Job ID = 4178551 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-05T03:54:33 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 : 55,291,041 reads read : 110,582,082 reads written : 55,291,041 reads 0-length : 55,291,041 rm: cannot remove ‘[DSE]RR*’: 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: 00:14:54 55291041 reads; of these: 55291041 (100.00%) were unpaired; of these: 5529977 (10.00%) aligned 0 times 41167253 (74.46%) aligned exactly 1 time 8593811 (15.54%) aligned >1 times 90.00% overall alignment rate Time searching: 00:14:59 Overall time: 00:14:59 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 24 files... [bam_rmdupse_core] 29228822 / 49761064 = 0.5874 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:43:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827823/SRX5827823.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827823/SRX5827823.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827823/SRX5827823.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827823/SRX5827823.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 @ Thu, 05 Dec 2019 13:43:38: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:43:38: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:43:45: 1000000 INFO @ Thu, 05 Dec 2019 13:43:51: 2000000 INFO @ Thu, 05 Dec 2019 13:43:58: 3000000 INFO @ Thu, 05 Dec 2019 13:44:04: 4000000 INFO @ Thu, 05 Dec 2019 13:44:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827823/SRX5827823.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827823/SRX5827823.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827823/SRX5827823.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827823/SRX5827823.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 @ Thu, 05 Dec 2019 13:44:06: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:44:06: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:44:11: 5000000 INFO @ Thu, 05 Dec 2019 13:44:12: 1000000 INFO @ Thu, 05 Dec 2019 13:44:17: 6000000 INFO @ Thu, 05 Dec 2019 13:44:18: 2000000 INFO @ Thu, 05 Dec 2019 13:44:24: 7000000 INFO @ Thu, 05 Dec 2019 13:44:24: 3000000 INFO @ Thu, 05 Dec 2019 13:44:30: 8000000 INFO @ Thu, 05 Dec 2019 13:44:31: 4000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:44:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827823/SRX5827823.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827823/SRX5827823.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827823/SRX5827823.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827823/SRX5827823.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 @ Thu, 05 Dec 2019 13:44:37: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:44:37: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:44:37: 5000000 INFO @ Thu, 05 Dec 2019 13:44:38: 9000000 INFO @ Thu, 05 Dec 2019 13:44:45: 1000000 INFO @ Thu, 05 Dec 2019 13:44:45: 10000000 INFO @ Thu, 05 Dec 2019 13:44:45: 6000000 INFO @ Thu, 05 Dec 2019 13:44:53: 2000000 INFO @ Thu, 05 Dec 2019 13:44:53: 7000000 INFO @ Thu, 05 Dec 2019 13:44:53: 11000000 INFO @ Thu, 05 Dec 2019 13:45:00: 3000000 INFO @ Thu, 05 Dec 2019 13:45:00: 8000000 INFO @ Thu, 05 Dec 2019 13:45:03: 12000000 INFO @ Thu, 05 Dec 2019 13:45:08: 4000000 INFO @ Thu, 05 Dec 2019 13:45:08: 9000000 INFO @ Thu, 05 Dec 2019 13:45:10: 13000000 INFO @ Thu, 05 Dec 2019 13:45:15: 10000000 INFO @ Thu, 05 Dec 2019 13:45:15: 5000000 INFO @ Thu, 05 Dec 2019 13:45:17: 14000000 INFO @ Thu, 05 Dec 2019 13:45:22: 11000000 INFO @ Thu, 05 Dec 2019 13:45:22: 6000000 INFO @ Thu, 05 Dec 2019 13:45:23: 15000000 INFO @ Thu, 05 Dec 2019 13:45:28: 12000000 INFO @ Thu, 05 Dec 2019 13:45:29: 7000000 INFO @ Thu, 05 Dec 2019 13:45:30: 16000000 INFO @ Thu, 05 Dec 2019 13:45:35: 13000000 INFO @ Thu, 05 Dec 2019 13:45:36: 8000000 INFO @ Thu, 05 Dec 2019 13:45:36: 17000000 INFO @ Thu, 05 Dec 2019 13:45:43: 14000000 INFO @ Thu, 05 Dec 2019 13:45:44: 18000000 INFO @ Thu, 05 Dec 2019 13:45:44: 9000000 INFO @ Thu, 05 Dec 2019 13:45:50: 15000000 INFO @ Thu, 05 Dec 2019 13:45:51: 10000000 INFO @ Thu, 05 Dec 2019 13:45:52: 19000000 INFO @ Thu, 05 Dec 2019 13:45:57: 16000000 INFO @ Thu, 05 Dec 2019 13:45:58: 11000000 INFO @ Thu, 05 Dec 2019 13:45:59: 20000000 INFO @ Thu, 05 Dec 2019 13:46:03: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:46:03: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:46:03: #1 total tags in treatment: 20532242 INFO @ Thu, 05 Dec 2019 13:46:03: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:46:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:46:03: #1 tags after filtering in treatment: 20532242 INFO @ Thu, 05 Dec 2019 13:46:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:46:03: #1 finished! INFO @ Thu, 05 Dec 2019 13:46:03: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:46:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:46:04: 17000000 INFO @ Thu, 05 Dec 2019 13:46:05: 12000000 INFO @ Thu, 05 Dec 2019 13:46:05: #2 number of paired peaks: 212 WARNING @ Thu, 05 Dec 2019 13:46:05: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Thu, 05 Dec 2019 13:46:05: start model_add_line... INFO @ Thu, 05 Dec 2019 13:46:05: start X-correlation... INFO @ Thu, 05 Dec 2019 13:46:05: end of X-cor INFO @ Thu, 05 Dec 2019 13:46:05: #2 finished! INFO @ Thu, 05 Dec 2019 13:46:05: #2 predicted fragment length is 120 bps INFO @ Thu, 05 Dec 2019 13:46:05: #2 alternative fragment length(s) may be 120 bps INFO @ Thu, 05 Dec 2019 13:46:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827823/SRX5827823.05_model.r INFO @ Thu, 05 Dec 2019 13:46:05: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:46:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:46:11: 13000000 INFO @ Thu, 05 Dec 2019 13:46:12: 18000000 INFO @ Thu, 05 Dec 2019 13:46:18: 14000000 INFO @ Thu, 05 Dec 2019 13:46:18: 19000000 INFO @ Thu, 05 Dec 2019 13:46:25: 15000000 INFO @ Thu, 05 Dec 2019 13:46:25: 20000000 INFO @ Thu, 05 Dec 2019 13:46:28: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:46:28: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:46:28: #1 total tags in treatment: 20532242 INFO @ Thu, 05 Dec 2019 13:46:28: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:46:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:46:29: #1 tags after filtering in treatment: 20532242 INFO @ Thu, 05 Dec 2019 13:46:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:46:29: #1 finished! INFO @ Thu, 05 Dec 2019 13:46:29: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:46:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:46:30: #2 number of paired peaks: 212 WARNING @ Thu, 05 Dec 2019 13:46:30: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Thu, 05 Dec 2019 13:46:30: start model_add_line... INFO @ Thu, 05 Dec 2019 13:46:30: start X-correlation... INFO @ Thu, 05 Dec 2019 13:46:30: end of X-cor INFO @ Thu, 05 Dec 2019 13:46:30: #2 finished! INFO @ Thu, 05 Dec 2019 13:46:30: #2 predicted fragment length is 120 bps INFO @ Thu, 05 Dec 2019 13:46:30: #2 alternative fragment length(s) may be 120 bps INFO @ Thu, 05 Dec 2019 13:46:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827823/SRX5827823.10_model.r INFO @ Thu, 05 Dec 2019 13:46:30: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:46:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:46:31: 16000000 INFO @ Thu, 05 Dec 2019 13:46:37: 17000000 INFO @ Thu, 05 Dec 2019 13:46:41: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:46:43: 18000000 INFO @ Thu, 05 Dec 2019 13:46:48: 19000000 INFO @ Thu, 05 Dec 2019 13:46:54: 20000000 INFO @ Thu, 05 Dec 2019 13:46:58: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:46:58: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:46:58: #1 total tags in treatment: 20532242 INFO @ Thu, 05 Dec 2019 13:46:58: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:46:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:46:58: #1 tags after filtering in treatment: 20532242 INFO @ Thu, 05 Dec 2019 13:46:58: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:46:58: #1 finished! INFO @ Thu, 05 Dec 2019 13:46:58: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:46:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:47:00: #2 number of paired peaks: 212 WARNING @ Thu, 05 Dec 2019 13:47:00: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Thu, 05 Dec 2019 13:47:00: start model_add_line... INFO @ Thu, 05 Dec 2019 13:47:00: start X-correlation... INFO @ Thu, 05 Dec 2019 13:47:00: end of X-cor INFO @ Thu, 05 Dec 2019 13:47:00: #2 finished! INFO @ Thu, 05 Dec 2019 13:47:00: #2 predicted fragment length is 120 bps INFO @ Thu, 05 Dec 2019 13:47:00: #2 alternative fragment length(s) may be 120 bps INFO @ Thu, 05 Dec 2019 13:47:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827823/SRX5827823.20_model.r INFO @ Thu, 05 Dec 2019 13:47:00: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:47:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:47:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827823/SRX5827823.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:47:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827823/SRX5827823.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:47:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827823/SRX5827823.05_summits.bed INFO @ Thu, 05 Dec 2019 13:47:02: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6086 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:47:08: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:47:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827823/SRX5827823.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:47:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827823/SRX5827823.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:47:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827823/SRX5827823.10_summits.bed INFO @ Thu, 05 Dec 2019 13:47:30: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3278 records, 4 fields): 120 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:47:39: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:48:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827823/SRX5827823.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:48:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827823/SRX5827823.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:48:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827823/SRX5827823.20_summits.bed INFO @ Thu, 05 Dec 2019 13:48:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1515 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。