Job ID = 1294703 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:45:48 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-03T00:48:00 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 : 14,404,929 reads read : 14,404,929 reads written : 14,404,929 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: 00:04:00 14404929 reads; of these: 14404929 (100.00%) were unpaired; of these: 628781 (4.37%) aligned 0 times 12522809 (86.93%) aligned exactly 1 time 1253339 (8.70%) aligned >1 times 95.63% overall alignment rate Time searching: 00:04:00 Overall time: 00:04:00 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 8 files... [bam_rmdupse_core] 1695723 / 13776148 = 0.1231 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 09:57:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287832/SRX287832.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287832/SRX287832.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287832/SRX287832.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287832/SRX287832.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 09:57:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:57:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:57:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287832/SRX287832.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287832/SRX287832.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287832/SRX287832.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287832/SRX287832.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 09:57:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:57:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:57:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287832/SRX287832.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287832/SRX287832.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287832/SRX287832.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287832/SRX287832.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 09:57:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:57:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:57:10: 1000000 INFO @ Mon, 03 Jun 2019 09:57:12: 1000000 INFO @ Mon, 03 Jun 2019 09:57:12: 1000000 INFO @ Mon, 03 Jun 2019 09:57:20: 2000000 INFO @ Mon, 03 Jun 2019 09:57:22: 2000000 INFO @ Mon, 03 Jun 2019 09:57:23: 2000000 INFO @ Mon, 03 Jun 2019 09:57:29: 3000000 INFO @ Mon, 03 Jun 2019 09:57:33: 3000000 INFO @ Mon, 03 Jun 2019 09:57:34: 3000000 INFO @ Mon, 03 Jun 2019 09:57:39: 4000000 INFO @ Mon, 03 Jun 2019 09:57:43: 4000000 INFO @ Mon, 03 Jun 2019 09:57:45: 4000000 INFO @ Mon, 03 Jun 2019 09:57:48: 5000000 INFO @ Mon, 03 Jun 2019 09:57:54: 5000000 INFO @ Mon, 03 Jun 2019 09:57:56: 5000000 INFO @ Mon, 03 Jun 2019 09:57:58: 6000000 INFO @ Mon, 03 Jun 2019 09:58:05: 6000000 INFO @ Mon, 03 Jun 2019 09:58:07: 6000000 INFO @ Mon, 03 Jun 2019 09:58:08: 7000000 INFO @ Mon, 03 Jun 2019 09:58:16: 7000000 INFO @ Mon, 03 Jun 2019 09:58:18: 8000000 INFO @ Mon, 03 Jun 2019 09:58:18: 7000000 INFO @ Mon, 03 Jun 2019 09:58:26: 8000000 INFO @ Mon, 03 Jun 2019 09:58:27: 9000000 INFO @ Mon, 03 Jun 2019 09:58:30: 8000000 INFO @ Mon, 03 Jun 2019 09:58:36: 10000000 INFO @ Mon, 03 Jun 2019 09:58:37: 9000000 INFO @ Mon, 03 Jun 2019 09:58:41: 9000000 INFO @ Mon, 03 Jun 2019 09:58:46: 11000000 INFO @ Mon, 03 Jun 2019 09:58:47: 10000000 INFO @ Mon, 03 Jun 2019 09:58:52: 10000000 INFO @ Mon, 03 Jun 2019 09:58:55: 12000000 INFO @ Mon, 03 Jun 2019 09:58:56: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:58:56: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:58:56: #1 total tags in treatment: 12080425 INFO @ Mon, 03 Jun 2019 09:58:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:58:56: #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 09:58:56: #1 tags after filtering in treatment: 12080425 INFO @ Mon, 03 Jun 2019 09:58:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:58:56: #1 finished! INFO @ Mon, 03 Jun 2019 09:58:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:58:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:58:57: 11000000 INFO @ Mon, 03 Jun 2019 09:58:58: #2 number of paired peaks: 6509 INFO @ Mon, 03 Jun 2019 09:58:58: start model_add_line... INFO @ Mon, 03 Jun 2019 09:58:58: start X-correlation... INFO @ Mon, 03 Jun 2019 09:58:58: end of X-cor INFO @ Mon, 03 Jun 2019 09:58:58: #2 finished! INFO @ Mon, 03 Jun 2019 09:58:58: #2 predicted fragment length is 191 bps INFO @ Mon, 03 Jun 2019 09:58:58: #2 alternative fragment length(s) may be 191 bps INFO @ Mon, 03 Jun 2019 09:58:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287832/SRX287832.10_model.r INFO @ Mon, 03 Jun 2019 09:58:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:58:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:59:03: 11000000 INFO @ Mon, 03 Jun 2019 09:59:08: 12000000 INFO @ Mon, 03 Jun 2019 09:59:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:59:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:59:08: #1 total tags in treatment: 12080425 INFO @ Mon, 03 Jun 2019 09:59:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:59:08: #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 09:59:09: #1 tags after filtering in treatment: 12080425 INFO @ Mon, 03 Jun 2019 09:59:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:59:09: #1 finished! INFO @ Mon, 03 Jun 2019 09:59:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:59:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:59:10: #2 number of paired peaks: 6509 INFO @ Mon, 03 Jun 2019 09:59:10: start model_add_line... INFO @ Mon, 03 Jun 2019 09:59:11: start X-correlation... INFO @ Mon, 03 Jun 2019 09:59:11: end of X-cor INFO @ Mon, 03 Jun 2019 09:59:11: #2 finished! INFO @ Mon, 03 Jun 2019 09:59:11: #2 predicted fragment length is 191 bps INFO @ Mon, 03 Jun 2019 09:59:11: #2 alternative fragment length(s) may be 191 bps INFO @ Mon, 03 Jun 2019 09:59:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287832/SRX287832.20_model.r INFO @ Mon, 03 Jun 2019 09:59:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:59:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:59:14: 12000000 INFO @ Mon, 03 Jun 2019 09:59:15: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:59:15: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:59:15: #1 total tags in treatment: 12080425 INFO @ Mon, 03 Jun 2019 09:59:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:59:15: #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 09:59:15: #1 tags after filtering in treatment: 12080425 INFO @ Mon, 03 Jun 2019 09:59:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:59:15: #1 finished! INFO @ Mon, 03 Jun 2019 09:59:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:59:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:59:17: #2 number of paired peaks: 6509 INFO @ Mon, 03 Jun 2019 09:59:17: start model_add_line... INFO @ Mon, 03 Jun 2019 09:59:17: start X-correlation... INFO @ Mon, 03 Jun 2019 09:59:17: end of X-cor INFO @ Mon, 03 Jun 2019 09:59:17: #2 finished! INFO @ Mon, 03 Jun 2019 09:59:17: #2 predicted fragment length is 191 bps INFO @ Mon, 03 Jun 2019 09:59:17: #2 alternative fragment length(s) may be 191 bps INFO @ Mon, 03 Jun 2019 09:59:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287832/SRX287832.05_model.r INFO @ Mon, 03 Jun 2019 09:59:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:59:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:59:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:59:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:59:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287832/SRX287832.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:59:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287832/SRX287832.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:59:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287832/SRX287832.10_summits.bed INFO @ Mon, 03 Jun 2019 09:59:56: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (7038 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:59:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:00:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287832/SRX287832.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:00:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287832/SRX287832.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:00:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287832/SRX287832.20_summits.bed INFO @ Mon, 03 Jun 2019 10:00:08: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4198 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:00:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287832/SRX287832.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:00:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287832/SRX287832.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:00:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287832/SRX287832.05_summits.bed INFO @ Mon, 03 Jun 2019 10:00:15: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9194 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。