Job ID = 4178563 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-05T04:03:23 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 ) 2019-12-05T04:03:23 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 ) 2019-12-05T04:03:23 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 ) 2019-12-05T04:03:23 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 : 29,146,312 reads read : 58,292,624 reads written : 29,146,312 reads 0-length : 29,146,312 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: 00:08:36 29146312 reads; of these: 29146312 (100.00%) were unpaired; of these: 4174578 (14.32%) aligned 0 times 21328497 (73.18%) aligned exactly 1 time 3643237 (12.50%) aligned >1 times 85.68% overall alignment rate Time searching: 00:08:36 Overall time: 00:08:36 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] 8301139 / 24971734 = 0.3324 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:31:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827835/SRX5827835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827835/SRX5827835.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827835/SRX5827835.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827835/SRX5827835.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 13:31:30: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:31:30: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:31:42: 1000000 INFO @ Thu, 05 Dec 2019 13:31:51: 2000000 INFO @ Thu, 05 Dec 2019 13:32:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827835/SRX5827835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827835/SRX5827835.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827835/SRX5827835.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827835/SRX5827835.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 13:32:00: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:32:00: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:32:00: 3000000 INFO @ Thu, 05 Dec 2019 13:32:10: 1000000 INFO @ Thu, 05 Dec 2019 13:32:10: 4000000 INFO @ Thu, 05 Dec 2019 13:32:19: 2000000 INFO @ Thu, 05 Dec 2019 13:32:21: 5000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:32:29: 3000000 INFO @ Thu, 05 Dec 2019 13:32:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827835/SRX5827835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827835/SRX5827835.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827835/SRX5827835.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827835/SRX5827835.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 13:32:30: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:32:30: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:32:31: 6000000 INFO @ Thu, 05 Dec 2019 13:32:38: 4000000 INFO @ Thu, 05 Dec 2019 13:32:40: 1000000 INFO @ Thu, 05 Dec 2019 13:32:41: 7000000 INFO @ Thu, 05 Dec 2019 13:32:48: 5000000 INFO @ Thu, 05 Dec 2019 13:32:50: 2000000 INFO @ Thu, 05 Dec 2019 13:32:54: 8000000 INFO @ Thu, 05 Dec 2019 13:32:58: 6000000 INFO @ Thu, 05 Dec 2019 13:33:01: 3000000 INFO @ Thu, 05 Dec 2019 13:33:06: 9000000 INFO @ Thu, 05 Dec 2019 13:33:09: 7000000 INFO @ Thu, 05 Dec 2019 13:33:11: 4000000 INFO @ Thu, 05 Dec 2019 13:33:18: 10000000 INFO @ Thu, 05 Dec 2019 13:33:19: 8000000 INFO @ Thu, 05 Dec 2019 13:33:20: 5000000 INFO @ Thu, 05 Dec 2019 13:33:29: 9000000 INFO @ Thu, 05 Dec 2019 13:33:29: 11000000 INFO @ Thu, 05 Dec 2019 13:33:30: 6000000 INFO @ Thu, 05 Dec 2019 13:33:38: 10000000 INFO @ Thu, 05 Dec 2019 13:33:40: 7000000 INFO @ Thu, 05 Dec 2019 13:33:41: 12000000 INFO @ Thu, 05 Dec 2019 13:33:49: 11000000 INFO @ Thu, 05 Dec 2019 13:33:50: 8000000 INFO @ Thu, 05 Dec 2019 13:33:52: 13000000 INFO @ Thu, 05 Dec 2019 13:33:58: 12000000 INFO @ Thu, 05 Dec 2019 13:34:00: 9000000 INFO @ Thu, 05 Dec 2019 13:34:04: 14000000 INFO @ Thu, 05 Dec 2019 13:34:08: 13000000 INFO @ Thu, 05 Dec 2019 13:34:10: 10000000 INFO @ Thu, 05 Dec 2019 13:34:16: 15000000 INFO @ Thu, 05 Dec 2019 13:34:18: 14000000 INFO @ Thu, 05 Dec 2019 13:34:19: 11000000 INFO @ Thu, 05 Dec 2019 13:34:26: 16000000 INFO @ Thu, 05 Dec 2019 13:34:29: 15000000 INFO @ Thu, 05 Dec 2019 13:34:29: 12000000 INFO @ Thu, 05 Dec 2019 13:34:33: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:34:33: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:34:33: #1 total tags in treatment: 16670595 INFO @ Thu, 05 Dec 2019 13:34:33: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:34:33: #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 13:34:33: #1 tags after filtering in treatment: 16670595 INFO @ Thu, 05 Dec 2019 13:34:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:34:33: #1 finished! INFO @ Thu, 05 Dec 2019 13:34:33: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:34:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:34:36: #2 number of paired peaks: 843 WARNING @ Thu, 05 Dec 2019 13:34:36: Fewer paired peaks (843) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 843 pairs to build model! INFO @ Thu, 05 Dec 2019 13:34:36: start model_add_line... INFO @ Thu, 05 Dec 2019 13:34:36: start X-correlation... INFO @ Thu, 05 Dec 2019 13:34:36: end of X-cor INFO @ Thu, 05 Dec 2019 13:34:36: #2 finished! INFO @ Thu, 05 Dec 2019 13:34:36: #2 predicted fragment length is 167 bps INFO @ Thu, 05 Dec 2019 13:34:36: #2 alternative fragment length(s) may be 167 bps INFO @ Thu, 05 Dec 2019 13:34:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827835/SRX5827835.05_model.r INFO @ Thu, 05 Dec 2019 13:34:36: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:34:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:34:41: 13000000 INFO @ Thu, 05 Dec 2019 13:34:41: 16000000 INFO @ Thu, 05 Dec 2019 13:34:50: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:34:50: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:34:50: #1 total tags in treatment: 16670595 INFO @ Thu, 05 Dec 2019 13:34:50: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:34:50: #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 13:34:50: #1 tags after filtering in treatment: 16670595 INFO @ Thu, 05 Dec 2019 13:34:50: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:34:50: #1 finished! INFO @ Thu, 05 Dec 2019 13:34:50: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:34:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:34:51: 14000000 INFO @ Thu, 05 Dec 2019 13:34:52: #2 number of paired peaks: 843 WARNING @ Thu, 05 Dec 2019 13:34:52: Fewer paired peaks (843) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 843 pairs to build model! INFO @ Thu, 05 Dec 2019 13:34:52: start model_add_line... INFO @ Thu, 05 Dec 2019 13:34:52: start X-correlation... INFO @ Thu, 05 Dec 2019 13:34:52: end of X-cor INFO @ Thu, 05 Dec 2019 13:34:52: #2 finished! INFO @ Thu, 05 Dec 2019 13:34:52: #2 predicted fragment length is 167 bps INFO @ Thu, 05 Dec 2019 13:34:52: #2 alternative fragment length(s) may be 167 bps INFO @ Thu, 05 Dec 2019 13:34:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827835/SRX5827835.10_model.r INFO @ Thu, 05 Dec 2019 13:34:55: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:34:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:35:02: 15000000 INFO @ Thu, 05 Dec 2019 13:35:11: 16000000 INFO @ Thu, 05 Dec 2019 13:35:18: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:35:18: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:35:18: #1 total tags in treatment: 16670595 INFO @ Thu, 05 Dec 2019 13:35:18: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:35:18: #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 13:35:18: #1 tags after filtering in treatment: 16670595 INFO @ Thu, 05 Dec 2019 13:35:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:35:18: #1 finished! INFO @ Thu, 05 Dec 2019 13:35:18: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:35:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:35:20: #2 number of paired peaks: 843 WARNING @ Thu, 05 Dec 2019 13:35:20: Fewer paired peaks (843) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 843 pairs to build model! INFO @ Thu, 05 Dec 2019 13:35:20: start model_add_line... INFO @ Thu, 05 Dec 2019 13:35:20: start X-correlation... INFO @ Thu, 05 Dec 2019 13:35:20: end of X-cor INFO @ Thu, 05 Dec 2019 13:35:20: #2 finished! INFO @ Thu, 05 Dec 2019 13:35:20: #2 predicted fragment length is 167 bps INFO @ Thu, 05 Dec 2019 13:35:20: #2 alternative fragment length(s) may be 167 bps INFO @ Thu, 05 Dec 2019 13:35:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827835/SRX5827835.20_model.r INFO @ Thu, 05 Dec 2019 13:35:20: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:35:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:35:32: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:35:47: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:35:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827835/SRX5827835.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:35:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827835/SRX5827835.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:35:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827835/SRX5827835.05_summits.bed INFO @ Thu, 05 Dec 2019 13:35:58: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6551 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:36:11: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:36:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827835/SRX5827835.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:36:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827835/SRX5827835.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:36:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827835/SRX5827835.10_summits.bed INFO @ Thu, 05 Dec 2019 13:36:12: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4158 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:36:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827835/SRX5827835.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:36:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827835/SRX5827835.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:36:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827835/SRX5827835.20_summits.bed INFO @ Thu, 05 Dec 2019 13:36:38: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2015 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。