Job ID = 1303645 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T11:31:14 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 ) 1900-01-00T00:00:00 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 ) 2019-06-03T11:31:14 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 ) 2019-06-03T11:40:16 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 ) 2019-06-03T11:40:16 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 ) 2019-06-03T11:40:16 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 ) 2019-06-03T11:44:22 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 ) 2019-06-03T11:44:23 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 ) 2019-06-03T11:44:41 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 : 78,223,783 reads read : 156,447,566 reads written : 78,223,783 reads 0-length : 78,223,783 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: 00:36:50 78223783 reads; of these: 78223783 (100.00%) were unpaired; of these: 11132785 (14.23%) aligned 0 times 50705096 (64.82%) aligned exactly 1 time 16385902 (20.95%) aligned >1 times 85.77% overall alignment rate Time searching: 00:36:50 Overall time: 00:36:50 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_rmdupse_core] 31298975 / 67090998 = 0.4665 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 22:08:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4941149/SRX4941149.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4941149/SRX4941149.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4941149/SRX4941149.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4941149/SRX4941149.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 22:08:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:08:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:08:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4941149/SRX4941149.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4941149/SRX4941149.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4941149/SRX4941149.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4941149/SRX4941149.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 22:08:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:08:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:09:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4941149/SRX4941149.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4941149/SRX4941149.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4941149/SRX4941149.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4941149/SRX4941149.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 22:09:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:09:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:09:07: 1000000 INFO @ Mon, 03 Jun 2019 22:09:11: 1000000 INFO @ Mon, 03 Jun 2019 22:09:11: 1000000 INFO @ Mon, 03 Jun 2019 22:09:15: 2000000 INFO @ Mon, 03 Jun 2019 22:09:22: 2000000 INFO @ Mon, 03 Jun 2019 22:09:22: 2000000 INFO @ Mon, 03 Jun 2019 22:09:23: 3000000 INFO @ Mon, 03 Jun 2019 22:09:31: 4000000 INFO @ Mon, 03 Jun 2019 22:09:33: 3000000 INFO @ Mon, 03 Jun 2019 22:09:33: 3000000 INFO @ Mon, 03 Jun 2019 22:09:39: 5000000 INFO @ Mon, 03 Jun 2019 22:09:44: 4000000 INFO @ Mon, 03 Jun 2019 22:09:44: 4000000 INFO @ Mon, 03 Jun 2019 22:09:47: 6000000 INFO @ Mon, 03 Jun 2019 22:09:55: 7000000 INFO @ Mon, 03 Jun 2019 22:09:55: 5000000 INFO @ Mon, 03 Jun 2019 22:09:55: 5000000 INFO @ Mon, 03 Jun 2019 22:10:03: 8000000 INFO @ Mon, 03 Jun 2019 22:10:05: 6000000 INFO @ Mon, 03 Jun 2019 22:10:06: 6000000 INFO @ Mon, 03 Jun 2019 22:10:10: 9000000 INFO @ Mon, 03 Jun 2019 22:10:15: 7000000 INFO @ Mon, 03 Jun 2019 22:10:17: 7000000 INFO @ Mon, 03 Jun 2019 22:10:18: 10000000 INFO @ Mon, 03 Jun 2019 22:10:25: 8000000 INFO @ Mon, 03 Jun 2019 22:10:26: 11000000 INFO @ Mon, 03 Jun 2019 22:10:28: 8000000 INFO @ Mon, 03 Jun 2019 22:10:34: 12000000 INFO @ Mon, 03 Jun 2019 22:10:35: 9000000 INFO @ Mon, 03 Jun 2019 22:10:38: 9000000 INFO @ Mon, 03 Jun 2019 22:10:42: 13000000 INFO @ Mon, 03 Jun 2019 22:10:45: 10000000 INFO @ Mon, 03 Jun 2019 22:10:49: 10000000 INFO @ Mon, 03 Jun 2019 22:10:50: 14000000 INFO @ Mon, 03 Jun 2019 22:10:55: 11000000 INFO @ Mon, 03 Jun 2019 22:10:58: 15000000 INFO @ Mon, 03 Jun 2019 22:11:00: 11000000 INFO @ Mon, 03 Jun 2019 22:11:05: 12000000 INFO @ Mon, 03 Jun 2019 22:11:06: 16000000 INFO @ Mon, 03 Jun 2019 22:11:10: 12000000 INFO @ Mon, 03 Jun 2019 22:11:14: 17000000 INFO @ Mon, 03 Jun 2019 22:11:15: 13000000 INFO @ Mon, 03 Jun 2019 22:11:21: 13000000 INFO @ Mon, 03 Jun 2019 22:11:22: 18000000 INFO @ Mon, 03 Jun 2019 22:11:25: 14000000 INFO @ Mon, 03 Jun 2019 22:11:30: 19000000 INFO @ Mon, 03 Jun 2019 22:11:32: 14000000 INFO @ Mon, 03 Jun 2019 22:11:35: 15000000 INFO @ Mon, 03 Jun 2019 22:11:38: 20000000 INFO @ Mon, 03 Jun 2019 22:11:42: 15000000 INFO @ Mon, 03 Jun 2019 22:11:45: 16000000 INFO @ Mon, 03 Jun 2019 22:11:46: 21000000 INFO @ Mon, 03 Jun 2019 22:11:53: 16000000 INFO @ Mon, 03 Jun 2019 22:11:54: 22000000 INFO @ Mon, 03 Jun 2019 22:11:55: 17000000 INFO @ Mon, 03 Jun 2019 22:12:02: 23000000 INFO @ Mon, 03 Jun 2019 22:12:04: 17000000 INFO @ Mon, 03 Jun 2019 22:12:05: 18000000 INFO @ Mon, 03 Jun 2019 22:12:10: 24000000 INFO @ Mon, 03 Jun 2019 22:12:14: 18000000 INFO @ Mon, 03 Jun 2019 22:12:15: 19000000 INFO @ Mon, 03 Jun 2019 22:12:17: 25000000 INFO @ Mon, 03 Jun 2019 22:12:25: 26000000 INFO @ Mon, 03 Jun 2019 22:12:25: 19000000 INFO @ Mon, 03 Jun 2019 22:12:25: 20000000 INFO @ Mon, 03 Jun 2019 22:12:32: 27000000 INFO @ Mon, 03 Jun 2019 22:12:35: 21000000 INFO @ Mon, 03 Jun 2019 22:12:36: 20000000 INFO @ Mon, 03 Jun 2019 22:12:40: 28000000 INFO @ Mon, 03 Jun 2019 22:12:45: 22000000 INFO @ Mon, 03 Jun 2019 22:12:46: 21000000 INFO @ Mon, 03 Jun 2019 22:12:48: 29000000 INFO @ Mon, 03 Jun 2019 22:12:55: 23000000 INFO @ Mon, 03 Jun 2019 22:12:56: 30000000 INFO @ Mon, 03 Jun 2019 22:12:57: 22000000 INFO @ Mon, 03 Jun 2019 22:13:04: 31000000 INFO @ Mon, 03 Jun 2019 22:13:05: 24000000 INFO @ Mon, 03 Jun 2019 22:13:07: 23000000 INFO @ Mon, 03 Jun 2019 22:13:11: 32000000 INFO @ Mon, 03 Jun 2019 22:13:15: 25000000 INFO @ Mon, 03 Jun 2019 22:13:18: 24000000 INFO @ Mon, 03 Jun 2019 22:13:19: 33000000 INFO @ Mon, 03 Jun 2019 22:13:24: 26000000 INFO @ Mon, 03 Jun 2019 22:13:27: 34000000 INFO @ Mon, 03 Jun 2019 22:13:28: 25000000 INFO @ Mon, 03 Jun 2019 22:13:34: 27000000 INFO @ Mon, 03 Jun 2019 22:13:34: 35000000 INFO @ Mon, 03 Jun 2019 22:13:38: 26000000 INFO @ Mon, 03 Jun 2019 22:13:41: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 22:13:41: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 22:13:41: #1 total tags in treatment: 35792023 INFO @ Mon, 03 Jun 2019 22:13:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:13:41: #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 22:13:42: #1 tags after filtering in treatment: 35792023 INFO @ Mon, 03 Jun 2019 22:13:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:13:42: #1 finished! INFO @ Mon, 03 Jun 2019 22:13:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:13:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:13:44: 28000000 INFO @ Mon, 03 Jun 2019 22:13:45: #2 number of paired peaks: 1848 INFO @ Mon, 03 Jun 2019 22:13:45: start model_add_line... INFO @ Mon, 03 Jun 2019 22:13:45: start X-correlation... INFO @ Mon, 03 Jun 2019 22:13:45: end of X-cor INFO @ Mon, 03 Jun 2019 22:13:45: #2 finished! INFO @ Mon, 03 Jun 2019 22:13:45: #2 predicted fragment length is 174 bps INFO @ Mon, 03 Jun 2019 22:13:45: #2 alternative fragment length(s) may be 4,174 bps INFO @ Mon, 03 Jun 2019 22:13:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4941149/SRX4941149.20_model.r INFO @ Mon, 03 Jun 2019 22:13:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:13:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:13:48: 27000000 INFO @ Mon, 03 Jun 2019 22:13:53: 29000000 INFO @ Mon, 03 Jun 2019 22:13:58: 28000000 INFO @ Mon, 03 Jun 2019 22:14:03: 30000000 INFO @ Mon, 03 Jun 2019 22:14:08: 29000000 INFO @ Mon, 03 Jun 2019 22:14:13: 31000000 INFO @ Mon, 03 Jun 2019 22:14:19: 30000000 INFO @ Mon, 03 Jun 2019 22:14:22: 32000000 INFO @ Mon, 03 Jun 2019 22:14:29: 31000000 INFO @ Mon, 03 Jun 2019 22:14:32: 33000000 INFO @ Mon, 03 Jun 2019 22:14:39: 32000000 INFO @ Mon, 03 Jun 2019 22:14:42: 34000000 INFO @ Mon, 03 Jun 2019 22:14:49: 33000000 INFO @ Mon, 03 Jun 2019 22:14:51: 35000000 INFO @ Mon, 03 Jun 2019 22:14:59: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 22:14:59: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 22:14:59: #1 total tags in treatment: 35792023 INFO @ Mon, 03 Jun 2019 22:14:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:14:59: #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 22:14:59: 34000000 INFO @ Mon, 03 Jun 2019 22:15:00: #1 tags after filtering in treatment: 35792023 INFO @ Mon, 03 Jun 2019 22:15:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:15:00: #1 finished! INFO @ Mon, 03 Jun 2019 22:15:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:15:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:15:03: #2 number of paired peaks: 1848 INFO @ Mon, 03 Jun 2019 22:15:03: start model_add_line... INFO @ Mon, 03 Jun 2019 22:15:03: start X-correlation... INFO @ Mon, 03 Jun 2019 22:15:03: end of X-cor INFO @ Mon, 03 Jun 2019 22:15:03: #2 finished! INFO @ Mon, 03 Jun 2019 22:15:03: #2 predicted fragment length is 174 bps INFO @ Mon, 03 Jun 2019 22:15:03: #2 alternative fragment length(s) may be 4,174 bps INFO @ Mon, 03 Jun 2019 22:15:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4941149/SRX4941149.05_model.r INFO @ Mon, 03 Jun 2019 22:15:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:15:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:15:09: 35000000 INFO @ Mon, 03 Jun 2019 22:15:17: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 22:15:17: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 22:15:17: #1 total tags in treatment: 35792023 INFO @ Mon, 03 Jun 2019 22:15:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:15:17: #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 22:15:18: #1 tags after filtering in treatment: 35792023 INFO @ Mon, 03 Jun 2019 22:15:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:15:18: #1 finished! INFO @ Mon, 03 Jun 2019 22:15:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:15:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:15:21: #2 number of paired peaks: 1848 INFO @ Mon, 03 Jun 2019 22:15:21: start model_add_line... INFO @ Mon, 03 Jun 2019 22:15:21: start X-correlation... INFO @ Mon, 03 Jun 2019 22:15:21: end of X-cor INFO @ Mon, 03 Jun 2019 22:15:21: #2 finished! INFO @ Mon, 03 Jun 2019 22:15:21: #2 predicted fragment length is 174 bps INFO @ Mon, 03 Jun 2019 22:15:21: #2 alternative fragment length(s) may be 4,174 bps INFO @ Mon, 03 Jun 2019 22:15:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4941149/SRX4941149.10_model.r INFO @ Mon, 03 Jun 2019 22:15:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:15:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:15:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:16:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4941149/SRX4941149.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:16:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4941149/SRX4941149.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:16:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4941149/SRX4941149.20_summits.bed INFO @ Mon, 03 Jun 2019 22:16:13: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8284 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:16:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:17:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:17:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4941149/SRX4941149.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:17:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4941149/SRX4941149.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:17:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4941149/SRX4941149.05_summits.bed INFO @ Mon, 03 Jun 2019 22:17:27: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (14151 records, 4 fields): 22 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 22:17:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4941149/SRX4941149.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:17:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4941149/SRX4941149.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:17:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4941149/SRX4941149.10_summits.bed INFO @ Mon, 03 Jun 2019 22:17:51: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (11565 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。