Job ID = 1294432 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T22:52:44 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 : 18,421,694 reads read : 18,421,694 reads written : 18,421,694 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: 00:06:13 18421694 reads; of these: 18421694 (100.00%) were unpaired; of these: 1104187 (5.99%) aligned 0 times 15212810 (82.58%) aligned exactly 1 time 2104697 (11.43%) aligned >1 times 94.01% overall alignment rate Time searching: 00:06:13 Overall time: 00:06:13 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] 2265369 / 17317507 = 0.1308 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 08:04:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287601/SRX287601.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287601/SRX287601.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287601/SRX287601.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287601/SRX287601.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 08:04:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:04:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:04:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287601/SRX287601.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287601/SRX287601.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287601/SRX287601.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287601/SRX287601.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 08:04:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:04:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:04:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287601/SRX287601.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287601/SRX287601.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287601/SRX287601.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287601/SRX287601.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 08:04:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:04:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:04:55: 1000000 INFO @ Mon, 03 Jun 2019 08:04:55: 1000000 INFO @ Mon, 03 Jun 2019 08:04:56: 1000000 INFO @ Mon, 03 Jun 2019 08:05:04: 2000000 INFO @ Mon, 03 Jun 2019 08:05:05: 2000000 INFO @ Mon, 03 Jun 2019 08:05:05: 2000000 INFO @ Mon, 03 Jun 2019 08:05:13: 3000000 INFO @ Mon, 03 Jun 2019 08:05:13: 3000000 INFO @ Mon, 03 Jun 2019 08:05:14: 3000000 INFO @ Mon, 03 Jun 2019 08:05:21: 4000000 INFO @ Mon, 03 Jun 2019 08:05:22: 4000000 INFO @ Mon, 03 Jun 2019 08:05:23: 4000000 INFO @ Mon, 03 Jun 2019 08:05:30: 5000000 INFO @ Mon, 03 Jun 2019 08:05:30: 5000000 INFO @ Mon, 03 Jun 2019 08:05:32: 5000000 INFO @ Mon, 03 Jun 2019 08:05:38: 6000000 INFO @ Mon, 03 Jun 2019 08:05:40: 6000000 INFO @ Mon, 03 Jun 2019 08:05:41: 6000000 INFO @ Mon, 03 Jun 2019 08:05:47: 7000000 INFO @ Mon, 03 Jun 2019 08:05:50: 7000000 INFO @ Mon, 03 Jun 2019 08:05:51: 7000000 INFO @ Mon, 03 Jun 2019 08:05:56: 8000000 INFO @ Mon, 03 Jun 2019 08:05:59: 8000000 INFO @ Mon, 03 Jun 2019 08:06:01: 8000000 INFO @ Mon, 03 Jun 2019 08:06:04: 9000000 INFO @ Mon, 03 Jun 2019 08:06:08: 9000000 INFO @ Mon, 03 Jun 2019 08:06:11: 9000000 INFO @ Mon, 03 Jun 2019 08:06:12: 10000000 INFO @ Mon, 03 Jun 2019 08:06:17: 10000000 INFO @ Mon, 03 Jun 2019 08:06:20: 11000000 INFO @ Mon, 03 Jun 2019 08:06:21: 10000000 INFO @ Mon, 03 Jun 2019 08:06:26: 11000000 INFO @ Mon, 03 Jun 2019 08:06:29: 12000000 INFO @ Mon, 03 Jun 2019 08:06:32: 11000000 INFO @ Mon, 03 Jun 2019 08:06:34: 12000000 INFO @ Mon, 03 Jun 2019 08:06:37: 13000000 INFO @ Mon, 03 Jun 2019 08:06:42: 12000000 INFO @ Mon, 03 Jun 2019 08:06:43: 13000000 INFO @ Mon, 03 Jun 2019 08:06:46: 14000000 INFO @ Mon, 03 Jun 2019 08:06:52: 14000000 INFO @ Mon, 03 Jun 2019 08:06:53: 13000000 INFO @ Mon, 03 Jun 2019 08:06:54: 15000000 INFO @ Mon, 03 Jun 2019 08:06:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:06:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:06:55: #1 total tags in treatment: 15052138 INFO @ Mon, 03 Jun 2019 08:06:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:06:55: #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 08:06:55: #1 tags after filtering in treatment: 15052138 INFO @ Mon, 03 Jun 2019 08:06:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:06:55: #1 finished! INFO @ Mon, 03 Jun 2019 08:06:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:06:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:06:56: #2 number of paired peaks: 1108 INFO @ Mon, 03 Jun 2019 08:06:56: start model_add_line... INFO @ Mon, 03 Jun 2019 08:06:57: start X-correlation... INFO @ Mon, 03 Jun 2019 08:06:57: end of X-cor INFO @ Mon, 03 Jun 2019 08:06:57: #2 finished! INFO @ Mon, 03 Jun 2019 08:06:57: #2 predicted fragment length is 288 bps INFO @ Mon, 03 Jun 2019 08:06:57: #2 alternative fragment length(s) may be 4,288 bps INFO @ Mon, 03 Jun 2019 08:06:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287601/SRX287601.05_model.r INFO @ Mon, 03 Jun 2019 08:06:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:06:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:07:00: 15000000 INFO @ Mon, 03 Jun 2019 08:07:01: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:07:01: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:07:01: #1 total tags in treatment: 15052138 INFO @ Mon, 03 Jun 2019 08:07:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:07:01: #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 08:07:01: #1 tags after filtering in treatment: 15052138 INFO @ Mon, 03 Jun 2019 08:07:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:07:01: #1 finished! INFO @ Mon, 03 Jun 2019 08:07:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:07:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:07:02: #2 number of paired peaks: 1108 INFO @ Mon, 03 Jun 2019 08:07:02: start model_add_line... INFO @ Mon, 03 Jun 2019 08:07:03: start X-correlation... INFO @ Mon, 03 Jun 2019 08:07:03: end of X-cor INFO @ Mon, 03 Jun 2019 08:07:03: #2 finished! INFO @ Mon, 03 Jun 2019 08:07:03: #2 predicted fragment length is 288 bps INFO @ Mon, 03 Jun 2019 08:07:03: #2 alternative fragment length(s) may be 4,288 bps INFO @ Mon, 03 Jun 2019 08:07:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287601/SRX287601.20_model.r INFO @ Mon, 03 Jun 2019 08:07:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:07:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:07:03: 14000000 INFO @ Mon, 03 Jun 2019 08:07:13: 15000000 INFO @ Mon, 03 Jun 2019 08:07:14: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:07:14: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:07:14: #1 total tags in treatment: 15052138 INFO @ Mon, 03 Jun 2019 08:07:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:07:14: #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 08:07:14: #1 tags after filtering in treatment: 15052138 INFO @ Mon, 03 Jun 2019 08:07:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:07:14: #1 finished! INFO @ Mon, 03 Jun 2019 08:07:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:07:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:07:15: #2 number of paired peaks: 1108 INFO @ Mon, 03 Jun 2019 08:07:15: start model_add_line... INFO @ Mon, 03 Jun 2019 08:07:16: start X-correlation... INFO @ Mon, 03 Jun 2019 08:07:16: end of X-cor INFO @ Mon, 03 Jun 2019 08:07:16: #2 finished! INFO @ Mon, 03 Jun 2019 08:07:16: #2 predicted fragment length is 288 bps INFO @ Mon, 03 Jun 2019 08:07:16: #2 alternative fragment length(s) may be 4,288 bps INFO @ Mon, 03 Jun 2019 08:07:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287601/SRX287601.10_model.r INFO @ Mon, 03 Jun 2019 08:07:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:07:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:07:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:07:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:08:05: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:08:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287601/SRX287601.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:08:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287601/SRX287601.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:08:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287601/SRX287601.05_summits.bed INFO @ Mon, 03 Jun 2019 08:08:08: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6181 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:08:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287601/SRX287601.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:08:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287601/SRX287601.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:08:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287601/SRX287601.20_summits.bed INFO @ Mon, 03 Jun 2019 08:08:15: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1499 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:08:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287601/SRX287601.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:08:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287601/SRX287601.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:08:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287601/SRX287601.10_summits.bed INFO @ Mon, 03 Jun 2019 08:08:28: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3524 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。