Job ID = 2590502 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,177,236 reads read : 28,354,472 reads written : 14,177,236 reads 0-length : 14,177,236 2019-08-12T13:08:09 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 14,357,215 reads read : 28,714,430 reads written : 14,357,215 reads 0-length : 14,357,215 spots read : 14,388,099 reads read : 28,776,198 reads written : 14,388,099 reads 0-length : 14,388,099 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: 00:00:01 Multiseed full-index search: 00:14:10 42922550 reads; of these: 42922550 (100.00%) were unpaired; of these: 1067925 (2.49%) aligned 0 times 33002563 (76.89%) aligned exactly 1 time 8852062 (20.62%) aligned >1 times 97.51% overall alignment rate Time searching: 00:14:11 Overall time: 00:14:11 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 20 files... [bam_rmdupse_core] 14062468 / 41854625 = 0.3360 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, 12 Aug 2019 22:41:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981729/SRX3981729.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981729/SRX3981729.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981729/SRX3981729.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981729/SRX3981729.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, 12 Aug 2019 22:41:51: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:41:51: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:41:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981729/SRX3981729.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981729/SRX3981729.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981729/SRX3981729.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981729/SRX3981729.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, 12 Aug 2019 22:41:52: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:41:52: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:41:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981729/SRX3981729.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981729/SRX3981729.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981729/SRX3981729.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981729/SRX3981729.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, 12 Aug 2019 22:41:53: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:41:53: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:41:58: 1000000 INFO @ Mon, 12 Aug 2019 22:41:59: 1000000 INFO @ Mon, 12 Aug 2019 22:42:01: 1000000 INFO @ Mon, 12 Aug 2019 22:42:05: 2000000 INFO @ Mon, 12 Aug 2019 22:42:06: 2000000 INFO @ Mon, 12 Aug 2019 22:42:09: 2000000 INFO @ Mon, 12 Aug 2019 22:42:12: 3000000 INFO @ Mon, 12 Aug 2019 22:42:13: 3000000 INFO @ Mon, 12 Aug 2019 22:42:16: 3000000 INFO @ Mon, 12 Aug 2019 22:42:20: 4000000 INFO @ Mon, 12 Aug 2019 22:42:20: 4000000 INFO @ Mon, 12 Aug 2019 22:42:24: 4000000 INFO @ Mon, 12 Aug 2019 22:42:27: 5000000 INFO @ Mon, 12 Aug 2019 22:42:28: 5000000 INFO @ Mon, 12 Aug 2019 22:42:32: 5000000 INFO @ Mon, 12 Aug 2019 22:42:34: 6000000 INFO @ Mon, 12 Aug 2019 22:42:35: 6000000 INFO @ Mon, 12 Aug 2019 22:42:40: 6000000 INFO @ Mon, 12 Aug 2019 22:42:41: 7000000 INFO @ Mon, 12 Aug 2019 22:42:42: 7000000 INFO @ Mon, 12 Aug 2019 22:42:48: 7000000 INFO @ Mon, 12 Aug 2019 22:42:48: 8000000 INFO @ Mon, 12 Aug 2019 22:42:49: 8000000 INFO @ Mon, 12 Aug 2019 22:42:56: 9000000 INFO @ Mon, 12 Aug 2019 22:42:56: 8000000 INFO @ Mon, 12 Aug 2019 22:42:57: 9000000 INFO @ Mon, 12 Aug 2019 22:43:03: 10000000 INFO @ Mon, 12 Aug 2019 22:43:04: 10000000 INFO @ Mon, 12 Aug 2019 22:43:04: 9000000 INFO @ Mon, 12 Aug 2019 22:43:10: 11000000 INFO @ Mon, 12 Aug 2019 22:43:11: 11000000 INFO @ Mon, 12 Aug 2019 22:43:12: 10000000 INFO @ Mon, 12 Aug 2019 22:43:17: 12000000 INFO @ Mon, 12 Aug 2019 22:43:18: 12000000 INFO @ Mon, 12 Aug 2019 22:43:19: 11000000 INFO @ Mon, 12 Aug 2019 22:43:24: 13000000 INFO @ Mon, 12 Aug 2019 22:43:25: 13000000 INFO @ Mon, 12 Aug 2019 22:43:27: 12000000 INFO @ Mon, 12 Aug 2019 22:43:32: 14000000 INFO @ Mon, 12 Aug 2019 22:43:32: 14000000 INFO @ Mon, 12 Aug 2019 22:43:35: 13000000 INFO @ Mon, 12 Aug 2019 22:43:39: 15000000 INFO @ Mon, 12 Aug 2019 22:43:39: 15000000 INFO @ Mon, 12 Aug 2019 22:43:43: 14000000 INFO @ Mon, 12 Aug 2019 22:43:46: 16000000 INFO @ Mon, 12 Aug 2019 22:43:47: 16000000 INFO @ Mon, 12 Aug 2019 22:43:51: 15000000 INFO @ Mon, 12 Aug 2019 22:43:53: 17000000 INFO @ Mon, 12 Aug 2019 22:43:54: 17000000 INFO @ Mon, 12 Aug 2019 22:43:58: 16000000 INFO @ Mon, 12 Aug 2019 22:44:00: 18000000 INFO @ Mon, 12 Aug 2019 22:44:01: 18000000 INFO @ Mon, 12 Aug 2019 22:44:06: 17000000 INFO @ Mon, 12 Aug 2019 22:44:08: 19000000 INFO @ Mon, 12 Aug 2019 22:44:09: 19000000 INFO @ Mon, 12 Aug 2019 22:44:14: 18000000 INFO @ Mon, 12 Aug 2019 22:44:15: 20000000 INFO @ Mon, 12 Aug 2019 22:44:16: 20000000 INFO @ Mon, 12 Aug 2019 22:44:22: 19000000 INFO @ Mon, 12 Aug 2019 22:44:22: 21000000 INFO @ Mon, 12 Aug 2019 22:44:23: 21000000 INFO @ Mon, 12 Aug 2019 22:44:30: 22000000 INFO @ Mon, 12 Aug 2019 22:44:30: 20000000 INFO @ Mon, 12 Aug 2019 22:44:30: 22000000 INFO @ Mon, 12 Aug 2019 22:44:37: 23000000 INFO @ Mon, 12 Aug 2019 22:44:37: 23000000 INFO @ Mon, 12 Aug 2019 22:44:38: 21000000 INFO @ Mon, 12 Aug 2019 22:44:44: 24000000 INFO @ Mon, 12 Aug 2019 22:44:45: 24000000 INFO @ Mon, 12 Aug 2019 22:44:46: 22000000 INFO @ Mon, 12 Aug 2019 22:44:51: 25000000 INFO @ Mon, 12 Aug 2019 22:44:52: 25000000 INFO @ Mon, 12 Aug 2019 22:44:54: 23000000 INFO @ Mon, 12 Aug 2019 22:44:58: 26000000 INFO @ Mon, 12 Aug 2019 22:44:59: 26000000 INFO @ Mon, 12 Aug 2019 22:45:01: 24000000 INFO @ Mon, 12 Aug 2019 22:45:06: 27000000 INFO @ Mon, 12 Aug 2019 22:45:06: 27000000 INFO @ Mon, 12 Aug 2019 22:45:09: 25000000 INFO @ Mon, 12 Aug 2019 22:45:12: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:45:12: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:45:12: #1 total tags in treatment: 27792157 INFO @ Mon, 12 Aug 2019 22:45:12: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:45:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:45:12: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:45:12: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:45:12: #1 total tags in treatment: 27792157 INFO @ Mon, 12 Aug 2019 22:45:12: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:45:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:45:12: #1 tags after filtering in treatment: 27792157 INFO @ Mon, 12 Aug 2019 22:45:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:45:12: #1 finished! INFO @ Mon, 12 Aug 2019 22:45:12: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:45:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:45:13: #1 tags after filtering in treatment: 27792157 INFO @ Mon, 12 Aug 2019 22:45:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:45:13: #1 finished! INFO @ Mon, 12 Aug 2019 22:45:13: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:45:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:45:15: #2 number of paired peaks: 3003 INFO @ Mon, 12 Aug 2019 22:45:15: start model_add_line... INFO @ Mon, 12 Aug 2019 22:45:15: start X-correlation... INFO @ Mon, 12 Aug 2019 22:45:15: end of X-cor INFO @ Mon, 12 Aug 2019 22:45:15: #2 finished! INFO @ Mon, 12 Aug 2019 22:45:15: #2 predicted fragment length is 211 bps INFO @ Mon, 12 Aug 2019 22:45:15: #2 alternative fragment length(s) may be 4,211 bps INFO @ Mon, 12 Aug 2019 22:45:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981729/SRX3981729.05_model.r INFO @ Mon, 12 Aug 2019 22:45:15: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:45:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:45:15: #2 number of paired peaks: 3003 INFO @ Mon, 12 Aug 2019 22:45:15: start model_add_line... INFO @ Mon, 12 Aug 2019 22:45:16: start X-correlation... INFO @ Mon, 12 Aug 2019 22:45:16: end of X-cor INFO @ Mon, 12 Aug 2019 22:45:16: #2 finished! INFO @ Mon, 12 Aug 2019 22:45:16: #2 predicted fragment length is 211 bps INFO @ Mon, 12 Aug 2019 22:45:16: #2 alternative fragment length(s) may be 4,211 bps INFO @ Mon, 12 Aug 2019 22:45:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981729/SRX3981729.10_model.r INFO @ Mon, 12 Aug 2019 22:45:16: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:45:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:45:17: 26000000 INFO @ Mon, 12 Aug 2019 22:45:24: 27000000 INFO @ Mon, 12 Aug 2019 22:45:31: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:45:31: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:45:31: #1 total tags in treatment: 27792157 INFO @ Mon, 12 Aug 2019 22:45:31: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:45:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:45:31: #1 tags after filtering in treatment: 27792157 INFO @ Mon, 12 Aug 2019 22:45:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:45:31: #1 finished! INFO @ Mon, 12 Aug 2019 22:45:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:45:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:45:34: #2 number of paired peaks: 3003 INFO @ Mon, 12 Aug 2019 22:45:34: start model_add_line... INFO @ Mon, 12 Aug 2019 22:45:34: start X-correlation... INFO @ Mon, 12 Aug 2019 22:45:34: end of X-cor INFO @ Mon, 12 Aug 2019 22:45:34: #2 finished! INFO @ Mon, 12 Aug 2019 22:45:34: #2 predicted fragment length is 211 bps INFO @ Mon, 12 Aug 2019 22:45:34: #2 alternative fragment length(s) may be 4,211 bps INFO @ Mon, 12 Aug 2019 22:45:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981729/SRX3981729.20_model.r INFO @ Mon, 12 Aug 2019 22:45:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:45:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:46:46: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:46:47: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:47:05: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:47:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981729/SRX3981729.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:47:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981729/SRX3981729.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:47:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981729/SRX3981729.05_summits.bed INFO @ Mon, 12 Aug 2019 22:47:17: Done! INFO @ Mon, 12 Aug 2019 22:47:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981729/SRX3981729.10_peaks.xls pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (10272 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:47:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981729/SRX3981729.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:47:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981729/SRX3981729.10_summits.bed INFO @ Mon, 12 Aug 2019 22:47:17: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7778 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:47:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981729/SRX3981729.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:47:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981729/SRX3981729.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:47:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981729/SRX3981729.20_summits.bed INFO @ Mon, 12 Aug 2019 22:47:35: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5159 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。