Job ID = 1299139 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T08:56:24 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 : 22,398,369 reads read : 22,398,369 reads written : 22,398,369 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: 00:09:34 22398369 reads; of these: 22398369 (100.00%) were unpaired; of these: 310375 (1.39%) aligned 0 times 13726097 (61.28%) aligned exactly 1 time 8361897 (37.33%) aligned >1 times 98.61% overall alignment rate Time searching: 00:09:34 Overall time: 00:09:34 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] 1019671 / 22087994 = 0.0462 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 18:21:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474520/SRX474520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474520/SRX474520.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474520/SRX474520.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474520/SRX474520.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 18:21:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:21:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:21:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474520/SRX474520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474520/SRX474520.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474520/SRX474520.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474520/SRX474520.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 18:21:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:21:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:21:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474520/SRX474520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474520/SRX474520.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474520/SRX474520.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474520/SRX474520.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 18:21:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:21:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:21:39: 1000000 INFO @ Mon, 03 Jun 2019 18:21:41: 1000000 INFO @ Mon, 03 Jun 2019 18:21:41: 1000000 INFO @ Mon, 03 Jun 2019 18:21:46: 2000000 INFO @ Mon, 03 Jun 2019 18:21:48: 2000000 INFO @ Mon, 03 Jun 2019 18:21:49: 2000000 INFO @ Mon, 03 Jun 2019 18:21:53: 3000000 INFO @ Mon, 03 Jun 2019 18:21:56: 3000000 INFO @ Mon, 03 Jun 2019 18:21:57: 3000000 INFO @ Mon, 03 Jun 2019 18:22:00: 4000000 INFO @ Mon, 03 Jun 2019 18:22:04: 4000000 INFO @ Mon, 03 Jun 2019 18:22:04: 4000000 INFO @ Mon, 03 Jun 2019 18:22:07: 5000000 INFO @ Mon, 03 Jun 2019 18:22:11: 5000000 INFO @ Mon, 03 Jun 2019 18:22:12: 5000000 INFO @ Mon, 03 Jun 2019 18:22:14: 6000000 INFO @ Mon, 03 Jun 2019 18:22:19: 6000000 INFO @ Mon, 03 Jun 2019 18:22:19: 6000000 INFO @ Mon, 03 Jun 2019 18:22:21: 7000000 INFO @ Mon, 03 Jun 2019 18:22:26: 7000000 INFO @ Mon, 03 Jun 2019 18:22:27: 7000000 INFO @ Mon, 03 Jun 2019 18:22:28: 8000000 INFO @ Mon, 03 Jun 2019 18:22:34: 8000000 INFO @ Mon, 03 Jun 2019 18:22:34: 9000000 INFO @ Mon, 03 Jun 2019 18:22:35: 8000000 INFO @ Mon, 03 Jun 2019 18:22:41: 10000000 INFO @ Mon, 03 Jun 2019 18:22:41: 9000000 INFO @ Mon, 03 Jun 2019 18:22:42: 9000000 INFO @ Mon, 03 Jun 2019 18:22:48: 11000000 INFO @ Mon, 03 Jun 2019 18:22:49: 10000000 INFO @ Mon, 03 Jun 2019 18:22:50: 10000000 INFO @ Mon, 03 Jun 2019 18:22:55: 12000000 INFO @ Mon, 03 Jun 2019 18:22:56: 11000000 INFO @ Mon, 03 Jun 2019 18:22:57: 11000000 INFO @ Mon, 03 Jun 2019 18:23:02: 13000000 INFO @ Mon, 03 Jun 2019 18:23:04: 12000000 INFO @ Mon, 03 Jun 2019 18:23:05: 12000000 INFO @ Mon, 03 Jun 2019 18:23:09: 14000000 INFO @ Mon, 03 Jun 2019 18:23:11: 13000000 INFO @ Mon, 03 Jun 2019 18:23:12: 13000000 INFO @ Mon, 03 Jun 2019 18:23:16: 15000000 INFO @ Mon, 03 Jun 2019 18:23:19: 14000000 INFO @ Mon, 03 Jun 2019 18:23:20: 14000000 INFO @ Mon, 03 Jun 2019 18:23:23: 16000000 INFO @ Mon, 03 Jun 2019 18:23:26: 15000000 INFO @ Mon, 03 Jun 2019 18:23:27: 15000000 INFO @ Mon, 03 Jun 2019 18:23:30: 17000000 INFO @ Mon, 03 Jun 2019 18:23:34: 16000000 INFO @ Mon, 03 Jun 2019 18:23:35: 16000000 INFO @ Mon, 03 Jun 2019 18:23:36: 18000000 INFO @ Mon, 03 Jun 2019 18:23:41: 17000000 INFO @ Mon, 03 Jun 2019 18:23:43: 17000000 INFO @ Mon, 03 Jun 2019 18:23:43: 19000000 INFO @ Mon, 03 Jun 2019 18:23:49: 18000000 INFO @ Mon, 03 Jun 2019 18:23:50: 20000000 INFO @ Mon, 03 Jun 2019 18:23:50: 18000000 INFO @ Mon, 03 Jun 2019 18:23:56: 19000000 INFO @ Mon, 03 Jun 2019 18:23:57: 21000000 INFO @ Mon, 03 Jun 2019 18:23:58: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 18:23:58: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 18:23:58: #1 total tags in treatment: 21068323 INFO @ Mon, 03 Jun 2019 18:23:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:23:58: #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 18:23:58: #1 tags after filtering in treatment: 21068323 INFO @ Mon, 03 Jun 2019 18:23:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:23:58: #1 finished! INFO @ Mon, 03 Jun 2019 18:23:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:23:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:23:58: 19000000 INFO @ Mon, 03 Jun 2019 18:24:00: #2 number of paired peaks: 191 WARNING @ Mon, 03 Jun 2019 18:24:00: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Mon, 03 Jun 2019 18:24:00: start model_add_line... INFO @ Mon, 03 Jun 2019 18:24:00: start X-correlation... INFO @ Mon, 03 Jun 2019 18:24:00: end of X-cor INFO @ Mon, 03 Jun 2019 18:24:00: #2 finished! INFO @ Mon, 03 Jun 2019 18:24:00: #2 predicted fragment length is 167 bps INFO @ Mon, 03 Jun 2019 18:24:00: #2 alternative fragment length(s) may be 167 bps INFO @ Mon, 03 Jun 2019 18:24:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474520/SRX474520.10_model.r INFO @ Mon, 03 Jun 2019 18:24:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:24:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:24:04: 20000000 INFO @ Mon, 03 Jun 2019 18:24:06: 20000000 INFO @ Mon, 03 Jun 2019 18:24:11: 21000000 INFO @ Mon, 03 Jun 2019 18:24:12: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 18:24:12: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 18:24:12: #1 total tags in treatment: 21068323 INFO @ Mon, 03 Jun 2019 18:24:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:24:12: #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 18:24:12: #1 tags after filtering in treatment: 21068323 INFO @ Mon, 03 Jun 2019 18:24:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:24:12: #1 finished! INFO @ Mon, 03 Jun 2019 18:24:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:24:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:24:13: 21000000 INFO @ Mon, 03 Jun 2019 18:24:14: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 18:24:14: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 18:24:14: #1 total tags in treatment: 21068323 INFO @ Mon, 03 Jun 2019 18:24:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:24:14: #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 18:24:14: #2 number of paired peaks: 191 WARNING @ Mon, 03 Jun 2019 18:24:14: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Mon, 03 Jun 2019 18:24:14: start model_add_line... INFO @ Mon, 03 Jun 2019 18:24:14: start X-correlation... INFO @ Mon, 03 Jun 2019 18:24:14: end of X-cor INFO @ Mon, 03 Jun 2019 18:24:14: #2 finished! INFO @ Mon, 03 Jun 2019 18:24:14: #2 predicted fragment length is 167 bps INFO @ Mon, 03 Jun 2019 18:24:14: #2 alternative fragment length(s) may be 167 bps INFO @ Mon, 03 Jun 2019 18:24:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474520/SRX474520.20_model.r INFO @ Mon, 03 Jun 2019 18:24:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:24:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:24:14: #1 tags after filtering in treatment: 21068323 INFO @ Mon, 03 Jun 2019 18:24:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:24:14: #1 finished! INFO @ Mon, 03 Jun 2019 18:24:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:24:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:24:16: #2 number of paired peaks: 191 WARNING @ Mon, 03 Jun 2019 18:24:16: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Mon, 03 Jun 2019 18:24:16: start model_add_line... INFO @ Mon, 03 Jun 2019 18:24:16: start X-correlation... INFO @ Mon, 03 Jun 2019 18:24:16: end of X-cor INFO @ Mon, 03 Jun 2019 18:24:16: #2 finished! INFO @ Mon, 03 Jun 2019 18:24:16: #2 predicted fragment length is 167 bps INFO @ Mon, 03 Jun 2019 18:24:16: #2 alternative fragment length(s) may be 167 bps INFO @ Mon, 03 Jun 2019 18:24:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474520/SRX474520.05_model.r INFO @ Mon, 03 Jun 2019 18:24:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:24:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:24:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:25:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:25:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:25:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474520/SRX474520.10_peaks.xls INFO @ Mon, 03 Jun 2019 18:25:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474520/SRX474520.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:25:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474520/SRX474520.10_summits.bed INFO @ Mon, 03 Jun 2019 18:25:25: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (4033 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:25:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474520/SRX474520.20_peaks.xls INFO @ Mon, 03 Jun 2019 18:25:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474520/SRX474520.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:25:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474520/SRX474520.20_summits.bed INFO @ Mon, 03 Jun 2019 18:25:39: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1939 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:25:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474520/SRX474520.05_peaks.xls INFO @ Mon, 03 Jun 2019 18:25:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474520/SRX474520.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:25:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474520/SRX474520.05_summits.bed INFO @ Mon, 03 Jun 2019 18:25:41: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7023 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。