Job ID = 1295083 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T02:39:10 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 : 16,523,290 reads read : 16,523,290 reads written : 16,523,290 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: 00:05:22 16523290 reads; of these: 16523290 (100.00%) were unpaired; of these: 1905328 (11.53%) aligned 0 times 11753314 (71.13%) aligned exactly 1 time 2864648 (17.34%) aligned >1 times 88.47% overall alignment rate Time searching: 00:05:22 Overall time: 00:05:22 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] 2607772 / 14617962 = 0.1784 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 11:51:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318781/SRX318781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318781/SRX318781.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318781/SRX318781.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318781/SRX318781.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 11:51:41: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:51:41: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:51:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318781/SRX318781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318781/SRX318781.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318781/SRX318781.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318781/SRX318781.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 11:51:41: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:51:41: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:51:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318781/SRX318781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318781/SRX318781.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318781/SRX318781.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318781/SRX318781.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 11:51:41: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:51:41: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:51:49: 1000000 INFO @ Mon, 03 Jun 2019 11:51:49: 1000000 INFO @ Mon, 03 Jun 2019 11:51:51: 1000000 INFO @ Mon, 03 Jun 2019 11:51:57: 2000000 INFO @ Mon, 03 Jun 2019 11:51:57: 2000000 INFO @ Mon, 03 Jun 2019 11:52:00: 2000000 INFO @ Mon, 03 Jun 2019 11:52:05: 3000000 INFO @ Mon, 03 Jun 2019 11:52:06: 3000000 INFO @ Mon, 03 Jun 2019 11:52:09: 3000000 INFO @ Mon, 03 Jun 2019 11:52:13: 4000000 INFO @ Mon, 03 Jun 2019 11:52:14: 4000000 INFO @ Mon, 03 Jun 2019 11:52:19: 4000000 INFO @ Mon, 03 Jun 2019 11:52:21: 5000000 INFO @ Mon, 03 Jun 2019 11:52:22: 5000000 INFO @ Mon, 03 Jun 2019 11:52:28: 5000000 INFO @ Mon, 03 Jun 2019 11:52:29: 6000000 INFO @ Mon, 03 Jun 2019 11:52:29: 6000000 INFO @ Mon, 03 Jun 2019 11:52:37: 7000000 INFO @ Mon, 03 Jun 2019 11:52:37: 6000000 INFO @ Mon, 03 Jun 2019 11:52:37: 7000000 INFO @ Mon, 03 Jun 2019 11:52:45: 8000000 INFO @ Mon, 03 Jun 2019 11:52:45: 8000000 INFO @ Mon, 03 Jun 2019 11:52:46: 7000000 INFO @ Mon, 03 Jun 2019 11:52:53: 9000000 INFO @ Mon, 03 Jun 2019 11:52:53: 9000000 INFO @ Mon, 03 Jun 2019 11:52:55: 8000000 INFO @ Mon, 03 Jun 2019 11:53:01: 10000000 INFO @ Mon, 03 Jun 2019 11:53:02: 10000000 INFO @ Mon, 03 Jun 2019 11:53:04: 9000000 INFO @ Mon, 03 Jun 2019 11:53:10: 11000000 INFO @ Mon, 03 Jun 2019 11:53:10: 11000000 INFO @ Mon, 03 Jun 2019 11:53:13: 10000000 INFO @ Mon, 03 Jun 2019 11:53:18: 12000000 INFO @ Mon, 03 Jun 2019 11:53:18: 12000000 INFO @ Mon, 03 Jun 2019 11:53:18: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:53:18: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:53:18: #1 total tags in treatment: 12010190 INFO @ Mon, 03 Jun 2019 11:53:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:53:18: #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 11:53:18: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:53:18: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:53:18: #1 total tags in treatment: 12010190 INFO @ Mon, 03 Jun 2019 11:53:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:53:18: #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 11:53:18: #1 tags after filtering in treatment: 12010190 INFO @ Mon, 03 Jun 2019 11:53:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:53:18: #1 finished! INFO @ Mon, 03 Jun 2019 11:53:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:53:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:53:18: #1 tags after filtering in treatment: 12010190 INFO @ Mon, 03 Jun 2019 11:53:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:53:18: #1 finished! INFO @ Mon, 03 Jun 2019 11:53:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:53:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:53:19: #2 number of paired peaks: 528 WARNING @ Mon, 03 Jun 2019 11:53:19: Fewer paired peaks (528) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 528 pairs to build model! INFO @ Mon, 03 Jun 2019 11:53:19: start model_add_line... INFO @ Mon, 03 Jun 2019 11:53:19: #2 number of paired peaks: 528 WARNING @ Mon, 03 Jun 2019 11:53:19: Fewer paired peaks (528) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 528 pairs to build model! INFO @ Mon, 03 Jun 2019 11:53:19: start model_add_line... INFO @ Mon, 03 Jun 2019 11:53:20: start X-correlation... INFO @ Mon, 03 Jun 2019 11:53:20: start X-correlation... INFO @ Mon, 03 Jun 2019 11:53:20: end of X-cor INFO @ Mon, 03 Jun 2019 11:53:20: #2 finished! INFO @ Mon, 03 Jun 2019 11:53:20: #2 predicted fragment length is 175 bps INFO @ Mon, 03 Jun 2019 11:53:20: #2 alternative fragment length(s) may be 175 bps INFO @ Mon, 03 Jun 2019 11:53:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318781/SRX318781.10_model.r INFO @ Mon, 03 Jun 2019 11:53:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:53:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:53:20: end of X-cor INFO @ Mon, 03 Jun 2019 11:53:20: #2 finished! INFO @ Mon, 03 Jun 2019 11:53:20: #2 predicted fragment length is 175 bps INFO @ Mon, 03 Jun 2019 11:53:20: #2 alternative fragment length(s) may be 175 bps INFO @ Mon, 03 Jun 2019 11:53:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318781/SRX318781.20_model.r INFO @ Mon, 03 Jun 2019 11:53:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:53:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:53:22: 11000000 INFO @ Mon, 03 Jun 2019 11:53:30: 12000000 INFO @ Mon, 03 Jun 2019 11:53:30: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:53:30: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:53:30: #1 total tags in treatment: 12010190 INFO @ Mon, 03 Jun 2019 11:53:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:53:30: #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 11:53:30: #1 tags after filtering in treatment: 12010190 INFO @ Mon, 03 Jun 2019 11:53:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:53:30: #1 finished! INFO @ Mon, 03 Jun 2019 11:53:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:53:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:53:32: #2 number of paired peaks: 528 WARNING @ Mon, 03 Jun 2019 11:53:32: Fewer paired peaks (528) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 528 pairs to build model! INFO @ Mon, 03 Jun 2019 11:53:32: start model_add_line... INFO @ Mon, 03 Jun 2019 11:53:32: start X-correlation... INFO @ Mon, 03 Jun 2019 11:53:32: end of X-cor INFO @ Mon, 03 Jun 2019 11:53:32: #2 finished! INFO @ Mon, 03 Jun 2019 11:53:32: #2 predicted fragment length is 175 bps INFO @ Mon, 03 Jun 2019 11:53:32: #2 alternative fragment length(s) may be 175 bps INFO @ Mon, 03 Jun 2019 11:53:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318781/SRX318781.05_model.r INFO @ Mon, 03 Jun 2019 11:53:32: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:53:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:53:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:53:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:54:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:54:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318781/SRX318781.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:54:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318781/SRX318781.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:54:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318781/SRX318781.20_summits.bed INFO @ Mon, 03 Jun 2019 11:54:12: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1641 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:54:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318781/SRX318781.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:54:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318781/SRX318781.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:54:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318781/SRX318781.10_summits.bed INFO @ Mon, 03 Jun 2019 11:54:12: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (3360 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:54:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318781/SRX318781.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:54:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318781/SRX318781.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:54:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318781/SRX318781.05_summits.bed INFO @ Mon, 03 Jun 2019 11:54:24: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5475 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。