Job ID = 4178548 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-05T04:00:31 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 ) 2019-12-05T04:00:31 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 ) 2019-12-05T04:00:31 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 ) 2019-12-05T04:00:31 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 ) 2019-12-05T04:00:31 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 : 37,931,333 reads read : 75,862,666 reads written : 37,931,333 reads 0-length : 37,931,333 rm: cannot remove ‘[DSE]RR*’: 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: 00:11:29 37931333 reads; of these: 37931333 (100.00%) were unpaired; of these: 4020587 (10.60%) aligned 0 times 28638274 (75.50%) aligned exactly 1 time 5272472 (13.90%) aligned >1 times 89.40% overall alignment rate Time searching: 00:11:29 Overall time: 00:11:30 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 16 files... [bam_rmdupse_core] 17912010 / 33910746 = 0.5282 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:29:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827820/SRX5827820.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827820/SRX5827820.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827820/SRX5827820.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827820/SRX5827820.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 @ Thu, 05 Dec 2019 13:29:00: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:29:00: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:29:07: 1000000 INFO @ Thu, 05 Dec 2019 13:29:14: 2000000 INFO @ Thu, 05 Dec 2019 13:29:21: 3000000 INFO @ Thu, 05 Dec 2019 13:29:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827820/SRX5827820.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827820/SRX5827820.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827820/SRX5827820.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827820/SRX5827820.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 @ Thu, 05 Dec 2019 13:29:28: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:29:28: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:29:29: 4000000 INFO @ Thu, 05 Dec 2019 13:29:36: 1000000 INFO @ Thu, 05 Dec 2019 13:29:36: 5000000 INFO @ Thu, 05 Dec 2019 13:29:44: 2000000 INFO @ Thu, 05 Dec 2019 13:29:44: 6000000 INFO @ Thu, 05 Dec 2019 13:29:51: 7000000 INFO @ Thu, 05 Dec 2019 13:29:51: 3000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:29:58: 8000000 INFO @ Thu, 05 Dec 2019 13:29:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827820/SRX5827820.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827820/SRX5827820.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827820/SRX5827820.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827820/SRX5827820.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 @ Thu, 05 Dec 2019 13:29:59: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:29:59: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:29:59: 4000000 INFO @ Thu, 05 Dec 2019 13:30:08: 1000000 INFO @ Thu, 05 Dec 2019 13:30:11: 5000000 INFO @ Thu, 05 Dec 2019 13:30:12: 9000000 INFO @ Thu, 05 Dec 2019 13:30:17: 2000000 INFO @ Thu, 05 Dec 2019 13:30:21: 10000000 INFO @ Thu, 05 Dec 2019 13:30:23: 6000000 INFO @ Thu, 05 Dec 2019 13:30:29: 3000000 INFO @ Thu, 05 Dec 2019 13:30:31: 11000000 INFO @ Thu, 05 Dec 2019 13:30:34: 7000000 INFO @ Thu, 05 Dec 2019 13:30:37: 4000000 INFO @ Thu, 05 Dec 2019 13:30:38: 12000000 INFO @ Thu, 05 Dec 2019 13:30:42: 8000000 INFO @ Thu, 05 Dec 2019 13:30:44: 5000000 INFO @ Thu, 05 Dec 2019 13:30:46: 13000000 INFO @ Thu, 05 Dec 2019 13:30:49: 9000000 INFO @ Thu, 05 Dec 2019 13:30:52: 6000000 INFO @ Thu, 05 Dec 2019 13:30:54: 14000000 INFO @ Thu, 05 Dec 2019 13:30:57: 10000000 INFO @ Thu, 05 Dec 2019 13:31:00: 7000000 INFO @ Thu, 05 Dec 2019 13:31:01: 15000000 INFO @ Thu, 05 Dec 2019 13:31:04: 11000000 INFO @ Thu, 05 Dec 2019 13:31:08: 8000000 INFO @ Thu, 05 Dec 2019 13:31:09: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:31:09: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:31:09: #1 total tags in treatment: 15998736 INFO @ Thu, 05 Dec 2019 13:31:09: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:31:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:31:09: #1 tags after filtering in treatment: 15998736 INFO @ Thu, 05 Dec 2019 13:31:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:31:09: #1 finished! INFO @ Thu, 05 Dec 2019 13:31:09: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:31:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:31:10: #2 number of paired peaks: 1414 INFO @ Thu, 05 Dec 2019 13:31:10: start model_add_line... INFO @ Thu, 05 Dec 2019 13:31:11: start X-correlation... INFO @ Thu, 05 Dec 2019 13:31:11: end of X-cor INFO @ Thu, 05 Dec 2019 13:31:11: #2 finished! INFO @ Thu, 05 Dec 2019 13:31:11: #2 predicted fragment length is 160 bps INFO @ Thu, 05 Dec 2019 13:31:11: #2 alternative fragment length(s) may be 160 bps INFO @ Thu, 05 Dec 2019 13:31:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827820/SRX5827820.05_model.r INFO @ Thu, 05 Dec 2019 13:31:11: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:31:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:31:12: 12000000 INFO @ Thu, 05 Dec 2019 13:31:16: 9000000 INFO @ Thu, 05 Dec 2019 13:31:20: 13000000 INFO @ Thu, 05 Dec 2019 13:31:23: 10000000 INFO @ Thu, 05 Dec 2019 13:31:28: 14000000 INFO @ Thu, 05 Dec 2019 13:31:31: 11000000 INFO @ Thu, 05 Dec 2019 13:31:43: 15000000 INFO @ Thu, 05 Dec 2019 13:31:45: 12000000 INFO @ Thu, 05 Dec 2019 13:31:55: 13000000 INFO @ Thu, 05 Dec 2019 13:31:56: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:31:56: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:31:56: #1 total tags in treatment: 15998736 INFO @ Thu, 05 Dec 2019 13:31:56: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:31:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:31:56: #1 tags after filtering in treatment: 15998736 INFO @ Thu, 05 Dec 2019 13:31:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:31:56: #1 finished! INFO @ Thu, 05 Dec 2019 13:31:56: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:31:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:31:58: #2 number of paired peaks: 1414 INFO @ Thu, 05 Dec 2019 13:31:58: start model_add_line... INFO @ Thu, 05 Dec 2019 13:31:58: start X-correlation... INFO @ Thu, 05 Dec 2019 13:31:58: end of X-cor INFO @ Thu, 05 Dec 2019 13:31:58: #2 finished! INFO @ Thu, 05 Dec 2019 13:31:58: #2 predicted fragment length is 160 bps INFO @ Thu, 05 Dec 2019 13:31:58: #2 alternative fragment length(s) may be 160 bps INFO @ Thu, 05 Dec 2019 13:31:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827820/SRX5827820.10_model.r INFO @ Thu, 05 Dec 2019 13:31:58: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:31:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:32:05: 14000000 INFO @ Thu, 05 Dec 2019 13:32:15: 15000000 INFO @ Thu, 05 Dec 2019 13:32:15: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:32:24: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:32:24: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:32:24: #1 total tags in treatment: 15998736 INFO @ Thu, 05 Dec 2019 13:32:24: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:32:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:32:24: #1 tags after filtering in treatment: 15998736 INFO @ Thu, 05 Dec 2019 13:32:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:32:24: #1 finished! INFO @ Thu, 05 Dec 2019 13:32:24: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:32:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:32:27: #2 number of paired peaks: 1414 INFO @ Thu, 05 Dec 2019 13:32:27: start model_add_line... INFO @ Thu, 05 Dec 2019 13:32:27: start X-correlation... INFO @ Thu, 05 Dec 2019 13:32:27: end of X-cor INFO @ Thu, 05 Dec 2019 13:32:27: #2 finished! INFO @ Thu, 05 Dec 2019 13:32:27: #2 predicted fragment length is 160 bps INFO @ Thu, 05 Dec 2019 13:32:27: #2 alternative fragment length(s) may be 160 bps INFO @ Thu, 05 Dec 2019 13:32:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827820/SRX5827820.20_model.r INFO @ Thu, 05 Dec 2019 13:32:27: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:32:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:32:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827820/SRX5827820.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:32:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827820/SRX5827820.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:32:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827820/SRX5827820.05_summits.bed INFO @ Thu, 05 Dec 2019 13:32:46: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4041 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:32:55: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:33:14: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:33:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827820/SRX5827820.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:33:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827820/SRX5827820.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:33:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827820/SRX5827820.10_summits.bed INFO @ Thu, 05 Dec 2019 13:33:18: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2613 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:33:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827820/SRX5827820.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:33:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827820/SRX5827820.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:33:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827820/SRX5827820.20_summits.bed INFO @ Thu, 05 Dec 2019 13:33:37: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1624 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。