Job ID = 1295143 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T03:20:50 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 ) 2019-06-03T03:20:50 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 ) 2019-06-03T03:20:50 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 : 29,667,530 reads read : 59,335,060 reads written : 29,667,530 reads 0-length : 29,667,530 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: 00:12:00 29667530 reads; of these: 29667530 (100.00%) were unpaired; of these: 1614462 (5.44%) aligned 0 times 24138229 (81.36%) aligned exactly 1 time 3914839 (13.20%) aligned >1 times 94.56% overall alignment rate Time searching: 00:12:00 Overall time: 00:12:00 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 12 files... [bam_rmdupse_core] 8402594 / 28053068 = 0.2995 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 12:46:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3279759/SRX3279759.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3279759/SRX3279759.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3279759/SRX3279759.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3279759/SRX3279759.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 12:46:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:46:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:46:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3279759/SRX3279759.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3279759/SRX3279759.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3279759/SRX3279759.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3279759/SRX3279759.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 12:46:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:46:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:46:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3279759/SRX3279759.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3279759/SRX3279759.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3279759/SRX3279759.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3279759/SRX3279759.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 12:46:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:46:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:46:16: 1000000 INFO @ Mon, 03 Jun 2019 12:46:16: 1000000 INFO @ Mon, 03 Jun 2019 12:46:18: 1000000 INFO @ Mon, 03 Jun 2019 12:46:26: 2000000 INFO @ Mon, 03 Jun 2019 12:46:26: 2000000 INFO @ Mon, 03 Jun 2019 12:46:29: 2000000 INFO @ Mon, 03 Jun 2019 12:46:35: 3000000 INFO @ Mon, 03 Jun 2019 12:46:37: 3000000 INFO @ Mon, 03 Jun 2019 12:46:41: 3000000 INFO @ Mon, 03 Jun 2019 12:46:45: 4000000 INFO @ Mon, 03 Jun 2019 12:46:47: 4000000 INFO @ Mon, 03 Jun 2019 12:46:52: 4000000 INFO @ Mon, 03 Jun 2019 12:46:55: 5000000 INFO @ Mon, 03 Jun 2019 12:46:57: 5000000 INFO @ Mon, 03 Jun 2019 12:47:04: 5000000 INFO @ Mon, 03 Jun 2019 12:47:05: 6000000 INFO @ Mon, 03 Jun 2019 12:47:06: 6000000 INFO @ Mon, 03 Jun 2019 12:47:15: 7000000 INFO @ Mon, 03 Jun 2019 12:47:16: 6000000 INFO @ Mon, 03 Jun 2019 12:47:16: 7000000 INFO @ Mon, 03 Jun 2019 12:47:25: 8000000 INFO @ Mon, 03 Jun 2019 12:47:26: 8000000 INFO @ Mon, 03 Jun 2019 12:47:27: 7000000 INFO @ Mon, 03 Jun 2019 12:47:35: 9000000 INFO @ Mon, 03 Jun 2019 12:47:36: 9000000 INFO @ Mon, 03 Jun 2019 12:47:39: 8000000 INFO @ Mon, 03 Jun 2019 12:47:45: 10000000 INFO @ Mon, 03 Jun 2019 12:47:46: 10000000 INFO @ Mon, 03 Jun 2019 12:47:51: 9000000 INFO @ Mon, 03 Jun 2019 12:47:55: 11000000 INFO @ Mon, 03 Jun 2019 12:47:56: 11000000 INFO @ Mon, 03 Jun 2019 12:48:03: 10000000 INFO @ Mon, 03 Jun 2019 12:48:05: 12000000 INFO @ Mon, 03 Jun 2019 12:48:06: 12000000 INFO @ Mon, 03 Jun 2019 12:48:14: 11000000 INFO @ Mon, 03 Jun 2019 12:48:16: 13000000 INFO @ Mon, 03 Jun 2019 12:48:16: 13000000 INFO @ Mon, 03 Jun 2019 12:48:25: 14000000 INFO @ Mon, 03 Jun 2019 12:48:26: 14000000 INFO @ Mon, 03 Jun 2019 12:48:26: 12000000 INFO @ Mon, 03 Jun 2019 12:48:35: 15000000 INFO @ Mon, 03 Jun 2019 12:48:36: 15000000 INFO @ Mon, 03 Jun 2019 12:48:38: 13000000 INFO @ Mon, 03 Jun 2019 12:48:44: 16000000 INFO @ Mon, 03 Jun 2019 12:48:46: 16000000 INFO @ Mon, 03 Jun 2019 12:48:49: 14000000 INFO @ Mon, 03 Jun 2019 12:48:54: 17000000 INFO @ Mon, 03 Jun 2019 12:48:56: 17000000 INFO @ Mon, 03 Jun 2019 12:49:01: 15000000 INFO @ Mon, 03 Jun 2019 12:49:04: 18000000 INFO @ Mon, 03 Jun 2019 12:49:06: 18000000 INFO @ Mon, 03 Jun 2019 12:49:12: 16000000 INFO @ Mon, 03 Jun 2019 12:49:13: 19000000 INFO @ Mon, 03 Jun 2019 12:49:17: 19000000 INFO @ Mon, 03 Jun 2019 12:49:20: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 12:49:20: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 12:49:20: #1 total tags in treatment: 19650474 INFO @ Mon, 03 Jun 2019 12:49:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:49:20: #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 12:49:20: #1 tags after filtering in treatment: 19650474 INFO @ Mon, 03 Jun 2019 12:49:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:49:20: #1 finished! INFO @ Mon, 03 Jun 2019 12:49:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:49:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:49:22: #2 number of paired peaks: 2703 INFO @ Mon, 03 Jun 2019 12:49:22: start model_add_line... INFO @ Mon, 03 Jun 2019 12:49:22: start X-correlation... INFO @ Mon, 03 Jun 2019 12:49:22: end of X-cor INFO @ Mon, 03 Jun 2019 12:49:22: #2 finished! INFO @ Mon, 03 Jun 2019 12:49:22: #2 predicted fragment length is 194 bps INFO @ Mon, 03 Jun 2019 12:49:22: #2 alternative fragment length(s) may be 194 bps INFO @ Mon, 03 Jun 2019 12:49:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3279759/SRX3279759.20_model.r INFO @ Mon, 03 Jun 2019 12:49:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:49:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:49:24: 17000000 INFO @ Mon, 03 Jun 2019 12:49:24: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 12:49:24: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 12:49:24: #1 total tags in treatment: 19650474 INFO @ Mon, 03 Jun 2019 12:49:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:49:24: #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 12:49:24: #1 tags after filtering in treatment: 19650474 INFO @ Mon, 03 Jun 2019 12:49:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:49:24: #1 finished! INFO @ Mon, 03 Jun 2019 12:49:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:49:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:49:27: #2 number of paired peaks: 2703 INFO @ Mon, 03 Jun 2019 12:49:27: start model_add_line... INFO @ Mon, 03 Jun 2019 12:49:27: start X-correlation... INFO @ Mon, 03 Jun 2019 12:49:27: end of X-cor INFO @ Mon, 03 Jun 2019 12:49:27: #2 finished! INFO @ Mon, 03 Jun 2019 12:49:27: #2 predicted fragment length is 194 bps INFO @ Mon, 03 Jun 2019 12:49:27: #2 alternative fragment length(s) may be 194 bps INFO @ Mon, 03 Jun 2019 12:49:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3279759/SRX3279759.10_model.r INFO @ Mon, 03 Jun 2019 12:49:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:49:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:49:35: 18000000 INFO @ Mon, 03 Jun 2019 12:49:46: 19000000 INFO @ Mon, 03 Jun 2019 12:49:53: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 12:49:53: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 12:49:53: #1 total tags in treatment: 19650474 INFO @ Mon, 03 Jun 2019 12:49:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:49:53: #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 12:49:54: #1 tags after filtering in treatment: 19650474 INFO @ Mon, 03 Jun 2019 12:49:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:49:54: #1 finished! INFO @ Mon, 03 Jun 2019 12:49:54: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:49:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:49:56: #2 number of paired peaks: 2703 INFO @ Mon, 03 Jun 2019 12:49:56: start model_add_line... INFO @ Mon, 03 Jun 2019 12:49:56: start X-correlation... INFO @ Mon, 03 Jun 2019 12:49:56: end of X-cor INFO @ Mon, 03 Jun 2019 12:49:56: #2 finished! INFO @ Mon, 03 Jun 2019 12:49:56: #2 predicted fragment length is 194 bps INFO @ Mon, 03 Jun 2019 12:49:56: #2 alternative fragment length(s) may be 194 bps INFO @ Mon, 03 Jun 2019 12:49:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3279759/SRX3279759.05_model.r INFO @ Mon, 03 Jun 2019 12:49:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:49:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:50:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:50:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:50:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3279759/SRX3279759.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:50:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3279759/SRX3279759.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:50:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3279759/SRX3279759.20_summits.bed INFO @ Mon, 03 Jun 2019 12:50:51: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5416 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:50:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3279759/SRX3279759.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:50:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3279759/SRX3279759.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:50:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3279759/SRX3279759.10_summits.bed INFO @ Mon, 03 Jun 2019 12:50:57: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6621 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:50:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:51:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3279759/SRX3279759.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:51:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3279759/SRX3279759.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:51:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3279759/SRX3279759.05_summits.bed INFO @ Mon, 03 Jun 2019 12:51:25: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7440 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。