Job ID = 1309194 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T14:06:25 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 ) 2019-06-03T14:08:51 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 ) 2019-06-03T14:10:52 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 ) spots read : 19,577,660 reads read : 19,577,660 reads written : 19,577,660 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:23 19577660 reads; of these: 19577660 (100.00%) were unpaired; of these: 8884684 (45.38%) aligned 0 times 9322610 (47.62%) aligned exactly 1 time 1370366 (7.00%) aligned >1 times 54.62% overall alignment rate Time searching: 00:04:24 Overall time: 00:04:24 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_rmdupse_core] 4234042 / 10692976 = 0.3960 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 23:23:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX826333/SRX826333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX826333/SRX826333.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX826333/SRX826333.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX826333/SRX826333.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 23:23:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:23:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:23:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX826333/SRX826333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX826333/SRX826333.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX826333/SRX826333.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX826333/SRX826333.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 23:23:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:23:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:23:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX826333/SRX826333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX826333/SRX826333.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX826333/SRX826333.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX826333/SRX826333.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 23:23:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:23:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:23:46: 1000000 INFO @ Mon, 03 Jun 2019 23:23:46: 1000000 INFO @ Mon, 03 Jun 2019 23:23:47: 1000000 INFO @ Mon, 03 Jun 2019 23:23:53: 2000000 INFO @ Mon, 03 Jun 2019 23:23:54: 2000000 INFO @ Mon, 03 Jun 2019 23:23:55: 2000000 INFO @ Mon, 03 Jun 2019 23:24:01: 3000000 INFO @ Mon, 03 Jun 2019 23:24:01: 3000000 INFO @ Mon, 03 Jun 2019 23:24:04: 3000000 INFO @ Mon, 03 Jun 2019 23:24:08: 4000000 INFO @ Mon, 03 Jun 2019 23:24:09: 4000000 INFO @ Mon, 03 Jun 2019 23:24:12: 4000000 INFO @ Mon, 03 Jun 2019 23:24:16: 5000000 INFO @ Mon, 03 Jun 2019 23:24:17: 5000000 INFO @ Mon, 03 Jun 2019 23:24:21: 5000000 INFO @ Mon, 03 Jun 2019 23:24:23: 6000000 INFO @ Mon, 03 Jun 2019 23:24:25: 6000000 INFO @ Mon, 03 Jun 2019 23:24:27: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 23:24:27: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 23:24:27: #1 total tags in treatment: 6458934 INFO @ Mon, 03 Jun 2019 23:24:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:24:27: #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 23:24:27: #1 tags after filtering in treatment: 6458934 INFO @ Mon, 03 Jun 2019 23:24:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:24:27: #1 finished! INFO @ Mon, 03 Jun 2019 23:24:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:24:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:24:28: #2 number of paired peaks: 1971 INFO @ Mon, 03 Jun 2019 23:24:28: start model_add_line... INFO @ Mon, 03 Jun 2019 23:24:28: start X-correlation... INFO @ Mon, 03 Jun 2019 23:24:28: end of X-cor INFO @ Mon, 03 Jun 2019 23:24:28: #2 finished! INFO @ Mon, 03 Jun 2019 23:24:28: #2 predicted fragment length is 186 bps INFO @ Mon, 03 Jun 2019 23:24:28: #2 alternative fragment length(s) may be 186 bps INFO @ Mon, 03 Jun 2019 23:24:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX826333/SRX826333.05_model.r INFO @ Mon, 03 Jun 2019 23:24:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:24:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:24:28: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 23:24:28: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 23:24:28: #1 total tags in treatment: 6458934 INFO @ Mon, 03 Jun 2019 23:24:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:24:28: #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 23:24:29: #1 tags after filtering in treatment: 6458934 INFO @ Mon, 03 Jun 2019 23:24:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:24:29: #1 finished! INFO @ Mon, 03 Jun 2019 23:24:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:24:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:24:29: 6000000 INFO @ Mon, 03 Jun 2019 23:24:29: #2 number of paired peaks: 1971 INFO @ Mon, 03 Jun 2019 23:24:29: start model_add_line... INFO @ Mon, 03 Jun 2019 23:24:29: start X-correlation... INFO @ Mon, 03 Jun 2019 23:24:29: end of X-cor INFO @ Mon, 03 Jun 2019 23:24:29: #2 finished! INFO @ Mon, 03 Jun 2019 23:24:29: #2 predicted fragment length is 186 bps INFO @ Mon, 03 Jun 2019 23:24:29: #2 alternative fragment length(s) may be 186 bps INFO @ Mon, 03 Jun 2019 23:24:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX826333/SRX826333.10_model.r INFO @ Mon, 03 Jun 2019 23:24:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:24:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:24:33: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 23:24:33: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 23:24:33: #1 total tags in treatment: 6458934 INFO @ Mon, 03 Jun 2019 23:24:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:24:33: #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 23:24:33: #1 tags after filtering in treatment: 6458934 INFO @ Mon, 03 Jun 2019 23:24:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:24:33: #1 finished! INFO @ Mon, 03 Jun 2019 23:24:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:24:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:24:34: #2 number of paired peaks: 1971 INFO @ Mon, 03 Jun 2019 23:24:34: start model_add_line... INFO @ Mon, 03 Jun 2019 23:24:34: start X-correlation... INFO @ Mon, 03 Jun 2019 23:24:34: end of X-cor INFO @ Mon, 03 Jun 2019 23:24:34: #2 finished! INFO @ Mon, 03 Jun 2019 23:24:34: #2 predicted fragment length is 186 bps INFO @ Mon, 03 Jun 2019 23:24:34: #2 alternative fragment length(s) may be 186 bps INFO @ Mon, 03 Jun 2019 23:24:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX826333/SRX826333.20_model.r INFO @ Mon, 03 Jun 2019 23:24:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:24:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:24:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:24:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:24:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:25:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX826333/SRX826333.05_peaks.xls INFO @ Mon, 03 Jun 2019 23:25:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX826333/SRX826333.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:25:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX826333/SRX826333.05_summits.bed INFO @ Mon, 03 Jun 2019 23:25:01: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5550 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:25:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX826333/SRX826333.10_peaks.xls INFO @ Mon, 03 Jun 2019 23:25:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX826333/SRX826333.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:25:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX826333/SRX826333.10_summits.bed INFO @ Mon, 03 Jun 2019 23:25:03: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3896 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:25:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX826333/SRX826333.20_peaks.xls INFO @ Mon, 03 Jun 2019 23:25:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX826333/SRX826333.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:25:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX826333/SRX826333.20_summits.bed INFO @ Mon, 03 Jun 2019 23:25:07: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2527 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。