Job ID = 1307697 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:27:34 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 ) 2019-06-03T13:32:45 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 : 28,599,273 reads read : 57,198,546 reads written : 28,599,273 reads 0-length : 28,599,273 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: 00:09:18 28599273 reads; of these: 28599273 (100.00%) were unpaired; of these: 6315704 (22.08%) aligned 0 times 18765095 (65.61%) aligned exactly 1 time 3518474 (12.30%) aligned >1 times 77.92% overall alignment rate Time searching: 00:09:18 Overall time: 00:09:18 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] 13092469 / 22283569 = 0.5875 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 22:54:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343113/SRX5343113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343113/SRX5343113.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343113/SRX5343113.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343113/SRX5343113.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 22:54:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:54:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:54:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343113/SRX5343113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343113/SRX5343113.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343113/SRX5343113.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343113/SRX5343113.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 22:54:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:54:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:54:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343113/SRX5343113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343113/SRX5343113.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343113/SRX5343113.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343113/SRX5343113.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 22:54:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:54:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:54:42: 1000000 INFO @ Mon, 03 Jun 2019 22:54:45: 1000000 INFO @ Mon, 03 Jun 2019 22:54:45: 1000000 INFO @ Mon, 03 Jun 2019 22:54:50: 2000000 INFO @ Mon, 03 Jun 2019 22:54:55: 2000000 INFO @ Mon, 03 Jun 2019 22:54:55: 2000000 INFO @ Mon, 03 Jun 2019 22:54:57: 3000000 INFO @ Mon, 03 Jun 2019 22:55:04: 4000000 INFO @ Mon, 03 Jun 2019 22:55:05: 3000000 INFO @ Mon, 03 Jun 2019 22:55:05: 3000000 INFO @ Mon, 03 Jun 2019 22:55:12: 5000000 INFO @ Mon, 03 Jun 2019 22:55:14: 4000000 INFO @ Mon, 03 Jun 2019 22:55:14: 4000000 INFO @ Mon, 03 Jun 2019 22:55:19: 6000000 INFO @ Mon, 03 Jun 2019 22:55:24: 5000000 INFO @ Mon, 03 Jun 2019 22:55:24: 5000000 INFO @ Mon, 03 Jun 2019 22:55:26: 7000000 INFO @ Mon, 03 Jun 2019 22:55:33: 6000000 INFO @ Mon, 03 Jun 2019 22:55:33: 6000000 INFO @ Mon, 03 Jun 2019 22:55:34: 8000000 INFO @ Mon, 03 Jun 2019 22:55:41: 9000000 INFO @ Mon, 03 Jun 2019 22:55:42: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:55:42: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:55:42: #1 total tags in treatment: 9191100 INFO @ Mon, 03 Jun 2019 22:55:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:55:42: #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 22:55:43: #1 tags after filtering in treatment: 9191100 INFO @ Mon, 03 Jun 2019 22:55:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:55:43: #1 finished! INFO @ Mon, 03 Jun 2019 22:55:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:55:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:55:43: 7000000 INFO @ Mon, 03 Jun 2019 22:55:43: 7000000 INFO @ Mon, 03 Jun 2019 22:55:44: #2 number of paired peaks: 6865 INFO @ Mon, 03 Jun 2019 22:55:44: start model_add_line... INFO @ Mon, 03 Jun 2019 22:55:44: start X-correlation... INFO @ Mon, 03 Jun 2019 22:55:44: end of X-cor INFO @ Mon, 03 Jun 2019 22:55:44: #2 finished! INFO @ Mon, 03 Jun 2019 22:55:44: #2 predicted fragment length is 170 bps INFO @ Mon, 03 Jun 2019 22:55:44: #2 alternative fragment length(s) may be 170 bps INFO @ Mon, 03 Jun 2019 22:55:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343113/SRX5343113.20_model.r INFO @ Mon, 03 Jun 2019 22:55:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:55:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:55:52: 8000000 INFO @ Mon, 03 Jun 2019 22:55:53: 8000000 INFO @ Mon, 03 Jun 2019 22:56:02: 9000000 INFO @ Mon, 03 Jun 2019 22:56:02: 9000000 INFO @ Mon, 03 Jun 2019 22:56:04: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:56:04: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:56:04: #1 total tags in treatment: 9191100 INFO @ Mon, 03 Jun 2019 22:56:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:56:04: #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 22:56:04: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:56:04: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:56:04: #1 total tags in treatment: 9191100 INFO @ Mon, 03 Jun 2019 22:56:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:56:04: #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 22:56:04: #1 tags after filtering in treatment: 9191100 INFO @ Mon, 03 Jun 2019 22:56:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:56:04: #1 finished! INFO @ Mon, 03 Jun 2019 22:56:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:56:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:56:04: #1 tags after filtering in treatment: 9191100 INFO @ Mon, 03 Jun 2019 22:56:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:56:04: #1 finished! INFO @ Mon, 03 Jun 2019 22:56:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:56:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:56:06: #2 number of paired peaks: 6865 INFO @ Mon, 03 Jun 2019 22:56:06: start model_add_line... INFO @ Mon, 03 Jun 2019 22:56:06: start X-correlation... INFO @ Mon, 03 Jun 2019 22:56:06: end of X-cor INFO @ Mon, 03 Jun 2019 22:56:06: #2 finished! INFO @ Mon, 03 Jun 2019 22:56:06: #2 predicted fragment length is 170 bps INFO @ Mon, 03 Jun 2019 22:56:06: #2 alternative fragment length(s) may be 170 bps INFO @ Mon, 03 Jun 2019 22:56:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343113/SRX5343113.10_model.r INFO @ Mon, 03 Jun 2019 22:56:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:56:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:56:06: #2 number of paired peaks: 6865 INFO @ Mon, 03 Jun 2019 22:56:06: start model_add_line... INFO @ Mon, 03 Jun 2019 22:56:06: start X-correlation... INFO @ Mon, 03 Jun 2019 22:56:06: end of X-cor INFO @ Mon, 03 Jun 2019 22:56:06: #2 finished! INFO @ Mon, 03 Jun 2019 22:56:06: #2 predicted fragment length is 170 bps INFO @ Mon, 03 Jun 2019 22:56:06: #2 alternative fragment length(s) may be 170 bps INFO @ Mon, 03 Jun 2019 22:56:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343113/SRX5343113.05_model.r INFO @ Mon, 03 Jun 2019 22:56:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:56:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:56:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:56:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343113/SRX5343113.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:56:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343113/SRX5343113.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:56:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343113/SRX5343113.20_summits.bed INFO @ Mon, 03 Jun 2019 22:56:29: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5995 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:56:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:56:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:56:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343113/SRX5343113.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:56:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343113/SRX5343113.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:56:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343113/SRX5343113.05_summits.bed INFO @ Mon, 03 Jun 2019 22:56:53: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8353 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:56:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343113/SRX5343113.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:56:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343113/SRX5343113.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:56:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343113/SRX5343113.10_summits.bed INFO @ Mon, 03 Jun 2019 22:56:53: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7441 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。