Job ID = 1295157 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T03:23:48 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 ) 2019-06-03T03:23:48 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 : 36,078,793 reads read : 72,157,586 reads written : 36,078,793 reads 0-length : 36,078,793 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: 00:08:01 36078793 reads; of these: 36078793 (100.00%) were unpaired; of these: 1023507 (2.84%) aligned 0 times 33336790 (92.40%) aligned exactly 1 time 1718496 (4.76%) aligned >1 times 97.16% overall alignment rate Time searching: 00:08:01 Overall time: 00:08:01 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 16 files... [bam_rmdupse_core] 16729892 / 35055286 = 0.4772 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 12:46:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3279766/SRX3279766.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3279766/SRX3279766.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3279766/SRX3279766.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3279766/SRX3279766.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 12:46:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:46:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:46:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3279766/SRX3279766.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3279766/SRX3279766.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3279766/SRX3279766.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3279766/SRX3279766.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 12:46:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:46:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:46:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3279766/SRX3279766.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3279766/SRX3279766.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3279766/SRX3279766.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3279766/SRX3279766.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 12:46:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:46:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:46:36: 1000000 INFO @ Mon, 03 Jun 2019 12:46:37: 1000000 INFO @ Mon, 03 Jun 2019 12:46:37: 1000000 INFO @ Mon, 03 Jun 2019 12:46:44: 2000000 INFO @ Mon, 03 Jun 2019 12:46:47: 2000000 INFO @ Mon, 03 Jun 2019 12:46:48: 2000000 INFO @ Mon, 03 Jun 2019 12:46:53: 3000000 INFO @ Mon, 03 Jun 2019 12:46:56: 3000000 INFO @ Mon, 03 Jun 2019 12:46:58: 3000000 INFO @ Mon, 03 Jun 2019 12:47:01: 4000000 INFO @ Mon, 03 Jun 2019 12:47:06: 4000000 INFO @ Mon, 03 Jun 2019 12:47:08: 4000000 INFO @ Mon, 03 Jun 2019 12:47:09: 5000000 INFO @ Mon, 03 Jun 2019 12:47:15: 5000000 INFO @ Mon, 03 Jun 2019 12:47:17: 5000000 INFO @ Mon, 03 Jun 2019 12:47:17: 6000000 INFO @ Mon, 03 Jun 2019 12:47:25: 6000000 INFO @ Mon, 03 Jun 2019 12:47:25: 7000000 INFO @ Mon, 03 Jun 2019 12:47:25: 6000000 INFO @ Mon, 03 Jun 2019 12:47:33: 7000000 INFO @ Mon, 03 Jun 2019 12:47:34: 8000000 INFO @ Mon, 03 Jun 2019 12:47:35: 7000000 INFO @ Mon, 03 Jun 2019 12:47:42: 9000000 INFO @ Mon, 03 Jun 2019 12:47:42: 8000000 INFO @ Mon, 03 Jun 2019 12:47:44: 8000000 INFO @ Mon, 03 Jun 2019 12:47:50: 10000000 INFO @ Mon, 03 Jun 2019 12:47:51: 9000000 INFO @ Mon, 03 Jun 2019 12:47:54: 9000000 INFO @ Mon, 03 Jun 2019 12:48:00: 11000000 INFO @ Mon, 03 Jun 2019 12:48:01: 10000000 INFO @ Mon, 03 Jun 2019 12:48:04: 10000000 INFO @ Mon, 03 Jun 2019 12:48:10: 12000000 INFO @ Mon, 03 Jun 2019 12:48:12: 11000000 INFO @ Mon, 03 Jun 2019 12:48:14: 11000000 INFO @ Mon, 03 Jun 2019 12:48:20: 13000000 INFO @ Mon, 03 Jun 2019 12:48:21: 12000000 INFO @ Mon, 03 Jun 2019 12:48:23: 12000000 INFO @ Mon, 03 Jun 2019 12:48:29: 14000000 INFO @ Mon, 03 Jun 2019 12:48:31: 13000000 INFO @ Mon, 03 Jun 2019 12:48:33: 13000000 INFO @ Mon, 03 Jun 2019 12:48:39: 15000000 INFO @ Mon, 03 Jun 2019 12:48:40: 14000000 INFO @ Mon, 03 Jun 2019 12:48:42: 14000000 INFO @ Mon, 03 Jun 2019 12:48:48: 16000000 INFO @ Mon, 03 Jun 2019 12:48:50: 15000000 INFO @ Mon, 03 Jun 2019 12:48:52: 15000000 INFO @ Mon, 03 Jun 2019 12:48:58: 17000000 INFO @ Mon, 03 Jun 2019 12:48:59: 16000000 INFO @ Mon, 03 Jun 2019 12:49:02: 16000000 INFO @ Mon, 03 Jun 2019 12:49:07: 18000000 INFO @ Mon, 03 Jun 2019 12:49:08: 17000000 INFO @ Mon, 03 Jun 2019 12:49:10: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 12:49:10: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 12:49:10: #1 total tags in treatment: 18325394 INFO @ Mon, 03 Jun 2019 12:49:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:49:10: #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 12:49:10: #1 tags after filtering in treatment: 18325394 INFO @ Mon, 03 Jun 2019 12:49:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:49:10: #1 finished! INFO @ Mon, 03 Jun 2019 12:49:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:49:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:49:10: 17000000 INFO @ Mon, 03 Jun 2019 12:49:14: #2 number of paired peaks: 16956 INFO @ Mon, 03 Jun 2019 12:49:14: start model_add_line... INFO @ Mon, 03 Jun 2019 12:49:14: start X-correlation... INFO @ Mon, 03 Jun 2019 12:49:14: end of X-cor INFO @ Mon, 03 Jun 2019 12:49:14: #2 finished! INFO @ Mon, 03 Jun 2019 12:49:14: #2 predicted fragment length is 158 bps INFO @ Mon, 03 Jun 2019 12:49:14: #2 alternative fragment length(s) may be 158 bps INFO @ Mon, 03 Jun 2019 12:49:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3279766/SRX3279766.05_model.r INFO @ Mon, 03 Jun 2019 12:49:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:49:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:49:15: 18000000 INFO @ Mon, 03 Jun 2019 12:49:17: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 12:49:17: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 12:49:17: #1 total tags in treatment: 18325394 INFO @ Mon, 03 Jun 2019 12:49:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:49:17: #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 12:49:17: #1 tags after filtering in treatment: 18325394 INFO @ Mon, 03 Jun 2019 12:49:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:49:17: #1 finished! INFO @ Mon, 03 Jun 2019 12:49:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:49:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:49:18: 18000000 INFO @ Mon, 03 Jun 2019 12:49:21: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 12:49:21: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 12:49:21: #1 total tags in treatment: 18325394 INFO @ Mon, 03 Jun 2019 12:49:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:49:21: #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 12:49:21: #1 tags after filtering in treatment: 18325394 INFO @ Mon, 03 Jun 2019 12:49:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:49:21: #1 finished! INFO @ Mon, 03 Jun 2019 12:49:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:49:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:49:21: #2 number of paired peaks: 16956 INFO @ Mon, 03 Jun 2019 12:49:21: start model_add_line... INFO @ Mon, 03 Jun 2019 12:49:22: start X-correlation... INFO @ Mon, 03 Jun 2019 12:49:22: end of X-cor INFO @ Mon, 03 Jun 2019 12:49:22: #2 finished! INFO @ Mon, 03 Jun 2019 12:49:22: #2 predicted fragment length is 158 bps INFO @ Mon, 03 Jun 2019 12:49:22: #2 alternative fragment length(s) may be 158 bps INFO @ Mon, 03 Jun 2019 12:49:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3279766/SRX3279766.20_model.r INFO @ Mon, 03 Jun 2019 12:49:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:49:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:49:25: #2 number of paired peaks: 16956 INFO @ Mon, 03 Jun 2019 12:49:25: start model_add_line... INFO @ Mon, 03 Jun 2019 12:49:25: start X-correlation... INFO @ Mon, 03 Jun 2019 12:49:25: end of X-cor INFO @ Mon, 03 Jun 2019 12:49:25: #2 finished! INFO @ Mon, 03 Jun 2019 12:49:25: #2 predicted fragment length is 158 bps INFO @ Mon, 03 Jun 2019 12:49:25: #2 alternative fragment length(s) may be 158 bps INFO @ Mon, 03 Jun 2019 12:49:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3279766/SRX3279766.10_model.r INFO @ Mon, 03 Jun 2019 12:49:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:49:25: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 12:50:15: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 12:50:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:50:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:50:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3279766/SRX3279766.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:50:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3279766/SRX3279766.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:50:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3279766/SRX3279766.05_summits.bed INFO @ Mon, 03 Jun 2019 12:50:34: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (8976 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:50:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3279766/SRX3279766.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:50:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3279766/SRX3279766.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:50:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3279766/SRX3279766.20_summits.bed INFO @ Mon, 03 Jun 2019 12:50:44: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7869 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:50:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3279766/SRX3279766.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:50:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3279766/SRX3279766.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:50:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3279766/SRX3279766.10_summits.bed INFO @ Mon, 03 Jun 2019 12:50:46: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (8525 records, 4 fields): 19 millis CompletedMACS2peakCalling