Job ID = 1293900 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T18:07:28 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 ) 2019-06-02T18:07:28 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 : 33,536,924 reads read : 33,536,924 reads written : 33,536,924 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: 00:09:48 33536924 reads; of these: 33536924 (100.00%) were unpaired; of these: 847538 (2.53%) aligned 0 times 25295011 (75.42%) aligned exactly 1 time 7394375 (22.05%) aligned >1 times 97.47% overall alignment rate Time searching: 00:09:48 Overall time: 00:09:48 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] 7660906 / 32689386 = 0.2344 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 03:32:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX146996/SRX146996.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX146996/SRX146996.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX146996/SRX146996.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX146996/SRX146996.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 03:32:49: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:32:49: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:32:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX146996/SRX146996.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX146996/SRX146996.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX146996/SRX146996.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX146996/SRX146996.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 03:32:49: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:32:49: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:32:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX146996/SRX146996.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX146996/SRX146996.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX146996/SRX146996.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX146996/SRX146996.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 03:32:49: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:32:49: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:32:59: 1000000 INFO @ Mon, 03 Jun 2019 03:32:59: 1000000 INFO @ Mon, 03 Jun 2019 03:33:00: 1000000 INFO @ Mon, 03 Jun 2019 03:33:09: 2000000 INFO @ Mon, 03 Jun 2019 03:33:09: 2000000 INFO @ Mon, 03 Jun 2019 03:33:11: 2000000 INFO @ Mon, 03 Jun 2019 03:33:19: 3000000 INFO @ Mon, 03 Jun 2019 03:33:20: 3000000 INFO @ Mon, 03 Jun 2019 03:33:21: 3000000 INFO @ Mon, 03 Jun 2019 03:33:28: 4000000 INFO @ Mon, 03 Jun 2019 03:33:30: 4000000 INFO @ Mon, 03 Jun 2019 03:33:31: 4000000 INFO @ Mon, 03 Jun 2019 03:33:38: 5000000 INFO @ Mon, 03 Jun 2019 03:33:39: 5000000 INFO @ Mon, 03 Jun 2019 03:33:40: 5000000 INFO @ Mon, 03 Jun 2019 03:33:48: 6000000 INFO @ Mon, 03 Jun 2019 03:33:49: 6000000 INFO @ Mon, 03 Jun 2019 03:33:50: 6000000 INFO @ Mon, 03 Jun 2019 03:33:57: 7000000 INFO @ Mon, 03 Jun 2019 03:33:58: 7000000 INFO @ Mon, 03 Jun 2019 03:34:00: 7000000 INFO @ Mon, 03 Jun 2019 03:34:07: 8000000 INFO @ Mon, 03 Jun 2019 03:34:08: 8000000 INFO @ Mon, 03 Jun 2019 03:34:10: 8000000 INFO @ Mon, 03 Jun 2019 03:34:16: 9000000 INFO @ Mon, 03 Jun 2019 03:34:17: 9000000 INFO @ Mon, 03 Jun 2019 03:34:20: 9000000 INFO @ Mon, 03 Jun 2019 03:34:26: 10000000 INFO @ Mon, 03 Jun 2019 03:34:27: 10000000 INFO @ Mon, 03 Jun 2019 03:34:30: 10000000 INFO @ Mon, 03 Jun 2019 03:34:35: 11000000 INFO @ Mon, 03 Jun 2019 03:34:36: 11000000 INFO @ Mon, 03 Jun 2019 03:34:40: 11000000 INFO @ Mon, 03 Jun 2019 03:34:45: 12000000 INFO @ Mon, 03 Jun 2019 03:34:46: 12000000 INFO @ Mon, 03 Jun 2019 03:34:50: 12000000 INFO @ Mon, 03 Jun 2019 03:34:54: 13000000 INFO @ Mon, 03 Jun 2019 03:34:56: 13000000 INFO @ Mon, 03 Jun 2019 03:34:59: 13000000 INFO @ Mon, 03 Jun 2019 03:35:03: 14000000 INFO @ Mon, 03 Jun 2019 03:35:06: 14000000 INFO @ Mon, 03 Jun 2019 03:35:09: 14000000 INFO @ Mon, 03 Jun 2019 03:35:13: 15000000 INFO @ Mon, 03 Jun 2019 03:35:15: 15000000 INFO @ Mon, 03 Jun 2019 03:35:19: 15000000 INFO @ Mon, 03 Jun 2019 03:35:22: 16000000 INFO @ Mon, 03 Jun 2019 03:35:25: 16000000 INFO @ Mon, 03 Jun 2019 03:35:29: 16000000 INFO @ Mon, 03 Jun 2019 03:35:32: 17000000 INFO @ Mon, 03 Jun 2019 03:35:35: 17000000 INFO @ Mon, 03 Jun 2019 03:35:40: 17000000 INFO @ Mon, 03 Jun 2019 03:35:43: 18000000 INFO @ Mon, 03 Jun 2019 03:35:45: 18000000 INFO @ Mon, 03 Jun 2019 03:35:51: 18000000 INFO @ Mon, 03 Jun 2019 03:35:53: 19000000 INFO @ Mon, 03 Jun 2019 03:35:55: 19000000 INFO @ Mon, 03 Jun 2019 03:36:01: 19000000 INFO @ Mon, 03 Jun 2019 03:36:02: 20000000 INFO @ Mon, 03 Jun 2019 03:36:05: 20000000 INFO @ Mon, 03 Jun 2019 03:36:11: 20000000 INFO @ Mon, 03 Jun 2019 03:36:11: 21000000 INFO @ Mon, 03 Jun 2019 03:36:14: 21000000 INFO @ Mon, 03 Jun 2019 03:36:20: 21000000 INFO @ Mon, 03 Jun 2019 03:36:20: 22000000 INFO @ Mon, 03 Jun 2019 03:36:24: 22000000 INFO @ Mon, 03 Jun 2019 03:36:30: 23000000 INFO @ Mon, 03 Jun 2019 03:36:30: 22000000 INFO @ Mon, 03 Jun 2019 03:36:33: 23000000 INFO @ Mon, 03 Jun 2019 03:36:39: 24000000 INFO @ Mon, 03 Jun 2019 03:36:39: 23000000 INFO @ Mon, 03 Jun 2019 03:36:42: 24000000 INFO @ Mon, 03 Jun 2019 03:36:48: 25000000 INFO @ Mon, 03 Jun 2019 03:36:48: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 03:36:48: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 03:36:48: #1 total tags in treatment: 25028480 INFO @ Mon, 03 Jun 2019 03:36:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:36:48: #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 03:36:49: #1 tags after filtering in treatment: 25028480 INFO @ Mon, 03 Jun 2019 03:36:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:36:49: #1 finished! INFO @ Mon, 03 Jun 2019 03:36:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:36:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:36:49: 24000000 INFO @ Mon, 03 Jun 2019 03:36:51: #2 number of paired peaks: 1152 INFO @ Mon, 03 Jun 2019 03:36:51: start model_add_line... INFO @ Mon, 03 Jun 2019 03:36:51: start X-correlation... INFO @ Mon, 03 Jun 2019 03:36:51: end of X-cor INFO @ Mon, 03 Jun 2019 03:36:51: #2 finished! INFO @ Mon, 03 Jun 2019 03:36:51: #2 predicted fragment length is 121 bps INFO @ Mon, 03 Jun 2019 03:36:51: #2 alternative fragment length(s) may be 4,121 bps INFO @ Mon, 03 Jun 2019 03:36:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX146996/SRX146996.10_model.r INFO @ Mon, 03 Jun 2019 03:36:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:36:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:36:52: 25000000 INFO @ Mon, 03 Jun 2019 03:36:53: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 03:36:53: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 03:36:53: #1 total tags in treatment: 25028480 INFO @ Mon, 03 Jun 2019 03:36:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:36:53: #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 03:36:53: #1 tags after filtering in treatment: 25028480 INFO @ Mon, 03 Jun 2019 03:36:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:36:53: #1 finished! INFO @ Mon, 03 Jun 2019 03:36:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:36:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:36:55: #2 number of paired peaks: 1152 INFO @ Mon, 03 Jun 2019 03:36:55: start model_add_line... INFO @ Mon, 03 Jun 2019 03:36:56: start X-correlation... INFO @ Mon, 03 Jun 2019 03:36:56: end of X-cor INFO @ Mon, 03 Jun 2019 03:36:56: #2 finished! INFO @ Mon, 03 Jun 2019 03:36:56: #2 predicted fragment length is 121 bps INFO @ Mon, 03 Jun 2019 03:36:56: #2 alternative fragment length(s) may be 4,121 bps INFO @ Mon, 03 Jun 2019 03:36:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX146996/SRX146996.05_model.r INFO @ Mon, 03 Jun 2019 03:36:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:36:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:36:57: 25000000 INFO @ Mon, 03 Jun 2019 03:36:58: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 03:36:58: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 03:36:58: #1 total tags in treatment: 25028480 INFO @ Mon, 03 Jun 2019 03:36:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:36:58: #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 03:36:58: #1 tags after filtering in treatment: 25028480 INFO @ Mon, 03 Jun 2019 03:36:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:36:58: #1 finished! INFO @ Mon, 03 Jun 2019 03:36:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:36:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:37:01: #2 number of paired peaks: 1152 INFO @ Mon, 03 Jun 2019 03:37:01: start model_add_line... INFO @ Mon, 03 Jun 2019 03:37:01: start X-correlation... INFO @ Mon, 03 Jun 2019 03:37:01: end of X-cor INFO @ Mon, 03 Jun 2019 03:37:01: #2 finished! INFO @ Mon, 03 Jun 2019 03:37:01: #2 predicted fragment length is 121 bps INFO @ Mon, 03 Jun 2019 03:37:01: #2 alternative fragment length(s) may be 4,121 bps INFO @ Mon, 03 Jun 2019 03:37:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX146996/SRX146996.20_model.r INFO @ Mon, 03 Jun 2019 03:37:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:37:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:37:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:38:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:38:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:38:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX146996/SRX146996.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:38:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX146996/SRX146996.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:38:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX146996/SRX146996.10_summits.bed INFO @ Mon, 03 Jun 2019 03:38:28: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6982 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:38:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX146996/SRX146996.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:38:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX146996/SRX146996.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:38:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX146996/SRX146996.05_summits.bed INFO @ Mon, 03 Jun 2019 03:38:36: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (18634 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:38:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX146996/SRX146996.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:38:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX146996/SRX146996.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:38:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX146996/SRX146996.20_summits.bed INFO @ Mon, 03 Jun 2019 03:38:38: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2131 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。