Job ID = 2590346 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T11:53:18 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 ) 2019-08-12T11:53:18 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 ) 2019-08-12T11:53:51 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 : 12,025,795 reads read : 24,051,590 reads written : 12,025,795 reads 0-length : 12,025,795 spots read : 11,846,281 reads read : 23,692,562 reads written : 11,846,281 reads 0-length : 11,846,281 spots read : 12,013,653 reads read : 24,027,306 reads written : 12,013,653 reads 0-length : 12,013,653 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: 00:10:54 35885729 reads; of these: 35885729 (100.00%) were unpaired; of these: 1477473 (4.12%) aligned 0 times 27181028 (75.74%) aligned exactly 1 time 7227228 (20.14%) aligned >1 times 95.88% overall alignment rate Time searching: 00:10:54 Overall time: 00:10:54 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 16 files... [bam_rmdupse_core] 5008272 / 34408256 = 0.1456 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 21:25:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981621/SRX3981621.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981621/SRX3981621.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981621/SRX3981621.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981621/SRX3981621.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 21:25:45: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:25:45: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:25:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981621/SRX3981621.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981621/SRX3981621.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981621/SRX3981621.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981621/SRX3981621.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 21:25:46: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:25:46: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:25:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981621/SRX3981621.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981621/SRX3981621.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981621/SRX3981621.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981621/SRX3981621.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 21:25:47: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:25:47: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:25:54: 1000000 INFO @ Mon, 12 Aug 2019 21:25:56: 1000000 INFO @ Mon, 12 Aug 2019 21:25:57: 1000000 INFO @ Mon, 12 Aug 2019 21:26:01: 2000000 INFO @ Mon, 12 Aug 2019 21:26:05: 2000000 INFO @ Mon, 12 Aug 2019 21:26:07: 2000000 INFO @ Mon, 12 Aug 2019 21:26:09: 3000000 INFO @ Mon, 12 Aug 2019 21:26:15: 3000000 INFO @ Mon, 12 Aug 2019 21:26:16: 4000000 INFO @ Mon, 12 Aug 2019 21:26:17: 3000000 INFO @ Mon, 12 Aug 2019 21:26:23: 5000000 INFO @ Mon, 12 Aug 2019 21:26:25: 4000000 INFO @ Mon, 12 Aug 2019 21:26:27: 4000000 INFO @ Mon, 12 Aug 2019 21:26:30: 6000000 INFO @ Mon, 12 Aug 2019 21:26:35: 5000000 INFO @ Mon, 12 Aug 2019 21:26:37: 5000000 INFO @ Mon, 12 Aug 2019 21:26:37: 7000000 INFO @ Mon, 12 Aug 2019 21:26:44: 8000000 INFO @ Mon, 12 Aug 2019 21:26:44: 6000000 INFO @ Mon, 12 Aug 2019 21:26:46: 6000000 INFO @ Mon, 12 Aug 2019 21:26:51: 9000000 INFO @ Mon, 12 Aug 2019 21:26:53: 7000000 INFO @ Mon, 12 Aug 2019 21:26:54: 7000000 INFO @ Mon, 12 Aug 2019 21:26:58: 10000000 INFO @ Mon, 12 Aug 2019 21:27:01: 8000000 INFO @ Mon, 12 Aug 2019 21:27:01: 8000000 INFO @ Mon, 12 Aug 2019 21:27:05: 11000000 INFO @ Mon, 12 Aug 2019 21:27:08: 9000000 INFO @ Mon, 12 Aug 2019 21:27:09: 9000000 INFO @ Mon, 12 Aug 2019 21:27:12: 12000000 INFO @ Mon, 12 Aug 2019 21:27:15: 10000000 INFO @ Mon, 12 Aug 2019 21:27:17: 10000000 INFO @ Mon, 12 Aug 2019 21:27:19: 13000000 INFO @ Mon, 12 Aug 2019 21:27:21: 11000000 INFO @ Mon, 12 Aug 2019 21:27:25: 11000000 INFO @ Mon, 12 Aug 2019 21:27:26: 14000000 INFO @ Mon, 12 Aug 2019 21:27:28: 12000000 INFO @ Mon, 12 Aug 2019 21:27:33: 15000000 INFO @ Mon, 12 Aug 2019 21:27:33: 12000000 INFO @ Mon, 12 Aug 2019 21:27:34: 13000000 INFO @ Mon, 12 Aug 2019 21:27:40: 16000000 INFO @ Mon, 12 Aug 2019 21:27:40: 14000000 INFO @ Mon, 12 Aug 2019 21:27:41: 13000000 INFO @ Mon, 12 Aug 2019 21:27:47: 17000000 INFO @ Mon, 12 Aug 2019 21:27:47: 15000000 INFO @ Mon, 12 Aug 2019 21:27:49: 14000000 INFO @ Mon, 12 Aug 2019 21:27:53: 16000000 INFO @ Mon, 12 Aug 2019 21:27:54: 18000000 INFO @ Mon, 12 Aug 2019 21:27:57: 15000000 INFO @ Mon, 12 Aug 2019 21:27:59: 17000000 INFO @ Mon, 12 Aug 2019 21:28:00: 19000000 INFO @ Mon, 12 Aug 2019 21:28:05: 16000000 INFO @ Mon, 12 Aug 2019 21:28:06: 18000000 INFO @ Mon, 12 Aug 2019 21:28:07: 20000000 INFO @ Mon, 12 Aug 2019 21:28:12: 19000000 INFO @ Mon, 12 Aug 2019 21:28:13: 17000000 INFO @ Mon, 12 Aug 2019 21:28:14: 21000000 INFO @ Mon, 12 Aug 2019 21:28:18: 20000000 INFO @ Mon, 12 Aug 2019 21:28:21: 18000000 INFO @ Mon, 12 Aug 2019 21:28:21: 22000000 INFO @ Mon, 12 Aug 2019 21:28:25: 21000000 INFO @ Mon, 12 Aug 2019 21:28:28: 23000000 INFO @ Mon, 12 Aug 2019 21:28:29: 19000000 INFO @ Mon, 12 Aug 2019 21:28:31: 22000000 INFO @ Mon, 12 Aug 2019 21:28:35: 24000000 INFO @ Mon, 12 Aug 2019 21:28:37: 20000000 INFO @ Mon, 12 Aug 2019 21:28:37: 23000000 INFO @ Mon, 12 Aug 2019 21:28:42: 25000000 INFO @ Mon, 12 Aug 2019 21:28:44: 24000000 INFO @ Mon, 12 Aug 2019 21:28:45: 21000000 INFO @ Mon, 12 Aug 2019 21:28:49: 26000000 INFO @ Mon, 12 Aug 2019 21:28:50: 25000000 INFO @ Mon, 12 Aug 2019 21:28:53: 22000000 INFO @ Mon, 12 Aug 2019 21:28:56: 27000000 INFO @ Mon, 12 Aug 2019 21:28:56: 26000000 INFO @ Mon, 12 Aug 2019 21:29:01: 23000000 INFO @ Mon, 12 Aug 2019 21:29:02: 28000000 INFO @ Mon, 12 Aug 2019 21:29:03: 27000000 INFO @ Mon, 12 Aug 2019 21:29:09: 24000000 INFO @ Mon, 12 Aug 2019 21:29:09: 28000000 INFO @ Mon, 12 Aug 2019 21:29:09: 29000000 INFO @ Mon, 12 Aug 2019 21:29:12: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:29:12: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:29:12: #1 total tags in treatment: 29399984 INFO @ Mon, 12 Aug 2019 21:29:12: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:29:12: #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 21:29:13: #1 tags after filtering in treatment: 29399984 INFO @ Mon, 12 Aug 2019 21:29:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:29:13: #1 finished! INFO @ Mon, 12 Aug 2019 21:29:13: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:29:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:29:16: #2 number of paired peaks: 322 WARNING @ Mon, 12 Aug 2019 21:29:16: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Mon, 12 Aug 2019 21:29:16: start model_add_line... INFO @ Mon, 12 Aug 2019 21:29:16: 29000000 INFO @ Mon, 12 Aug 2019 21:29:16: start X-correlation... INFO @ Mon, 12 Aug 2019 21:29:16: end of X-cor INFO @ Mon, 12 Aug 2019 21:29:16: #2 finished! INFO @ Mon, 12 Aug 2019 21:29:16: #2 predicted fragment length is 117 bps INFO @ Mon, 12 Aug 2019 21:29:16: #2 alternative fragment length(s) may be 3,117 bps INFO @ Mon, 12 Aug 2019 21:29:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981621/SRX3981621.10_model.r INFO @ Mon, 12 Aug 2019 21:29:16: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:29:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:29:17: 25000000 INFO @ Mon, 12 Aug 2019 21:29:18: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:29:18: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:29:18: #1 total tags in treatment: 29399984 INFO @ Mon, 12 Aug 2019 21:29:18: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:29:18: #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 21:29:19: #1 tags after filtering in treatment: 29399984 INFO @ Mon, 12 Aug 2019 21:29:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:29:19: #1 finished! INFO @ Mon, 12 Aug 2019 21:29:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:29:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:29:21: #2 number of paired peaks: 322 WARNING @ Mon, 12 Aug 2019 21:29:21: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Mon, 12 Aug 2019 21:29:21: start model_add_line... INFO @ Mon, 12 Aug 2019 21:29:22: start X-correlation... INFO @ Mon, 12 Aug 2019 21:29:22: end of X-cor INFO @ Mon, 12 Aug 2019 21:29:22: #2 finished! INFO @ Mon, 12 Aug 2019 21:29:22: #2 predicted fragment length is 117 bps INFO @ Mon, 12 Aug 2019 21:29:22: #2 alternative fragment length(s) may be 3,117 bps INFO @ Mon, 12 Aug 2019 21:29:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981621/SRX3981621.20_model.r INFO @ Mon, 12 Aug 2019 21:29:22: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:29:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:29:24: 26000000 INFO @ Mon, 12 Aug 2019 21:29:32: 27000000 INFO @ Mon, 12 Aug 2019 21:29:40: 28000000 INFO @ Mon, 12 Aug 2019 21:29:48: 29000000 INFO @ Mon, 12 Aug 2019 21:29:51: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:29:51: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:29:51: #1 total tags in treatment: 29399984 INFO @ Mon, 12 Aug 2019 21:29:51: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:29:51: #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 21:29:52: #1 tags after filtering in treatment: 29399984 INFO @ Mon, 12 Aug 2019 21:29:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:29:52: #1 finished! INFO @ Mon, 12 Aug 2019 21:29:52: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:29:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:29:54: #2 number of paired peaks: 322 WARNING @ Mon, 12 Aug 2019 21:29:54: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Mon, 12 Aug 2019 21:29:54: start model_add_line... INFO @ Mon, 12 Aug 2019 21:29:55: start X-correlation... INFO @ Mon, 12 Aug 2019 21:29:55: end of X-cor INFO @ Mon, 12 Aug 2019 21:29:55: #2 finished! INFO @ Mon, 12 Aug 2019 21:29:55: #2 predicted fragment length is 117 bps INFO @ Mon, 12 Aug 2019 21:29:55: #2 alternative fragment length(s) may be 3,117 bps INFO @ Mon, 12 Aug 2019 21:29:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981621/SRX3981621.05_model.r INFO @ Mon, 12 Aug 2019 21:29:55: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:29:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:30:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:30:35: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:31:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981621/SRX3981621.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:31:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981621/SRX3981621.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:31:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981621/SRX3981621.10_summits.bed INFO @ Mon, 12 Aug 2019 21:31:03: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4856 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:31:07: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:31:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981621/SRX3981621.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:31:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981621/SRX3981621.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:31:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981621/SRX3981621.20_summits.bed INFO @ Mon, 12 Aug 2019 21:31:10: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1352 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:31:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981621/SRX3981621.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:31:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981621/SRX3981621.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:31:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981621/SRX3981621.05_summits.bed INFO @ Mon, 12 Aug 2019 21:31:43: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (9422 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。