Job ID = 1295732 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 21,141,173 reads read : 42,282,346 reads written : 42,282,346 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 04:30:35 21141173 reads; of these: 21141173 (100.00%) were paired; of these: 6995217 (33.09%) aligned concordantly 0 times 8348501 (39.49%) aligned concordantly exactly 1 time 5797455 (27.42%) aligned concordantly >1 times ---- 6995217 pairs aligned concordantly 0 times; of these: 147217 (2.10%) aligned discordantly 1 time ---- 6848000 pairs aligned 0 times concordantly or discordantly; of these: 13696000 mates make up the pairs; of these: 4919810 (35.92%) aligned 0 times 432438 (3.16%) aligned exactly 1 time 8343752 (60.92%) aligned >1 times 88.36% overall alignment rate Time searching: 04:30:35 Overall time: 04:30:35 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 28 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1854282 / 2412438 = 0.7686 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 @ Mon, 03 Jun 2019 20:42:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4453994/SRX4453994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4453994/SRX4453994.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4453994/SRX4453994.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4453994/SRX4453994.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 @ Mon, 03 Jun 2019 20:42:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:42:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:42:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4453994/SRX4453994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4453994/SRX4453994.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4453994/SRX4453994.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4453994/SRX4453994.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 @ Mon, 03 Jun 2019 20:42:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:42:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:42:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4453994/SRX4453994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4453994/SRX4453994.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4453994/SRX4453994.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4453994/SRX4453994.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 @ Mon, 03 Jun 2019 20:42:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:42:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:42:40: 1000000 INFO @ Mon, 03 Jun 2019 20:42:41: 1000000 INFO @ Mon, 03 Jun 2019 20:42:43: 1000000 INFO @ Mon, 03 Jun 2019 20:42:51: 2000000 INFO @ Mon, 03 Jun 2019 20:42:52: 2000000 INFO @ Mon, 03 Jun 2019 20:42:56: 2000000 INFO @ Mon, 03 Jun 2019 20:43:02: 3000000 INFO @ Mon, 03 Jun 2019 20:43:04: 3000000 INFO @ Mon, 03 Jun 2019 20:43:10: 3000000 INFO @ Mon, 03 Jun 2019 20:43:13: 4000000 INFO @ Mon, 03 Jun 2019 20:43:14: 4000000 INFO @ Mon, 03 Jun 2019 20:43:23: 4000000 INFO @ Mon, 03 Jun 2019 20:43:24: 5000000 INFO @ Mon, 03 Jun 2019 20:43:25: 5000000 INFO @ Mon, 03 Jun 2019 20:43:34: 6000000 INFO @ Mon, 03 Jun 2019 20:43:36: 6000000 INFO @ Mon, 03 Jun 2019 20:43:37: 5000000 INFO @ Mon, 03 Jun 2019 20:43:44: 7000000 INFO @ Mon, 03 Jun 2019 20:43:46: 7000000 INFO @ Mon, 03 Jun 2019 20:43:50: 6000000 INFO @ Mon, 03 Jun 2019 20:43:55: 8000000 INFO @ Mon, 03 Jun 2019 20:43:57: 8000000 INFO @ Mon, 03 Jun 2019 20:44:02: 7000000 INFO @ Mon, 03 Jun 2019 20:44:06: 9000000 INFO @ Mon, 03 Jun 2019 20:44:08: 9000000 INFO @ Mon, 03 Jun 2019 20:44:16: 10000000 INFO @ Mon, 03 Jun 2019 20:44:16: 8000000 INFO @ Mon, 03 Jun 2019 20:44:18: 10000000 INFO @ Mon, 03 Jun 2019 20:44:26: 11000000 INFO @ Mon, 03 Jun 2019 20:44:29: 9000000 INFO @ Mon, 03 Jun 2019 20:44:30: 11000000 INFO @ Mon, 03 Jun 2019 20:44:37: 12000000 INFO @ Mon, 03 Jun 2019 20:44:40: 12000000 INFO @ Mon, 03 Jun 2019 20:44:42: 10000000 INFO @ Mon, 03 Jun 2019 20:44:47: 13000000 INFO @ Mon, 03 Jun 2019 20:44:51: 13000000 INFO @ Mon, 03 Jun 2019 20:44:56: 11000000 INFO @ Mon, 03 Jun 2019 20:44:58: 14000000 INFO @ Mon, 03 Jun 2019 20:45:03: 14000000 INFO @ Mon, 03 Jun 2019 20:45:08: 15000000 INFO @ Mon, 03 Jun 2019 20:45:10: 12000000 INFO @ Mon, 03 Jun 2019 20:45:14: 15000000 INFO @ Mon, 03 Jun 2019 20:45:19: 16000000 INFO @ Mon, 03 Jun 2019 20:45:24: 13000000 INFO @ Mon, 03 Jun 2019 20:45:26: 16000000 INFO @ Mon, 03 Jun 2019 20:45:30: 17000000 INFO @ Mon, 03 Jun 2019 20:45:37: 14000000 INFO @ Mon, 03 Jun 2019 20:45:37: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 20:45:42: 18000000 BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 20:45:50: 18000000 INFO @ Mon, 03 Jun 2019 20:45:50: 15000000 INFO @ Mon, 03 Jun 2019 20:45:55: 19000000 INFO @ Mon, 03 Jun 2019 20:46:03: 19000000 INFO @ Mon, 03 Jun 2019 20:46:04: 16000000 INFO @ Mon, 03 Jun 2019 20:46:08: 20000000 INFO @ Mon, 03 Jun 2019 20:46:16: 20000000 INFO @ Mon, 03 Jun 2019 20:46:18: 17000000 INFO @ Mon, 03 Jun 2019 20:46:20: 21000000 INFO @ Mon, 03 Jun 2019 20:46:28: 21000000 INFO @ Mon, 03 Jun 2019 20:46:32: 22000000 INFO @ Mon, 03 Jun 2019 20:46:34: 18000000 INFO @ Mon, 03 Jun 2019 20:46:42: 22000000 INFO @ Mon, 03 Jun 2019 20:46:46: 23000000 INFO @ Mon, 03 Jun 2019 20:46:50: 19000000 INFO @ Mon, 03 Jun 2019 20:46:56: 23000000 INFO @ Mon, 03 Jun 2019 20:46:58: 24000000 INFO @ Mon, 03 Jun 2019 20:47:06: 20000000 INFO @ Mon, 03 Jun 2019 20:47:08: 24000000 INFO @ Mon, 03 Jun 2019 20:47:10: 25000000 INFO @ Mon, 03 Jun 2019 20:47:20: 25000000 INFO @ Mon, 03 Jun 2019 20:47:21: 21000000 INFO @ Mon, 03 Jun 2019 20:47:22: 26000000 INFO @ Mon, 03 Jun 2019 20:47:33: 26000000 INFO @ Mon, 03 Jun 2019 20:47:34: 27000000 INFO @ Mon, 03 Jun 2019 20:47:36: 22000000 INFO @ Mon, 03 Jun 2019 20:47:45: 27000000 INFO @ Mon, 03 Jun 2019 20:47:45: 28000000 INFO @ Mon, 03 Jun 2019 20:47:51: 23000000 INFO @ Mon, 03 Jun 2019 20:47:57: 28000000 INFO @ Mon, 03 Jun 2019 20:47:57: 29000000 INFO @ Mon, 03 Jun 2019 20:48:06: 24000000 INFO @ Mon, 03 Jun 2019 20:48:09: 29000000 INFO @ Mon, 03 Jun 2019 20:48:09: 30000000 INFO @ Mon, 03 Jun 2019 20:48:21: 25000000 INFO @ Mon, 03 Jun 2019 20:48:21: 30000000 INFO @ Mon, 03 Jun 2019 20:48:22: 31000000 INFO @ Mon, 03 Jun 2019 20:48:33: 32000000 INFO @ Mon, 03 Jun 2019 20:48:34: 31000000 INFO @ Mon, 03 Jun 2019 20:48:36: 26000000 INFO @ Mon, 03 Jun 2019 20:48:43: 33000000 INFO @ Mon, 03 Jun 2019 20:48:45: 32000000 INFO @ Mon, 03 Jun 2019 20:48:50: 27000000 INFO @ Mon, 03 Jun 2019 20:48:50: #1 tag size is determined as 118 bps INFO @ Mon, 03 Jun 2019 20:48:50: #1 tag size = 118 INFO @ Mon, 03 Jun 2019 20:48:50: #1 total tags in treatment: 12323859 INFO @ Mon, 03 Jun 2019 20:48:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:48:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 20:48:50: #1 tags after filtering in treatment: 1512139 INFO @ Mon, 03 Jun 2019 20:48:50: #1 Redundant rate of treatment: 0.88 INFO @ Mon, 03 Jun 2019 20:48:50: #1 finished! INFO @ Mon, 03 Jun 2019 20:48:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:48:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:48:51: #2 number of paired peaks: 5012 INFO @ Mon, 03 Jun 2019 20:48:51: start model_add_line... INFO @ Mon, 03 Jun 2019 20:48:51: start X-correlation... INFO @ Mon, 03 Jun 2019 20:48:51: end of X-cor INFO @ Mon, 03 Jun 2019 20:48:51: #2 finished! INFO @ Mon, 03 Jun 2019 20:48:51: #2 predicted fragment length is 132 bps INFO @ Mon, 03 Jun 2019 20:48:51: #2 alternative fragment length(s) may be 132 bps INFO @ Mon, 03 Jun 2019 20:48:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4453994/SRX4453994.10_model.r WARNING @ Mon, 03 Jun 2019 20:48:51: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:48:51: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Mon, 03 Jun 2019 20:48:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 20:48:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:48:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:48:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:48:56: 33000000 INFO @ Mon, 03 Jun 2019 20:48:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4453994/SRX4453994.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:48:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4453994/SRX4453994.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:48:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4453994/SRX4453994.10_summits.bed INFO @ Mon, 03 Jun 2019 20:48:58: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1316 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:49:03: #1 tag size is determined as 118 bps INFO @ Mon, 03 Jun 2019 20:49:03: #1 tag size = 118 INFO @ Mon, 03 Jun 2019 20:49:03: #1 total tags in treatment: 12323859 INFO @ Mon, 03 Jun 2019 20:49:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:49:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 20:49:03: #1 tags after filtering in treatment: 1512139 INFO @ Mon, 03 Jun 2019 20:49:03: #1 Redundant rate of treatment: 0.88 INFO @ Mon, 03 Jun 2019 20:49:03: #1 finished! INFO @ Mon, 03 Jun 2019 20:49:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:49:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:49:03: 28000000 INFO @ Mon, 03 Jun 2019 20:49:04: #2 number of paired peaks: 5012 INFO @ Mon, 03 Jun 2019 20:49:04: start model_add_line... INFO @ Mon, 03 Jun 2019 20:49:04: start X-correlation... INFO @ Mon, 03 Jun 2019 20:49:04: end of X-cor INFO @ Mon, 03 Jun 2019 20:49:04: #2 finished! INFO @ Mon, 03 Jun 2019 20:49:04: #2 predicted fragment length is 132 bps INFO @ Mon, 03 Jun 2019 20:49:04: #2 alternative fragment length(s) may be 132 bps INFO @ Mon, 03 Jun 2019 20:49:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4453994/SRX4453994.05_model.r WARNING @ Mon, 03 Jun 2019 20:49:04: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:49:04: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Mon, 03 Jun 2019 20:49:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 20:49:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:49:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:49:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:49:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4453994/SRX4453994.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:49:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4453994/SRX4453994.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:49:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4453994/SRX4453994.05_summits.bed INFO @ Mon, 03 Jun 2019 20:49:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3605 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:49:17: 29000000 INFO @ Mon, 03 Jun 2019 20:49:31: 30000000 INFO @ Mon, 03 Jun 2019 20:49:45: 31000000 INFO @ Mon, 03 Jun 2019 20:49:57: 32000000 INFO @ Mon, 03 Jun 2019 20:50:10: 33000000 INFO @ Mon, 03 Jun 2019 20:50:17: #1 tag size is determined as 118 bps INFO @ Mon, 03 Jun 2019 20:50:17: #1 tag size = 118 INFO @ Mon, 03 Jun 2019 20:50:17: #1 total tags in treatment: 12323859 INFO @ Mon, 03 Jun 2019 20:50:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:50:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 20:50:17: #1 tags after filtering in treatment: 1512139 INFO @ Mon, 03 Jun 2019 20:50:17: #1 Redundant rate of treatment: 0.88 INFO @ Mon, 03 Jun 2019 20:50:17: #1 finished! INFO @ Mon, 03 Jun 2019 20:50:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:50:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:50:18: #2 number of paired peaks: 5012 INFO @ Mon, 03 Jun 2019 20:50:18: start model_add_line... INFO @ Mon, 03 Jun 2019 20:50:18: start X-correlation... INFO @ Mon, 03 Jun 2019 20:50:18: end of X-cor INFO @ Mon, 03 Jun 2019 20:50:18: #2 finished! INFO @ Mon, 03 Jun 2019 20:50:18: #2 predicted fragment length is 132 bps INFO @ Mon, 03 Jun 2019 20:50:18: #2 alternative fragment length(s) may be 132 bps INFO @ Mon, 03 Jun 2019 20:50:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4453994/SRX4453994.20_model.r WARNING @ Mon, 03 Jun 2019 20:50:18: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:50:18: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Mon, 03 Jun 2019 20:50:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 20:50:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:50:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:50:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:50:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4453994/SRX4453994.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:50:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4453994/SRX4453994.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:50:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4453994/SRX4453994.20_summits.bed INFO @ Mon, 03 Jun 2019 20:50:25: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (390 records, 4 fields): 4 millis CompletedMACS2peakCalling