Job ID = 1307690 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:32:28 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 ) spots read : 27,894,518 reads read : 55,789,036 reads written : 27,894,518 reads 0-length : 27,894,518 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: 00:08:56 27894518 reads; of these: 27894518 (100.00%) were unpaired; of these: 6196025 (22.21%) aligned 0 times 18688767 (67.00%) aligned exactly 1 time 3009726 (10.79%) aligned >1 times 77.79% overall alignment rate Time searching: 00:08:56 Overall time: 00:08:56 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] 9355989 / 21698493 = 0.4312 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 22:54:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343112/SRX5343112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343112/SRX5343112.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343112/SRX5343112.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343112/SRX5343112.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 22:54:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:54:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:54:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343112/SRX5343112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343112/SRX5343112.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343112/SRX5343112.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343112/SRX5343112.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 22:54:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343112/SRX5343112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343112/SRX5343112.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343112/SRX5343112.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343112/SRX5343112.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 22:54:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:54:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:54:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:54:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:54:24: 1000000 INFO @ Mon, 03 Jun 2019 22:54:25: 1000000 INFO @ Mon, 03 Jun 2019 22:54:25: 1000000 INFO @ Mon, 03 Jun 2019 22:54:31: 2000000 INFO @ Mon, 03 Jun 2019 22:54:34: 2000000 INFO @ Mon, 03 Jun 2019 22:54:34: 2000000 INFO @ Mon, 03 Jun 2019 22:54:39: 3000000 INFO @ Mon, 03 Jun 2019 22:54:43: 3000000 INFO @ Mon, 03 Jun 2019 22:54:43: 3000000 INFO @ Mon, 03 Jun 2019 22:54:46: 4000000 INFO @ Mon, 03 Jun 2019 22:54:52: 4000000 INFO @ Mon, 03 Jun 2019 22:54:52: 4000000 INFO @ Mon, 03 Jun 2019 22:54:54: 5000000 INFO @ Mon, 03 Jun 2019 22:55:01: 5000000 INFO @ Mon, 03 Jun 2019 22:55:01: 5000000 INFO @ Mon, 03 Jun 2019 22:55:01: 6000000 INFO @ Mon, 03 Jun 2019 22:55:09: 7000000 INFO @ Mon, 03 Jun 2019 22:55:10: 6000000 INFO @ Mon, 03 Jun 2019 22:55:10: 6000000 INFO @ Mon, 03 Jun 2019 22:55:16: 8000000 INFO @ Mon, 03 Jun 2019 22:55:19: 7000000 INFO @ Mon, 03 Jun 2019 22:55:19: 7000000 INFO @ Mon, 03 Jun 2019 22:55:24: 9000000 INFO @ Mon, 03 Jun 2019 22:55:28: 8000000 INFO @ Mon, 03 Jun 2019 22:55:28: 8000000 INFO @ Mon, 03 Jun 2019 22:55:31: 10000000 INFO @ Mon, 03 Jun 2019 22:55:37: 9000000 INFO @ Mon, 03 Jun 2019 22:55:37: 9000000 INFO @ Mon, 03 Jun 2019 22:55:40: 11000000 INFO @ Mon, 03 Jun 2019 22:55:46: 10000000 INFO @ Mon, 03 Jun 2019 22:55:46: 10000000 INFO @ Mon, 03 Jun 2019 22:55:49: 12000000 INFO @ Mon, 03 Jun 2019 22:55:51: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:55:51: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:55:51: #1 total tags in treatment: 12342504 INFO @ Mon, 03 Jun 2019 22:55:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:55:51: #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 22:55:52: #1 tags after filtering in treatment: 12342504 INFO @ Mon, 03 Jun 2019 22:55:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:55:52: #1 finished! INFO @ Mon, 03 Jun 2019 22:55:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:55:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:55:54: #2 number of paired peaks: 8034 INFO @ Mon, 03 Jun 2019 22:55:54: start model_add_line... INFO @ Mon, 03 Jun 2019 22:55:54: start X-correlation... INFO @ Mon, 03 Jun 2019 22:55:54: end of X-cor INFO @ Mon, 03 Jun 2019 22:55:54: #2 finished! INFO @ Mon, 03 Jun 2019 22:55:54: #2 predicted fragment length is 158 bps INFO @ Mon, 03 Jun 2019 22:55:54: #2 alternative fragment length(s) may be 158 bps INFO @ Mon, 03 Jun 2019 22:55:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343112/SRX5343112.20_model.r INFO @ Mon, 03 Jun 2019 22:55:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:55:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:55:55: 11000000 INFO @ Mon, 03 Jun 2019 22:55:55: 11000000 INFO @ Mon, 03 Jun 2019 22:56:04: 12000000 INFO @ Mon, 03 Jun 2019 22:56:04: 12000000 INFO @ Mon, 03 Jun 2019 22:56:07: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:56:07: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:56:07: #1 total tags in treatment: 12342504 INFO @ Mon, 03 Jun 2019 22:56:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:56:07: #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 22:56:07: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:56:07: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:56:07: #1 total tags in treatment: 12342504 INFO @ Mon, 03 Jun 2019 22:56:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:56:07: #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 22:56:07: #1 tags after filtering in treatment: 12342504 INFO @ Mon, 03 Jun 2019 22:56:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:56:07: #1 finished! INFO @ Mon, 03 Jun 2019 22:56:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:56:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:56:07: #1 tags after filtering in treatment: 12342504 INFO @ Mon, 03 Jun 2019 22:56:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:56:07: #1 finished! INFO @ Mon, 03 Jun 2019 22:56:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:56:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:56:09: #2 number of paired peaks: 8034 INFO @ Mon, 03 Jun 2019 22:56:09: start model_add_line... INFO @ Mon, 03 Jun 2019 22:56:09: #2 number of paired peaks: 8034 INFO @ Mon, 03 Jun 2019 22:56:09: start model_add_line... INFO @ Mon, 03 Jun 2019 22:56:09: start X-correlation... INFO @ Mon, 03 Jun 2019 22:56:09: start X-correlation... INFO @ Mon, 03 Jun 2019 22:56:09: end of X-cor INFO @ Mon, 03 Jun 2019 22:56:09: #2 finished! INFO @ Mon, 03 Jun 2019 22:56:09: #2 predicted fragment length is 158 bps INFO @ Mon, 03 Jun 2019 22:56:09: #2 alternative fragment length(s) may be 158 bps INFO @ Mon, 03 Jun 2019 22:56:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343112/SRX5343112.10_model.r INFO @ Mon, 03 Jun 2019 22:56:09: end of X-cor INFO @ Mon, 03 Jun 2019 22:56:09: #2 finished! INFO @ Mon, 03 Jun 2019 22:56:09: #2 predicted fragment length is 158 bps INFO @ Mon, 03 Jun 2019 22:56:09: #2 alternative fragment length(s) may be 158 bps INFO @ Mon, 03 Jun 2019 22:56:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343112/SRX5343112.05_model.r INFO @ Mon, 03 Jun 2019 22:56:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:56:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:56:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:56:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:56:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:56:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:56:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:56:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343112/SRX5343112.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:56:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343112/SRX5343112.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:56:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343112/SRX5343112.20_summits.bed INFO @ Mon, 03 Jun 2019 22:56:50: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (6592 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:57:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343112/SRX5343112.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:57:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343112/SRX5343112.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:57:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343112/SRX5343112.10_summits.bed INFO @ Mon, 03 Jun 2019 22:57:07: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7884 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:57:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343112/SRX5343112.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:57:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343112/SRX5343112.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:57:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343112/SRX5343112.05_summits.bed INFO @ Mon, 03 Jun 2019 22:57:08: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (8831 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。