Job ID = 1293647 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T16:31:06 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 : 41,546,488 reads read : 41,546,488 reads written : 41,546,488 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: 00:09:17 41546488 reads; of these: 41546488 (100.00%) were unpaired; of these: 2596917 (6.25%) aligned 0 times 34628631 (83.35%) aligned exactly 1 time 4320940 (10.40%) aligned >1 times 93.75% overall alignment rate Time searching: 00:09:17 Overall time: 00:09:17 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] 13683541 / 38949571 = 0.3513 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 01:52:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104961/SRX104961.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104961/SRX104961.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104961/SRX104961.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104961/SRX104961.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 01:52:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:52:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:52:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104961/SRX104961.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104961/SRX104961.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104961/SRX104961.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104961/SRX104961.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 01:52:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:52:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:52:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104961/SRX104961.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104961/SRX104961.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104961/SRX104961.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104961/SRX104961.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 01:52:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:52:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:52:24: 1000000 INFO @ Mon, 03 Jun 2019 01:52:25: 1000000 INFO @ Mon, 03 Jun 2019 01:52:26: 1000000 INFO @ Mon, 03 Jun 2019 01:52:32: 2000000 INFO @ Mon, 03 Jun 2019 01:52:33: 2000000 INFO @ Mon, 03 Jun 2019 01:52:36: 2000000 INFO @ Mon, 03 Jun 2019 01:52:40: 3000000 INFO @ Mon, 03 Jun 2019 01:52:41: 3000000 INFO @ Mon, 03 Jun 2019 01:52:46: 3000000 INFO @ Mon, 03 Jun 2019 01:52:47: 4000000 INFO @ Mon, 03 Jun 2019 01:52:49: 4000000 INFO @ Mon, 03 Jun 2019 01:52:54: 5000000 INFO @ Mon, 03 Jun 2019 01:52:55: 4000000 INFO @ Mon, 03 Jun 2019 01:52:57: 5000000 INFO @ Mon, 03 Jun 2019 01:53:01: 6000000 INFO @ Mon, 03 Jun 2019 01:53:05: 5000000 INFO @ Mon, 03 Jun 2019 01:53:05: 6000000 INFO @ Mon, 03 Jun 2019 01:53:09: 7000000 INFO @ Mon, 03 Jun 2019 01:53:13: 7000000 INFO @ Mon, 03 Jun 2019 01:53:14: 6000000 INFO @ Mon, 03 Jun 2019 01:53:16: 8000000 INFO @ Mon, 03 Jun 2019 01:53:21: 8000000 INFO @ Mon, 03 Jun 2019 01:53:23: 9000000 INFO @ Mon, 03 Jun 2019 01:53:24: 7000000 INFO @ Mon, 03 Jun 2019 01:53:29: 9000000 INFO @ Mon, 03 Jun 2019 01:53:30: 10000000 INFO @ Mon, 03 Jun 2019 01:53:33: 8000000 INFO @ Mon, 03 Jun 2019 01:53:37: 10000000 INFO @ Mon, 03 Jun 2019 01:53:38: 11000000 INFO @ Mon, 03 Jun 2019 01:53:43: 9000000 INFO @ Mon, 03 Jun 2019 01:53:44: 11000000 INFO @ Mon, 03 Jun 2019 01:53:45: 12000000 INFO @ Mon, 03 Jun 2019 01:53:52: 10000000 INFO @ Mon, 03 Jun 2019 01:53:53: 12000000 INFO @ Mon, 03 Jun 2019 01:53:53: 13000000 INFO @ Mon, 03 Jun 2019 01:54:01: 13000000 INFO @ Mon, 03 Jun 2019 01:54:01: 14000000 INFO @ Mon, 03 Jun 2019 01:54:02: 11000000 INFO @ Mon, 03 Jun 2019 01:54:09: 14000000 INFO @ Mon, 03 Jun 2019 01:54:09: 15000000 INFO @ Mon, 03 Jun 2019 01:54:11: 12000000 INFO @ Mon, 03 Jun 2019 01:54:17: 15000000 INFO @ Mon, 03 Jun 2019 01:54:17: 16000000 INFO @ Mon, 03 Jun 2019 01:54:21: 13000000 INFO @ Mon, 03 Jun 2019 01:54:25: 16000000 INFO @ Mon, 03 Jun 2019 01:54:25: 17000000 INFO @ Mon, 03 Jun 2019 01:54:30: 14000000 INFO @ Mon, 03 Jun 2019 01:54:33: 17000000 INFO @ Mon, 03 Jun 2019 01:54:33: 18000000 INFO @ Mon, 03 Jun 2019 01:54:40: 15000000 INFO @ Mon, 03 Jun 2019 01:54:41: 18000000 INFO @ Mon, 03 Jun 2019 01:54:41: 19000000 INFO @ Mon, 03 Jun 2019 01:54:49: 19000000 INFO @ Mon, 03 Jun 2019 01:54:49: 20000000 INFO @ Mon, 03 Jun 2019 01:54:49: 16000000 INFO @ Mon, 03 Jun 2019 01:54:57: 20000000 INFO @ Mon, 03 Jun 2019 01:54:57: 21000000 INFO @ Mon, 03 Jun 2019 01:54:59: 17000000 INFO @ Mon, 03 Jun 2019 01:55:05: 22000000 INFO @ Mon, 03 Jun 2019 01:55:05: 21000000 INFO @ Mon, 03 Jun 2019 01:55:08: 18000000 INFO @ Mon, 03 Jun 2019 01:55:13: 23000000 INFO @ Mon, 03 Jun 2019 01:55:13: 22000000 INFO @ Mon, 03 Jun 2019 01:55:18: 19000000 INFO @ Mon, 03 Jun 2019 01:55:21: 24000000 INFO @ Mon, 03 Jun 2019 01:55:21: 23000000 INFO @ Mon, 03 Jun 2019 01:55:27: 20000000 INFO @ Mon, 03 Jun 2019 01:55:29: 25000000 INFO @ Mon, 03 Jun 2019 01:55:29: 24000000 INFO @ Mon, 03 Jun 2019 01:55:31: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 01:55:31: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 01:55:31: #1 total tags in treatment: 25266030 INFO @ Mon, 03 Jun 2019 01:55:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:55:31: #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 01:55:32: #1 tags after filtering in treatment: 25266030 INFO @ Mon, 03 Jun 2019 01:55:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:55:32: #1 finished! INFO @ Mon, 03 Jun 2019 01:55:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:55:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:55:34: #2 number of paired peaks: 459 WARNING @ Mon, 03 Jun 2019 01:55:34: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Mon, 03 Jun 2019 01:55:34: start model_add_line... INFO @ Mon, 03 Jun 2019 01:55:34: start X-correlation... INFO @ Mon, 03 Jun 2019 01:55:34: end of X-cor INFO @ Mon, 03 Jun 2019 01:55:34: #2 finished! INFO @ Mon, 03 Jun 2019 01:55:34: #2 predicted fragment length is 124 bps INFO @ Mon, 03 Jun 2019 01:55:34: #2 alternative fragment length(s) may be 124 bps INFO @ Mon, 03 Jun 2019 01:55:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX104961/SRX104961.05_model.r INFO @ Mon, 03 Jun 2019 01:55:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:55:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:55:36: 21000000 INFO @ Mon, 03 Jun 2019 01:55:37: 25000000 INFO @ Mon, 03 Jun 2019 01:55:39: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 01:55:39: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 01:55:39: #1 total tags in treatment: 25266030 INFO @ Mon, 03 Jun 2019 01:55:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:55:39: #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 01:55:40: #1 tags after filtering in treatment: 25266030 INFO @ Mon, 03 Jun 2019 01:55:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:55:40: #1 finished! INFO @ Mon, 03 Jun 2019 01:55:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:55:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:55:42: #2 number of paired peaks: 459 WARNING @ Mon, 03 Jun 2019 01:55:42: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Mon, 03 Jun 2019 01:55:42: start model_add_line... INFO @ Mon, 03 Jun 2019 01:55:42: start X-correlation... INFO @ Mon, 03 Jun 2019 01:55:42: end of X-cor INFO @ Mon, 03 Jun 2019 01:55:42: #2 finished! INFO @ Mon, 03 Jun 2019 01:55:42: #2 predicted fragment length is 124 bps INFO @ Mon, 03 Jun 2019 01:55:42: #2 alternative fragment length(s) may be 124 bps INFO @ Mon, 03 Jun 2019 01:55:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX104961/SRX104961.20_model.r INFO @ Mon, 03 Jun 2019 01:55:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:55:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:55:45: 22000000 INFO @ Mon, 03 Jun 2019 01:55:54: 23000000 INFO @ Mon, 03 Jun 2019 01:56:03: 24000000 INFO @ Mon, 03 Jun 2019 01:56:12: 25000000 INFO @ Mon, 03 Jun 2019 01:56:15: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 01:56:15: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 01:56:15: #1 total tags in treatment: 25266030 INFO @ Mon, 03 Jun 2019 01:56:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:56:15: #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 01:56:15: #1 tags after filtering in treatment: 25266030 INFO @ Mon, 03 Jun 2019 01:56:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:56:15: #1 finished! INFO @ Mon, 03 Jun 2019 01:56:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:56:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:56:17: #2 number of paired peaks: 459 WARNING @ Mon, 03 Jun 2019 01:56:17: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Mon, 03 Jun 2019 01:56:17: start model_add_line... INFO @ Mon, 03 Jun 2019 01:56:18: start X-correlation... INFO @ Mon, 03 Jun 2019 01:56:18: end of X-cor INFO @ Mon, 03 Jun 2019 01:56:18: #2 finished! INFO @ Mon, 03 Jun 2019 01:56:18: #2 predicted fragment length is 124 bps INFO @ Mon, 03 Jun 2019 01:56:18: #2 alternative fragment length(s) may be 124 bps INFO @ Mon, 03 Jun 2019 01:56:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX104961/SRX104961.10_model.r INFO @ Mon, 03 Jun 2019 01:56:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:56:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:56:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:56:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:57:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX104961/SRX104961.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:57:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX104961/SRX104961.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:57:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX104961/SRX104961.05_summits.bed INFO @ Mon, 03 Jun 2019 01:57:11: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (12191 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:57:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX104961/SRX104961.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:57:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX104961/SRX104961.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:57:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX104961/SRX104961.20_summits.bed INFO @ Mon, 03 Jun 2019 01:57:18: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4921 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:57:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:57:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX104961/SRX104961.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:57:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX104961/SRX104961.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:57:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX104961/SRX104961.10_summits.bed INFO @ Mon, 03 Jun 2019 01:57:54: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8139 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。