:00:45: 7000000 INFO @ Mon, 04 Nov 2019 03:00:45: 9000000 INFO @ Mon, 04 Nov 2019 03:00:50: 13000000 INFO @ Mon, 04 Nov 2019 03:00:55: 8000000 INFO @ Mon, 04 Nov 2019 03:00:56: 10000000 INFO @ Mon, 04 Nov 2019 03:01:02: 14000000 INFO @ Mon, 04 Nov 2019 03:01:05: 9000000 INFO @ Mon, 04 Nov 2019 03:01:08: 11000000 INFO @ Mon, 04 Nov 2019 03:01:13: 15000000 INFO @ Mon, 04 Nov 2019 03:01:16: 10000000 INFO @ Mon, 04 Nov 2019 03:01:19: 12000000 INFO @ Mon, 04 Nov 2019 03:01:24: 16000000 INFO @ Mon, 04 Nov 2019 03:01:26: 11000000 INFO @ Mon, 04 Nov 2019 03:01:30: 13000000 INFO @ Mon, 04 Nov 2019 03:01:35: 17000000 INFO @ Mon, 04 Nov 2019 03:01:36: 12000000 INFO @ Mon, 04 Nov 2019 03:01:41: 14000000 INFO @ Mon, 04 Nov 2019 03:01:46: 18000000 INFO @ Mon, 04 Nov 2019 03:01:46: 13000000 INFO @ Mon, 04 Nov 2019 03:01:52: 15000000 INFO @ Mon, 04 Nov 2019 03:01:56: 14000000 INFO @ Mon, 04 Nov 2019 03:01:57: 19000000 INFO @ Mon, 04 Nov 2019 03:02:03: 16000000 INFO @ Mon, 04 Nov 2019 03:02:06: 15000000 INFO @ Mon, 04 Nov 2019 03:02:08: 20000000 INFO @ Mon, 04 Nov 2019 03:02:14: 17000000 INFO @ Mon, 04 Nov 2019 03:02:16: 16000000 INFO @ Mon, 04 Nov 2019 03:02:19: 21000000 INFO @ Mon, 04 Nov 2019 03:02:25: 18000000 INFO @ Mon, 04 Nov 2019 03:02:26: 17000000 INFO @ Mon, 04 Nov 2019 03:02:30: 22000000 INFO @ Mon, 04 Nov 2019 03:02:36: 19000000 INFO @ Mon, 04 Nov 2019 03:02:36: 18000000 INFO @ Mon, 04 Nov 2019 03:02:41: 23000000 INFO @ Mon, 04 Nov 2019 03:02:46: 19000000 INFO @ Mon, 04 Nov 2019 03:02:47: 20000000 INFO @ Mon, 04 Nov 2019 03:02:53: 24000000 INFO @ Mon, 04 Nov 2019 03:02:56: 20000000 INFO @ Mon, 04 Nov 2019 03:02:59: 21000000 INFO @ Mon, 04 Nov 2019 03:03:05: 25000000 INFO @ Mon, 04 Nov 2019 03:03:06: 21000000 INFO @ Mon, 04 Nov 2019 03:03:12: 22000000 INFO @ Mon, 04 Nov 2019 03:03:16: 22000000 INFO @ Mon, 04 Nov 2019 03:03:17: 26000000 INFO @ Mon, 04 Nov 2019 03:03:23: 23000000 INFO @ Mon, 04 Nov 2019 03:03:27: 23000000 INFO @ Mon, 04 Nov 2019 03:03:29: 27000000 INFO @ Mon, 04 Nov 2019 03:03:32: #1 tag size is determined as 75 bps INFO @ Mon, 04 Nov 2019 03:03:32: #1 tag size = 75 INFO @ Mon, 04 Nov 2019 03:03:32: #1 total tags in treatment: 27240168 INFO @ Mon, 04 Nov 2019 03:03:32: #1 user defined the maximum tags... INFO @ Mon, 04 Nov 2019 03:03:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 04 Nov 2019 03:03:33: #1 tags after filtering in treatment: 27240077 INFO @ Mon, 04 Nov 2019 03:03:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 04 Nov 2019 03:03:33: #1 finished! INFO @ Mon, 04 Nov 2019 03:03:33: #2 Build Peak Model... INFO @ Mon, 04 Nov 2019 03:03:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 04 Nov 2019 03:03:35: 24000000 INFO @ Mon, 04 Nov 2019 03:03:37: 24000000 INFO @ Mon, 04 Nov 2019 03:03:37: #2 number of paired peaks: 5507 INFO @ Mon, 04 Nov 2019 03:03:37: start model_add_line... INFO @ Mon, 04 Nov 2019 03:03:37: start X-correlation... INFO @ Mon, 04 Nov 2019 03:03:37: end of X-cor INFO @ Mon, 04 Nov 2019 03:03:37: #2 finished! INFO @ Mon, 04 Nov 2019 03:03:37: #2 predicted fragment length is 77 bps INFO @ Mon, 04 Nov 2019 03:03:37: #2 alternative fragment length(s) may be 77 bps INFO @ Mon, 04 Nov 2019 03:03:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4098374/SRX4098374.05_model.r WARNING @ Mon, 04 Nov 2019 03:03:37: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 04 Nov 2019 03:03:37: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Mon, 04 Nov 2019 03:03:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 04 Nov 2019 03:03:37: #3 Call peaks... INFO @ Mon, 04 Nov 2019 03:03:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 04 Nov 2019 03:03:46: 25000000 INFO @ Mon, 04 Nov 2019 03:03:47: 25000000 INFO @ Mon, 04 Nov 2019 03:03:57: 26000000 INFO @ Mon, 04 Nov 2019 03:03:57: 26000000 INFO @ Mon, 04 Nov 2019 03:04:07: 27000000 INFO @ Mon, 04 Nov 2019 03:04:08: 27000000 INFO @ Mon, 04 Nov 2019 03:04:10: #1 tag size is determined as 75 bps INFO @ Mon, 04 Nov 2019 03:04:10: #1 tag size = 75 INFO @ Mon, 04 Nov 2019 03:04:10: #1 total tags in treatment: 27240168 INFO @ Mon, 04 Nov 2019 03:04:10: #1 user defined the maximum tags... INFO @ Mon, 04 Nov 2019 03:04:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 04 Nov 2019 03:04:10: #1 tags after filtering in treatment: 27240077 INFO @ Mon, 04 Nov 2019 03:04:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 04 Nov 2019 03:04:10: #1 finished! INFO @ Mon, 04 Nov 2019 03:04:10: #2 Build Peak Model... INFO @ Mon, 04 Nov 2019 03:04:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 04 Nov 2019 03:04:11: #1 tag size is determined as 75 bps INFO @ Mon, 04 Nov 2019 03:04:11: #1 tag size = 75 INFO @ Mon, 04 Nov 2019 03:04:11: #1 total tags in treatment: 27240168 INFO @ Mon, 04 Nov 2019 03:04:11: #1 user defined the maximum tags... INFO @ Mon, 04 Nov 2019 03:04:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 04 Nov 2019 03:04:12: #1 tags after filtering in treatment: 27240077 INFO @ Mon, 04 Nov 2019 03:04:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 04 Nov 2019 03:04:12: #1 finished! INFO @ Mon, 04 Nov 2019 03:04:12: #2 Build Peak Model... INFO @ Mon, 04 Nov 2019 03:04:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 04 Nov 2019 03:04:14: #2 number of paired peaks: 5507 INFO @ Mon, 04 Nov 2019 03:04:14: start model_add_line... INFO @ Mon, 04 Nov 2019 03:04:14: start X-correlation... INFO @ Mon, 04 Nov 2019 03:04:14: end of X-cor INFO @ Mon, 04 Nov 2019 03:04:14: #2 finished! INFO @ Mon, 04 Nov 2019 03:04:14: #2 predicted fragment length is 77 bps INFO @ Mon, 04 Nov 2019 03:04:14: #2 alternative fragment length(s) may be 77 bps INFO @ Mon, 04 Nov 2019 03:04:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4098374/SRX4098374.20_model.r WARNING @ Mon, 04 Nov 2019 03:04:14: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 04 Nov 2019 03:04:14: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Mon, 04 Nov 2019 03:04:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 04 Nov 2019 03:04:14: #3 Call peaks... INFO @ Mon, 04 Nov 2019 03:04:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 04 Nov 2019 03:04:15: #2 number of paired peaks: 5507 INFO @ Mon, 04 Nov 2019 03:04:15: start model_add_line... INFO @ Mon, 04 Nov 2019 03:04:15: start X-correlation... INFO @ Mon, 04 Nov 2019 03:04:15: end of X-cor INFO @ Mon, 04 Nov 2019 03:04:15: #2 finished! INFO @ Mon, 04 Nov 2019 03:04:15: #2 predicted fragment length is 77 bps INFO @ Mon, 04 Nov 2019 03:04:15: #2 alternative fragment length(s) may be 77 bps INFO @ Mon, 04 Nov 2019 03:04:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4098374/SRX4098374.10_model.r WARNING @ Mon, 04 Nov 2019 03:04:15: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 04 Nov 2019 03:04:15: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Mon, 04 Nov 2019 03:04:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 04 Nov 2019 03:04:15: #3 Call peaks... INFO @ Mon, 04 Nov 2019 03:04:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 04 Nov 2019 03:05:10: #3 Call peaks for each chromosome... INFO @ Mon, 04 Nov 2019 03:05:47: #3 Call peaks for each chromosome... INFO @ Mon, 04 Nov 2019 03:05:50: #3 Call peaks for each chromosome... INFO @ Mon, 04 Nov 2019 03:05:58: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4098374/SRX4098374.05_peaks.xls INFO @ Mon, 04 Nov 2019 03:05:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4098374/SRX4098374.05_peaks.narrowPeak INFO @ Mon, 04 Nov 2019 03:05:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4098374/SRX4098374.05_summits.bed INFO @ Mon, 04 Nov 2019 03:05:58: Done! pass1 - making usageList (66 chroms): 8 millis pass2 - checking and writing primary data (1767 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 04 Nov 2019 03:06:36: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4098374/SRX4098374.10_peaks.xls INFO @ Mon, 04 Nov 2019 03:06:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4098374/SRX4098374.10_peaks.narrowPeak INFO @ Mon, 04 Nov 2019 03:06:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4098374/SRX4098374.10_summits.bed INFO @ Mon, 04 Nov 2019 03:06:36: Done! pass1 - making usageList (55 chroms): 1 millis pass2 - checking and writing primary data (922 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 04 Nov 2019 03:06:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4098374/SRX4098374.20_peaks.xls INFO @ Mon, 04 Nov 2019 03:06:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4098374/SRX4098374.20_peaks.narrowPeak INFO @ Mon, 04 Nov 2019 03:06:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4098374/SRX4098374.20_summits.bed INFO @ Mon, 04 Nov 2019 03:06:41: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (480 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。