Job ID = 1294565 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:57:43 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 ) 2019-06-02T23:58:56 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 ) 2019-06-02T23:59:46 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 ) 2019-06-02T23:59:46 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 ) 2019-06-03T00:00:27 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 ) 2019-06-03T00:00:27 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 ) 2019-06-03T00:03:53 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 ) 2019-06-03T00:04:18 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 ) spots read : 19,622,225 reads read : 19,622,225 reads written : 19,622,225 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:04 19622225 reads; of these: 19622225 (100.00%) were unpaired; of these: 1114760 (5.68%) aligned 0 times 13453680 (68.56%) aligned exactly 1 time 5053785 (25.76%) aligned >1 times 94.32% overall alignment rate Time searching: 00:08:05 Overall time: 00:08:05 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] 4727468 / 18507465 = 0.2554 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 09:19:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287744/SRX287744.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287744/SRX287744.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287744/SRX287744.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287744/SRX287744.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 09:19:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:19:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:19:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287744/SRX287744.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287744/SRX287744.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287744/SRX287744.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287744/SRX287744.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 09:19:49: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:19:49: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:19:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287744/SRX287744.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287744/SRX287744.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287744/SRX287744.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287744/SRX287744.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 09:19:49: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:19:49: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:19:58: 1000000 INFO @ Mon, 03 Jun 2019 09:19:58: 1000000 INFO @ Mon, 03 Jun 2019 09:20:00: 1000000 INFO @ Mon, 03 Jun 2019 09:20:06: 2000000 INFO @ Mon, 03 Jun 2019 09:20:06: 2000000 INFO @ Mon, 03 Jun 2019 09:20:11: 2000000 INFO @ Mon, 03 Jun 2019 09:20:15: 3000000 INFO @ Mon, 03 Jun 2019 09:20:15: 3000000 INFO @ Mon, 03 Jun 2019 09:20:22: 3000000 INFO @ Mon, 03 Jun 2019 09:20:23: 4000000 INFO @ Mon, 03 Jun 2019 09:20:24: 4000000 INFO @ Mon, 03 Jun 2019 09:20:31: 5000000 INFO @ Mon, 03 Jun 2019 09:20:32: 5000000 INFO @ Mon, 03 Jun 2019 09:20:32: 4000000 INFO @ Mon, 03 Jun 2019 09:20:39: 6000000 INFO @ Mon, 03 Jun 2019 09:20:40: 6000000 INFO @ Mon, 03 Jun 2019 09:20:43: 5000000 INFO @ Mon, 03 Jun 2019 09:20:47: 7000000 INFO @ Mon, 03 Jun 2019 09:20:49: 7000000 INFO @ Mon, 03 Jun 2019 09:20:54: 6000000 INFO @ Mon, 03 Jun 2019 09:20:55: 8000000 INFO @ Mon, 03 Jun 2019 09:20:58: 8000000 INFO @ Mon, 03 Jun 2019 09:21:04: 9000000 INFO @ Mon, 03 Jun 2019 09:21:04: 7000000 INFO @ Mon, 03 Jun 2019 09:21:07: 9000000 INFO @ Mon, 03 Jun 2019 09:21:12: 10000000 INFO @ Mon, 03 Jun 2019 09:21:15: 10000000 INFO @ Mon, 03 Jun 2019 09:21:15: 8000000 INFO @ Mon, 03 Jun 2019 09:21:20: 11000000 INFO @ Mon, 03 Jun 2019 09:21:23: 11000000 INFO @ Mon, 03 Jun 2019 09:21:26: 9000000 INFO @ Mon, 03 Jun 2019 09:21:28: 12000000 INFO @ Mon, 03 Jun 2019 09:21:32: 12000000 INFO @ Mon, 03 Jun 2019 09:21:36: 10000000 INFO @ Mon, 03 Jun 2019 09:21:37: 13000000 INFO @ Mon, 03 Jun 2019 09:21:40: 13000000 INFO @ Mon, 03 Jun 2019 09:21:44: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:21:44: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:21:44: #1 total tags in treatment: 13779997 INFO @ Mon, 03 Jun 2019 09:21:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:21:44: #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 09:21:44: #1 tags after filtering in treatment: 13779997 INFO @ Mon, 03 Jun 2019 09:21:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:21:44: #1 finished! INFO @ Mon, 03 Jun 2019 09:21:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:21:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:21:45: #2 number of paired peaks: 1049 INFO @ Mon, 03 Jun 2019 09:21:45: start model_add_line... INFO @ Mon, 03 Jun 2019 09:21:46: start X-correlation... INFO @ Mon, 03 Jun 2019 09:21:46: 11000000 INFO @ Mon, 03 Jun 2019 09:21:46: end of X-cor INFO @ Mon, 03 Jun 2019 09:21:46: #2 finished! INFO @ Mon, 03 Jun 2019 09:21:46: #2 predicted fragment length is 316 bps INFO @ Mon, 03 Jun 2019 09:21:46: #2 alternative fragment length(s) may be 316 bps INFO @ Mon, 03 Jun 2019 09:21:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287744/SRX287744.05_model.r INFO @ Mon, 03 Jun 2019 09:21:46: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:21:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:21:47: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:21:47: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:21:47: #1 total tags in treatment: 13779997 INFO @ Mon, 03 Jun 2019 09:21:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:21:47: #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 09:21:47: #1 tags after filtering in treatment: 13779997 INFO @ Mon, 03 Jun 2019 09:21:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:21:47: #1 finished! INFO @ Mon, 03 Jun 2019 09:21:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:21:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:21:48: #2 number of paired peaks: 1049 INFO @ Mon, 03 Jun 2019 09:21:48: start model_add_line... INFO @ Mon, 03 Jun 2019 09:21:48: start X-correlation... INFO @ Mon, 03 Jun 2019 09:21:49: end of X-cor INFO @ Mon, 03 Jun 2019 09:21:49: #2 finished! INFO @ Mon, 03 Jun 2019 09:21:49: #2 predicted fragment length is 316 bps INFO @ Mon, 03 Jun 2019 09:21:49: #2 alternative fragment length(s) may be 316 bps INFO @ Mon, 03 Jun 2019 09:21:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287744/SRX287744.10_model.r INFO @ Mon, 03 Jun 2019 09:21:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:21:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:21:55: 12000000 INFO @ Mon, 03 Jun 2019 09:22:04: 13000000 INFO @ Mon, 03 Jun 2019 09:22:11: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:22:11: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:22:11: #1 total tags in treatment: 13779997 INFO @ Mon, 03 Jun 2019 09:22:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:22:11: #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 09:22:12: #1 tags after filtering in treatment: 13779997 INFO @ Mon, 03 Jun 2019 09:22:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:22:12: #1 finished! INFO @ Mon, 03 Jun 2019 09:22:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:22:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:22:13: #2 number of paired peaks: 1049 INFO @ Mon, 03 Jun 2019 09:22:13: start model_add_line... INFO @ Mon, 03 Jun 2019 09:22:13: start X-correlation... INFO @ Mon, 03 Jun 2019 09:22:13: end of X-cor INFO @ Mon, 03 Jun 2019 09:22:13: #2 finished! INFO @ Mon, 03 Jun 2019 09:22:13: #2 predicted fragment length is 316 bps INFO @ Mon, 03 Jun 2019 09:22:13: #2 alternative fragment length(s) may be 316 bps INFO @ Mon, 03 Jun 2019 09:22:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287744/SRX287744.20_model.r INFO @ Mon, 03 Jun 2019 09:22:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:22:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:22:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:22:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:22:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287744/SRX287744.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:22:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287744/SRX287744.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:22:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287744/SRX287744.05_summits.bed INFO @ Mon, 03 Jun 2019 09:22:48: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2562 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:22:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287744/SRX287744.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:22:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287744/SRX287744.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:22:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287744/SRX287744.10_summits.bed INFO @ Mon, 03 Jun 2019 09:22:50: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1990 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:22:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:23:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287744/SRX287744.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:23:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287744/SRX287744.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:23:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287744/SRX287744.20_summits.bed INFO @ Mon, 03 Jun 2019 09:23:15: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1512 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。