Job ID = 1294960 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T02:01:26 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 : 16,366,646 reads read : 16,366,646 reads written : 16,366,646 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: 00:05:08 16366646 reads; of these: 16366646 (100.00%) were unpaired; of these: 975452 (5.96%) aligned 0 times 12539230 (76.61%) aligned exactly 1 time 2851964 (17.43%) aligned >1 times 94.04% overall alignment rate Time searching: 00:05:08 Overall time: 00:05:08 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 8 files... [bam_rmdupse_core] 2051971 / 15391194 = 0.1333 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 11:12:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288021/SRX288021.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288021/SRX288021.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288021/SRX288021.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288021/SRX288021.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 11:12:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:12:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:12:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288021/SRX288021.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288021/SRX288021.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288021/SRX288021.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288021/SRX288021.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 11:12:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:12:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:12:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288021/SRX288021.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288021/SRX288021.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288021/SRX288021.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288021/SRX288021.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 11:12:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:12:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:12:59: 1000000 INFO @ Mon, 03 Jun 2019 11:12:59: 1000000 INFO @ Mon, 03 Jun 2019 11:13:00: 1000000 INFO @ Mon, 03 Jun 2019 11:13:08: 2000000 INFO @ Mon, 03 Jun 2019 11:13:09: 2000000 INFO @ Mon, 03 Jun 2019 11:13:09: 2000000 INFO @ Mon, 03 Jun 2019 11:13:17: 3000000 INFO @ Mon, 03 Jun 2019 11:13:18: 3000000 INFO @ Mon, 03 Jun 2019 11:13:19: 3000000 INFO @ Mon, 03 Jun 2019 11:13:26: 4000000 INFO @ Mon, 03 Jun 2019 11:13:26: 4000000 INFO @ Mon, 03 Jun 2019 11:13:27: 4000000 INFO @ Mon, 03 Jun 2019 11:13:34: 5000000 INFO @ Mon, 03 Jun 2019 11:13:35: 5000000 INFO @ Mon, 03 Jun 2019 11:13:36: 5000000 INFO @ Mon, 03 Jun 2019 11:13:42: 6000000 INFO @ Mon, 03 Jun 2019 11:13:43: 6000000 INFO @ Mon, 03 Jun 2019 11:13:45: 6000000 INFO @ Mon, 03 Jun 2019 11:13:51: 7000000 INFO @ Mon, 03 Jun 2019 11:13:51: 7000000 INFO @ Mon, 03 Jun 2019 11:13:54: 7000000 INFO @ Mon, 03 Jun 2019 11:13:59: 8000000 INFO @ Mon, 03 Jun 2019 11:14:00: 8000000 INFO @ Mon, 03 Jun 2019 11:14:02: 8000000 INFO @ Mon, 03 Jun 2019 11:14:08: 9000000 INFO @ Mon, 03 Jun 2019 11:14:08: 9000000 INFO @ Mon, 03 Jun 2019 11:14:10: 9000000 INFO @ Mon, 03 Jun 2019 11:14:16: 10000000 INFO @ Mon, 03 Jun 2019 11:14:16: 10000000 INFO @ Mon, 03 Jun 2019 11:14:18: 10000000 INFO @ Mon, 03 Jun 2019 11:14:24: 11000000 INFO @ Mon, 03 Jun 2019 11:14:25: 11000000 INFO @ Mon, 03 Jun 2019 11:14:27: 11000000 INFO @ Mon, 03 Jun 2019 11:14:33: 12000000 INFO @ Mon, 03 Jun 2019 11:14:34: 12000000 INFO @ Mon, 03 Jun 2019 11:14:36: 12000000 INFO @ Mon, 03 Jun 2019 11:14:41: 13000000 INFO @ Mon, 03 Jun 2019 11:14:43: 13000000 INFO @ Mon, 03 Jun 2019 11:14:44: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:14:44: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:14:44: #1 total tags in treatment: 13339223 INFO @ Mon, 03 Jun 2019 11:14:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:14:44: #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 11:14:44: #1 tags after filtering in treatment: 13339223 INFO @ Mon, 03 Jun 2019 11:14:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:14:44: #1 finished! INFO @ Mon, 03 Jun 2019 11:14:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:14:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:14:45: 13000000 INFO @ Mon, 03 Jun 2019 11:14:45: #2 number of paired peaks: 2627 INFO @ Mon, 03 Jun 2019 11:14:45: start model_add_line... INFO @ Mon, 03 Jun 2019 11:14:46: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:14:46: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:14:46: #1 total tags in treatment: 13339223 INFO @ Mon, 03 Jun 2019 11:14:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:14:46: #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 11:14:46: start X-correlation... INFO @ Mon, 03 Jun 2019 11:14:46: end of X-cor INFO @ Mon, 03 Jun 2019 11:14:46: #2 finished! INFO @ Mon, 03 Jun 2019 11:14:46: #2 predicted fragment length is 206 bps INFO @ Mon, 03 Jun 2019 11:14:46: #2 alternative fragment length(s) may be 206 bps INFO @ Mon, 03 Jun 2019 11:14:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288021/SRX288021.05_model.r INFO @ Mon, 03 Jun 2019 11:14:46: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:14:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:14:46: #1 tags after filtering in treatment: 13339223 INFO @ Mon, 03 Jun 2019 11:14:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:14:46: #1 finished! INFO @ Mon, 03 Jun 2019 11:14:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:14:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:14:47: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:14:47: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:14:47: #1 total tags in treatment: 13339223 INFO @ Mon, 03 Jun 2019 11:14:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:14:47: #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 11:14:47: #2 number of paired peaks: 2627 INFO @ Mon, 03 Jun 2019 11:14:47: start model_add_line... INFO @ Mon, 03 Jun 2019 11:14:48: start X-correlation... INFO @ Mon, 03 Jun 2019 11:14:48: end of X-cor INFO @ Mon, 03 Jun 2019 11:14:48: #2 finished! INFO @ Mon, 03 Jun 2019 11:14:48: #2 predicted fragment length is 206 bps INFO @ Mon, 03 Jun 2019 11:14:48: #2 alternative fragment length(s) may be 206 bps INFO @ Mon, 03 Jun 2019 11:14:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288021/SRX288021.10_model.r INFO @ Mon, 03 Jun 2019 11:14:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:14:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:14:48: #1 tags after filtering in treatment: 13339223 INFO @ Mon, 03 Jun 2019 11:14:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:14:48: #1 finished! INFO @ Mon, 03 Jun 2019 11:14:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:14:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:14:49: #2 number of paired peaks: 2627 INFO @ Mon, 03 Jun 2019 11:14:49: start model_add_line... INFO @ Mon, 03 Jun 2019 11:14:49: start X-correlation... INFO @ Mon, 03 Jun 2019 11:14:49: end of X-cor INFO @ Mon, 03 Jun 2019 11:14:49: #2 finished! INFO @ Mon, 03 Jun 2019 11:14:49: #2 predicted fragment length is 206 bps INFO @ Mon, 03 Jun 2019 11:14:49: #2 alternative fragment length(s) may be 206 bps INFO @ Mon, 03 Jun 2019 11:14:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288021/SRX288021.20_model.r INFO @ Mon, 03 Jun 2019 11:14:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:14:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:15:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:15:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:15:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:15:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288021/SRX288021.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:15:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288021/SRX288021.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:15:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288021/SRX288021.05_summits.bed INFO @ Mon, 03 Jun 2019 11:15:47: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7874 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:15:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288021/SRX288021.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:15:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288021/SRX288021.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:15:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288021/SRX288021.10_summits.bed INFO @ Mon, 03 Jun 2019 11:15:49: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (6211 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:15:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288021/SRX288021.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:15:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288021/SRX288021.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:15:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288021/SRX288021.20_summits.bed INFO @ Mon, 03 Jun 2019 11:15:51: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4476 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。