Job ID = 1294845 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T01:23:28 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 ) 2019-06-03T01:33:41 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 : 26,373,715 reads read : 26,373,715 reads written : 26,373,715 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: 00:08:29 26373715 reads; of these: 26373715 (100.00%) were unpaired; of these: 1307572 (4.96%) aligned 0 times 20129603 (76.32%) aligned exactly 1 time 4936540 (18.72%) aligned >1 times 95.04% overall alignment rate Time searching: 00:08:29 Overall time: 00:08:29 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] 3482085 / 25066143 = 0.1389 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 10:52:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287940/SRX287940.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287940/SRX287940.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287940/SRX287940.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287940/SRX287940.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 10:52:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:52:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:52:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287940/SRX287940.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287940/SRX287940.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287940/SRX287940.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287940/SRX287940.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 10:52:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:52:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:52:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287940/SRX287940.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287940/SRX287940.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287940/SRX287940.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287940/SRX287940.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 10:52:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:52:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:53:00: 1000000 INFO @ Mon, 03 Jun 2019 10:53:03: 1000000 INFO @ Mon, 03 Jun 2019 10:53:03: 1000000 INFO @ Mon, 03 Jun 2019 10:53:07: 2000000 INFO @ Mon, 03 Jun 2019 10:53:13: 2000000 INFO @ Mon, 03 Jun 2019 10:53:13: 2000000 INFO @ Mon, 03 Jun 2019 10:53:14: 3000000 INFO @ Mon, 03 Jun 2019 10:53:21: 4000000 INFO @ Mon, 03 Jun 2019 10:53:23: 3000000 INFO @ Mon, 03 Jun 2019 10:53:24: 3000000 INFO @ Mon, 03 Jun 2019 10:53:29: 5000000 INFO @ Mon, 03 Jun 2019 10:53:33: 4000000 INFO @ Mon, 03 Jun 2019 10:53:34: 4000000 INFO @ Mon, 03 Jun 2019 10:53:36: 6000000 INFO @ Mon, 03 Jun 2019 10:53:43: 5000000 INFO @ Mon, 03 Jun 2019 10:53:43: 7000000 INFO @ Mon, 03 Jun 2019 10:53:44: 5000000 INFO @ Mon, 03 Jun 2019 10:53:51: 8000000 INFO @ Mon, 03 Jun 2019 10:53:52: 6000000 INFO @ Mon, 03 Jun 2019 10:53:54: 6000000 INFO @ Mon, 03 Jun 2019 10:53:58: 9000000 INFO @ Mon, 03 Jun 2019 10:54:01: 7000000 INFO @ Mon, 03 Jun 2019 10:54:04: 7000000 INFO @ Mon, 03 Jun 2019 10:54:06: 10000000 INFO @ Mon, 03 Jun 2019 10:54:10: 8000000 INFO @ Mon, 03 Jun 2019 10:54:13: 11000000 INFO @ Mon, 03 Jun 2019 10:54:14: 8000000 INFO @ Mon, 03 Jun 2019 10:54:20: 9000000 INFO @ Mon, 03 Jun 2019 10:54:20: 12000000 INFO @ Mon, 03 Jun 2019 10:54:24: 9000000 INFO @ Mon, 03 Jun 2019 10:54:27: 13000000 INFO @ Mon, 03 Jun 2019 10:54:29: 10000000 INFO @ Mon, 03 Jun 2019 10:54:34: 10000000 INFO @ Mon, 03 Jun 2019 10:54:34: 14000000 INFO @ Mon, 03 Jun 2019 10:54:39: 11000000 INFO @ Mon, 03 Jun 2019 10:54:42: 15000000 INFO @ Mon, 03 Jun 2019 10:54:44: 11000000 INFO @ Mon, 03 Jun 2019 10:54:48: 12000000 INFO @ Mon, 03 Jun 2019 10:54:49: 16000000 INFO @ Mon, 03 Jun 2019 10:54:54: 12000000 INFO @ Mon, 03 Jun 2019 10:54:56: 17000000 INFO @ Mon, 03 Jun 2019 10:54:58: 13000000 INFO @ Mon, 03 Jun 2019 10:55:04: 18000000 INFO @ Mon, 03 Jun 2019 10:55:04: 13000000 INFO @ Mon, 03 Jun 2019 10:55:08: 14000000 INFO @ Mon, 03 Jun 2019 10:55:11: 19000000 INFO @ Mon, 03 Jun 2019 10:55:14: 14000000 INFO @ Mon, 03 Jun 2019 10:55:17: 15000000 INFO @ Mon, 03 Jun 2019 10:55:18: 20000000 INFO @ Mon, 03 Jun 2019 10:55:24: 15000000 INFO @ Mon, 03 Jun 2019 10:55:26: 21000000 INFO @ Mon, 03 Jun 2019 10:55:26: 16000000 INFO @ Mon, 03 Jun 2019 10:55:30: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:55:30: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:55:30: #1 total tags in treatment: 21584058 INFO @ Mon, 03 Jun 2019 10:55:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:55:30: #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 10:55:31: #1 tags after filtering in treatment: 21584058 INFO @ Mon, 03 Jun 2019 10:55:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:55:31: #1 finished! INFO @ Mon, 03 Jun 2019 10:55:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:55:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:55:32: #2 number of paired peaks: 155 WARNING @ Mon, 03 Jun 2019 10:55:32: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Mon, 03 Jun 2019 10:55:32: start model_add_line... INFO @ Mon, 03 Jun 2019 10:55:33: start X-correlation... INFO @ Mon, 03 Jun 2019 10:55:33: end of X-cor INFO @ Mon, 03 Jun 2019 10:55:33: #2 finished! INFO @ Mon, 03 Jun 2019 10:55:33: #2 predicted fragment length is 158 bps INFO @ Mon, 03 Jun 2019 10:55:33: #2 alternative fragment length(s) may be 158 bps INFO @ Mon, 03 Jun 2019 10:55:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287940/SRX287940.20_model.r INFO @ Mon, 03 Jun 2019 10:55:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:55:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:55:33: 16000000 INFO @ Mon, 03 Jun 2019 10:55:36: 17000000 INFO @ Mon, 03 Jun 2019 10:55:43: 17000000 INFO @ Mon, 03 Jun 2019 10:55:46: 18000000 INFO @ Mon, 03 Jun 2019 10:55:53: 18000000 INFO @ Mon, 03 Jun 2019 10:55:56: 19000000 INFO @ Mon, 03 Jun 2019 10:56:02: 19000000 INFO @ Mon, 03 Jun 2019 10:56:05: 20000000 INFO @ Mon, 03 Jun 2019 10:56:11: 20000000 INFO @ Mon, 03 Jun 2019 10:56:15: 21000000 INFO @ Mon, 03 Jun 2019 10:56:20: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:56:20: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:56:20: #1 total tags in treatment: 21584058 INFO @ Mon, 03 Jun 2019 10:56:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:56:20: #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 10:56:21: 21000000 INFO @ Mon, 03 Jun 2019 10:56:21: #1 tags after filtering in treatment: 21584058 INFO @ Mon, 03 Jun 2019 10:56:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:56:21: #1 finished! INFO @ Mon, 03 Jun 2019 10:56:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:56:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:56:23: #2 number of paired peaks: 155 WARNING @ Mon, 03 Jun 2019 10:56:23: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Mon, 03 Jun 2019 10:56:23: start model_add_line... INFO @ Mon, 03 Jun 2019 10:56:23: start X-correlation... INFO @ Mon, 03 Jun 2019 10:56:23: end of X-cor INFO @ Mon, 03 Jun 2019 10:56:23: #2 finished! INFO @ Mon, 03 Jun 2019 10:56:23: #2 predicted fragment length is 158 bps INFO @ Mon, 03 Jun 2019 10:56:23: #2 alternative fragment length(s) may be 158 bps INFO @ Mon, 03 Jun 2019 10:56:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287940/SRX287940.10_model.r INFO @ Mon, 03 Jun 2019 10:56:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:56:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:56:26: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:56:26: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:56:26: #1 total tags in treatment: 21584058 INFO @ Mon, 03 Jun 2019 10:56:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:56:26: #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 10:56:26: #1 tags after filtering in treatment: 21584058 INFO @ Mon, 03 Jun 2019 10:56:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:56:26: #1 finished! INFO @ Mon, 03 Jun 2019 10:56:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:56:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:56:28: #2 number of paired peaks: 155 WARNING @ Mon, 03 Jun 2019 10:56:28: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Mon, 03 Jun 2019 10:56:28: start model_add_line... INFO @ Mon, 03 Jun 2019 10:56:28: start X-correlation... INFO @ Mon, 03 Jun 2019 10:56:28: end of X-cor INFO @ Mon, 03 Jun 2019 10:56:28: #2 finished! INFO @ Mon, 03 Jun 2019 10:56:28: #2 predicted fragment length is 158 bps INFO @ Mon, 03 Jun 2019 10:56:28: #2 alternative fragment length(s) may be 158 bps INFO @ Mon, 03 Jun 2019 10:56:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287940/SRX287940.05_model.r INFO @ Mon, 03 Jun 2019 10:56:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:56:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:56:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:56:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287940/SRX287940.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:56:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287940/SRX287940.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:56:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287940/SRX287940.20_summits.bed INFO @ Mon, 03 Jun 2019 10:56:58: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (2453 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:57:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:57:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:57:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287940/SRX287940.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:57:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287940/SRX287940.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:57:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287940/SRX287940.10_summits.bed INFO @ Mon, 03 Jun 2019 10:57:49: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (5604 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:57:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287940/SRX287940.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:57:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287940/SRX287940.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:57:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287940/SRX287940.05_summits.bed INFO @ Mon, 03 Jun 2019 10:57:55: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (8687 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。