Job ID = 1294786 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T01:01:46 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 ) 2019-06-03T01:01:46 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 ) 2019-06-03T01:01:46 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 ) spots read : 23,049,469 reads read : 23,049,469 reads written : 23,049,469 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: 00:08:33 23049469 reads; of these: 23049469 (100.00%) were unpaired; of these: 1380389 (5.99%) aligned 0 times 15197351 (65.93%) aligned exactly 1 time 6471729 (28.08%) aligned >1 times 94.01% overall alignment rate Time searching: 00:08:33 Overall time: 00:08:33 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] 3146397 / 21669080 = 0.1452 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 10:28:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287876/SRX287876.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287876/SRX287876.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287876/SRX287876.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287876/SRX287876.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 10:28:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:28:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:28:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287876/SRX287876.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287876/SRX287876.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287876/SRX287876.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287876/SRX287876.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 10:28:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:28:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:28:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287876/SRX287876.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287876/SRX287876.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287876/SRX287876.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287876/SRX287876.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 10:28:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:28:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:28:53: 1000000 INFO @ Mon, 03 Jun 2019 10:28:53: 1000000 INFO @ Mon, 03 Jun 2019 10:28:54: 1000000 INFO @ Mon, 03 Jun 2019 10:29:00: 2000000 INFO @ Mon, 03 Jun 2019 10:29:01: 2000000 INFO @ Mon, 03 Jun 2019 10:29:02: 2000000 INFO @ Mon, 03 Jun 2019 10:29:06: 3000000 INFO @ Mon, 03 Jun 2019 10:29:09: 3000000 INFO @ Mon, 03 Jun 2019 10:29:10: 3000000 INFO @ Mon, 03 Jun 2019 10:29:13: 4000000 INFO @ Mon, 03 Jun 2019 10:29:17: 4000000 INFO @ Mon, 03 Jun 2019 10:29:19: 4000000 INFO @ Mon, 03 Jun 2019 10:29:20: 5000000 INFO @ Mon, 03 Jun 2019 10:29:24: 5000000 INFO @ Mon, 03 Jun 2019 10:29:27: 5000000 INFO @ Mon, 03 Jun 2019 10:29:27: 6000000 INFO @ Mon, 03 Jun 2019 10:29:32: 6000000 INFO @ Mon, 03 Jun 2019 10:29:34: 7000000 INFO @ Mon, 03 Jun 2019 10:29:35: 6000000 INFO @ Mon, 03 Jun 2019 10:29:39: 7000000 INFO @ Mon, 03 Jun 2019 10:29:41: 8000000 INFO @ Mon, 03 Jun 2019 10:29:43: 7000000 INFO @ Mon, 03 Jun 2019 10:29:47: 8000000 INFO @ Mon, 03 Jun 2019 10:29:48: 9000000 INFO @ Mon, 03 Jun 2019 10:29:52: 8000000 INFO @ Mon, 03 Jun 2019 10:29:56: 9000000 INFO @ Mon, 03 Jun 2019 10:29:56: 10000000 INFO @ Mon, 03 Jun 2019 10:30:00: 9000000 INFO @ Mon, 03 Jun 2019 10:30:04: 11000000 INFO @ Mon, 03 Jun 2019 10:30:04: 10000000 INFO @ Mon, 03 Jun 2019 10:30:09: 10000000 INFO @ Mon, 03 Jun 2019 10:30:11: 12000000 INFO @ Mon, 03 Jun 2019 10:30:12: 11000000 INFO @ Mon, 03 Jun 2019 10:30:17: 11000000 INFO @ Mon, 03 Jun 2019 10:30:19: 13000000 INFO @ Mon, 03 Jun 2019 10:30:20: 12000000 INFO @ Mon, 03 Jun 2019 10:30:25: 12000000 INFO @ Mon, 03 Jun 2019 10:30:26: 14000000 INFO @ Mon, 03 Jun 2019 10:30:28: 13000000 INFO @ Mon, 03 Jun 2019 10:30:33: 13000000 INFO @ Mon, 03 Jun 2019 10:30:34: 15000000 INFO @ Mon, 03 Jun 2019 10:30:37: 14000000 INFO @ Mon, 03 Jun 2019 10:30:41: 14000000 INFO @ Mon, 03 Jun 2019 10:30:41: 16000000 INFO @ Mon, 03 Jun 2019 10:30:45: 15000000 INFO @ Mon, 03 Jun 2019 10:30:49: 15000000 INFO @ Mon, 03 Jun 2019 10:30:49: 17000000 INFO @ Mon, 03 Jun 2019 10:30:53: 16000000 INFO @ Mon, 03 Jun 2019 10:30:57: 16000000 INFO @ Mon, 03 Jun 2019 10:30:57: 18000000 INFO @ Mon, 03 Jun 2019 10:31:01: 17000000 INFO @ Mon, 03 Jun 2019 10:31:02: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:31:02: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:31:02: #1 total tags in treatment: 18522683 INFO @ Mon, 03 Jun 2019 10:31:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:31:02: #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 10:31:02: #1 tags after filtering in treatment: 18522683 INFO @ Mon, 03 Jun 2019 10:31:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:31:02: #1 finished! INFO @ Mon, 03 Jun 2019 10:31:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:31:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:31:04: #2 number of paired peaks: 323 WARNING @ Mon, 03 Jun 2019 10:31:04: Fewer paired peaks (323) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 323 pairs to build model! INFO @ Mon, 03 Jun 2019 10:31:04: start model_add_line... INFO @ Mon, 03 Jun 2019 10:31:04: start X-correlation... INFO @ Mon, 03 Jun 2019 10:31:04: end of X-cor INFO @ Mon, 03 Jun 2019 10:31:04: #2 finished! INFO @ Mon, 03 Jun 2019 10:31:04: #2 predicted fragment length is 186 bps INFO @ Mon, 03 Jun 2019 10:31:04: #2 alternative fragment length(s) may be 186 bps INFO @ Mon, 03 Jun 2019 10:31:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287876/SRX287876.20_model.r INFO @ Mon, 03 Jun 2019 10:31:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:31:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:31:05: 17000000 INFO @ Mon, 03 Jun 2019 10:31:10: 18000000 INFO @ Mon, 03 Jun 2019 10:31:13: 18000000 INFO @ Mon, 03 Jun 2019 10:31:14: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:31:14: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:31:14: #1 total tags in treatment: 18522683 INFO @ Mon, 03 Jun 2019 10:31:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:31:14: #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 10:31:15: #1 tags after filtering in treatment: 18522683 INFO @ Mon, 03 Jun 2019 10:31:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:31:15: #1 finished! INFO @ Mon, 03 Jun 2019 10:31:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:31:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:31:16: #2 number of paired peaks: 323 WARNING @ Mon, 03 Jun 2019 10:31:16: Fewer paired peaks (323) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 323 pairs to build model! INFO @ Mon, 03 Jun 2019 10:31:16: start model_add_line... INFO @ Mon, 03 Jun 2019 10:31:16: start X-correlation... INFO @ Mon, 03 Jun 2019 10:31:16: end of X-cor INFO @ Mon, 03 Jun 2019 10:31:16: #2 finished! INFO @ Mon, 03 Jun 2019 10:31:16: #2 predicted fragment length is 186 bps INFO @ Mon, 03 Jun 2019 10:31:16: #2 alternative fragment length(s) may be 186 bps INFO @ Mon, 03 Jun 2019 10:31:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287876/SRX287876.05_model.r INFO @ Mon, 03 Jun 2019 10:31:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:31:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:31:18: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:31:18: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:31:18: #1 total tags in treatment: 18522683 INFO @ Mon, 03 Jun 2019 10:31:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:31:18: #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 10:31:18: #1 tags after filtering in treatment: 18522683 INFO @ Mon, 03 Jun 2019 10:31:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:31:18: #1 finished! INFO @ Mon, 03 Jun 2019 10:31:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:31:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:31:20: #2 number of paired peaks: 323 WARNING @ Mon, 03 Jun 2019 10:31:20: Fewer paired peaks (323) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 323 pairs to build model! INFO @ Mon, 03 Jun 2019 10:31:20: start model_add_line... INFO @ Mon, 03 Jun 2019 10:31:20: start X-correlation... INFO @ Mon, 03 Jun 2019 10:31:20: end of X-cor INFO @ Mon, 03 Jun 2019 10:31:20: #2 finished! INFO @ Mon, 03 Jun 2019 10:31:20: #2 predicted fragment length is 186 bps INFO @ Mon, 03 Jun 2019 10:31:20: #2 alternative fragment length(s) may be 186 bps INFO @ Mon, 03 Jun 2019 10:31:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287876/SRX287876.10_model.r INFO @ Mon, 03 Jun 2019 10:31:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:31:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:31:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:32:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:32:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:32:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287876/SRX287876.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:32:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287876/SRX287876.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:32:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287876/SRX287876.20_summits.bed INFO @ Mon, 03 Jun 2019 10:32:21: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1587 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:32:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287876/SRX287876.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:32:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287876/SRX287876.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:32:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287876/SRX287876.05_summits.bed INFO @ Mon, 03 Jun 2019 10:32:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4688 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:32:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287876/SRX287876.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:32:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287876/SRX287876.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:32:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287876/SRX287876.10_summits.bed INFO @ Mon, 03 Jun 2019 10:32:38: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2820 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。