Job ID = 1294672 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:32:15 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 ) 2019-06-03T00:32:15 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 ) 2019-06-03T00:32:15 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 ) 2019-06-03T00:32:15 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 ) 2019-06-03T00:35:07 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 : 12,631,769 reads read : 12,631,769 reads written : 12,631,769 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: 00:03:43 12631769 reads; of these: 12631769 (100.00%) were unpaired; of these: 426832 (3.38%) aligned 0 times 10712108 (84.80%) aligned exactly 1 time 1492829 (11.82%) aligned >1 times 96.62% overall alignment rate Time searching: 00:03:43 Overall time: 00:03:43 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 8 files... [bam_rmdupse_core] 1898740 / 12204937 = 0.1556 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 09:46:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287816/SRX287816.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287816/SRX287816.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287816/SRX287816.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287816/SRX287816.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 09:46:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:46:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:46:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287816/SRX287816.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287816/SRX287816.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287816/SRX287816.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287816/SRX287816.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 09:46:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:46:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:46:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287816/SRX287816.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287816/SRX287816.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287816/SRX287816.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287816/SRX287816.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 09:46:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:46:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:47:01: 1000000 INFO @ Mon, 03 Jun 2019 09:47:02: 1000000 INFO @ Mon, 03 Jun 2019 09:47:03: 1000000 INFO @ Mon, 03 Jun 2019 09:47:09: 2000000 INFO @ Mon, 03 Jun 2019 09:47:11: 2000000 INFO @ Mon, 03 Jun 2019 09:47:14: 2000000 INFO @ Mon, 03 Jun 2019 09:47:17: 3000000 INFO @ Mon, 03 Jun 2019 09:47:19: 3000000 INFO @ Mon, 03 Jun 2019 09:47:24: 3000000 INFO @ Mon, 03 Jun 2019 09:47:24: 4000000 INFO @ Mon, 03 Jun 2019 09:47:27: 4000000 INFO @ Mon, 03 Jun 2019 09:47:32: 5000000 INFO @ Mon, 03 Jun 2019 09:47:34: 4000000 INFO @ Mon, 03 Jun 2019 09:47:36: 5000000 INFO @ Mon, 03 Jun 2019 09:47:40: 6000000 INFO @ Mon, 03 Jun 2019 09:47:44: 5000000 INFO @ Mon, 03 Jun 2019 09:47:45: 6000000 INFO @ Mon, 03 Jun 2019 09:47:47: 7000000 INFO @ Mon, 03 Jun 2019 09:47:53: 7000000 INFO @ Mon, 03 Jun 2019 09:47:55: 8000000 INFO @ Mon, 03 Jun 2019 09:47:55: 6000000 INFO @ Mon, 03 Jun 2019 09:48:01: 8000000 INFO @ Mon, 03 Jun 2019 09:48:03: 9000000 INFO @ Mon, 03 Jun 2019 09:48:06: 7000000 INFO @ Mon, 03 Jun 2019 09:48:10: 9000000 INFO @ Mon, 03 Jun 2019 09:48:10: 10000000 INFO @ Mon, 03 Jun 2019 09:48:13: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:48:13: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:48:13: #1 total tags in treatment: 10306197 INFO @ Mon, 03 Jun 2019 09:48:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:48:13: #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 09:48:13: #1 tags after filtering in treatment: 10306197 INFO @ Mon, 03 Jun 2019 09:48:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:48:13: #1 finished! INFO @ Mon, 03 Jun 2019 09:48:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:48:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:48:15: #2 number of paired peaks: 9399 INFO @ Mon, 03 Jun 2019 09:48:15: start model_add_line... INFO @ Mon, 03 Jun 2019 09:48:15: start X-correlation... INFO @ Mon, 03 Jun 2019 09:48:15: end of X-cor INFO @ Mon, 03 Jun 2019 09:48:15: #2 finished! INFO @ Mon, 03 Jun 2019 09:48:15: #2 predicted fragment length is 221 bps INFO @ Mon, 03 Jun 2019 09:48:15: #2 alternative fragment length(s) may be 3,221 bps INFO @ Mon, 03 Jun 2019 09:48:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287816/SRX287816.20_model.r INFO @ Mon, 03 Jun 2019 09:48:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:48:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:48:16: 8000000 INFO @ Mon, 03 Jun 2019 09:48:18: 10000000 INFO @ Mon, 03 Jun 2019 09:48:21: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:48:21: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:48:21: #1 total tags in treatment: 10306197 INFO @ Mon, 03 Jun 2019 09:48:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:48:21: #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 09:48:21: #1 tags after filtering in treatment: 10306197 INFO @ Mon, 03 Jun 2019 09:48:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:48:21: #1 finished! INFO @ Mon, 03 Jun 2019 09:48:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:48:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:48:23: #2 number of paired peaks: 9399 INFO @ Mon, 03 Jun 2019 09:48:23: start model_add_line... INFO @ Mon, 03 Jun 2019 09:48:23: start X-correlation... INFO @ Mon, 03 Jun 2019 09:48:23: end of X-cor INFO @ Mon, 03 Jun 2019 09:48:23: #2 finished! INFO @ Mon, 03 Jun 2019 09:48:23: #2 predicted fragment length is 221 bps INFO @ Mon, 03 Jun 2019 09:48:23: #2 alternative fragment length(s) may be 3,221 bps INFO @ Mon, 03 Jun 2019 09:48:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287816/SRX287816.10_model.r INFO @ Mon, 03 Jun 2019 09:48:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:48:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:48:26: 9000000 INFO @ Mon, 03 Jun 2019 09:48:36: 10000000 INFO @ Mon, 03 Jun 2019 09:48:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:48:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:48:39: #1 total tags in treatment: 10306197 INFO @ Mon, 03 Jun 2019 09:48:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:48:39: #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 09:48:39: #1 tags after filtering in treatment: 10306197 INFO @ Mon, 03 Jun 2019 09:48:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:48:39: #1 finished! INFO @ Mon, 03 Jun 2019 09:48:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:48:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:48:41: #2 number of paired peaks: 9399 INFO @ Mon, 03 Jun 2019 09:48:41: start model_add_line... INFO @ Mon, 03 Jun 2019 09:48:41: start X-correlation... INFO @ Mon, 03 Jun 2019 09:48:41: end of X-cor INFO @ Mon, 03 Jun 2019 09:48:41: #2 finished! INFO @ Mon, 03 Jun 2019 09:48:41: #2 predicted fragment length is 221 bps INFO @ Mon, 03 Jun 2019 09:48:41: #2 alternative fragment length(s) may be 3,221 bps INFO @ Mon, 03 Jun 2019 09:48:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287816/SRX287816.05_model.r INFO @ Mon, 03 Jun 2019 09:48:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:48:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:48:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:48:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:49:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287816/SRX287816.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:49:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287816/SRX287816.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:49:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287816/SRX287816.20_summits.bed INFO @ Mon, 03 Jun 2019 09:49:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2412 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:49:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287816/SRX287816.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:49:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287816/SRX287816.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:49:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287816/SRX287816.10_summits.bed INFO @ Mon, 03 Jun 2019 09:49:12: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5738 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:49:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:49:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287816/SRX287816.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:49:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287816/SRX287816.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:49:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287816/SRX287816.05_summits.bed INFO @ Mon, 03 Jun 2019 09:49:29: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8636 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。