Job ID = 4178600 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-05T04:28:20 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 ) 2019-12-05T04:28:20 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 : 39,064,443 reads read : 39,064,443 reads written : 39,064,443 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: 00:09:30 39064443 reads; of these: 39064443 (100.00%) were unpaired; of these: 2039485 (5.22%) aligned 0 times 32092456 (82.15%) aligned exactly 1 time 4932502 (12.63%) aligned >1 times 94.78% overall alignment rate Time searching: 00:09:30 Overall time: 00:09:30 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] 20029510 / 37024958 = 0.5410 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:48:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6468479/SRX6468479.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6468479/SRX6468479.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6468479/SRX6468479.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6468479/SRX6468479.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 13:48:44: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:48:44: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:48:55: 1000000 INFO @ Thu, 05 Dec 2019 13:49:05: 2000000 INFO @ Thu, 05 Dec 2019 13:49:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6468479/SRX6468479.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6468479/SRX6468479.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6468479/SRX6468479.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6468479/SRX6468479.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 13:49:14: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:49:14: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:49:16: 3000000 INFO @ Thu, 05 Dec 2019 13:49:25: 1000000 INFO @ Thu, 05 Dec 2019 13:49:27: 4000000 INFO @ Thu, 05 Dec 2019 13:49:35: 2000000 INFO @ Thu, 05 Dec 2019 13:49:38: 5000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:49:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6468479/SRX6468479.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6468479/SRX6468479.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6468479/SRX6468479.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6468479/SRX6468479.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 13:49:44: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:49:44: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:49:44: 3000000 INFO @ Thu, 05 Dec 2019 13:49:50: 6000000 INFO @ Thu, 05 Dec 2019 13:49:54: 4000000 INFO @ Thu, 05 Dec 2019 13:49:56: 1000000 INFO @ Thu, 05 Dec 2019 13:50:01: 7000000 INFO @ Thu, 05 Dec 2019 13:50:03: 5000000 INFO @ Thu, 05 Dec 2019 13:50:06: 2000000 INFO @ Thu, 05 Dec 2019 13:50:12: 6000000 INFO @ Thu, 05 Dec 2019 13:50:12: 8000000 INFO @ Thu, 05 Dec 2019 13:50:16: 3000000 INFO @ Thu, 05 Dec 2019 13:50:21: 7000000 INFO @ Thu, 05 Dec 2019 13:50:24: 9000000 INFO @ Thu, 05 Dec 2019 13:50:26: 4000000 INFO @ Thu, 05 Dec 2019 13:50:30: 8000000 INFO @ Thu, 05 Dec 2019 13:50:35: 10000000 INFO @ Thu, 05 Dec 2019 13:50:36: 5000000 INFO @ Thu, 05 Dec 2019 13:50:39: 9000000 INFO @ Thu, 05 Dec 2019 13:50:45: 11000000 INFO @ Thu, 05 Dec 2019 13:50:45: 6000000 INFO @ Thu, 05 Dec 2019 13:50:47: 10000000 INFO @ Thu, 05 Dec 2019 13:50:54: 7000000 INFO @ Thu, 05 Dec 2019 13:50:56: 12000000 INFO @ Thu, 05 Dec 2019 13:50:56: 11000000 INFO @ Thu, 05 Dec 2019 13:51:03: 8000000 INFO @ Thu, 05 Dec 2019 13:51:04: 12000000 INFO @ Thu, 05 Dec 2019 13:51:07: 13000000 INFO @ Thu, 05 Dec 2019 13:51:12: 9000000 INFO @ Thu, 05 Dec 2019 13:51:13: 13000000 INFO @ Thu, 05 Dec 2019 13:51:18: 14000000 INFO @ Thu, 05 Dec 2019 13:51:21: 10000000 INFO @ Thu, 05 Dec 2019 13:51:21: 14000000 INFO @ Thu, 05 Dec 2019 13:51:30: 15000000 INFO @ Thu, 05 Dec 2019 13:51:31: 15000000 INFO @ Thu, 05 Dec 2019 13:51:31: 11000000 INFO @ Thu, 05 Dec 2019 13:51:40: 16000000 INFO @ Thu, 05 Dec 2019 13:51:43: 12000000 INFO @ Thu, 05 Dec 2019 13:51:43: 16000000 INFO @ Thu, 05 Dec 2019 13:51:48: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:51:48: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:51:48: #1 total tags in treatment: 16995448 INFO @ Thu, 05 Dec 2019 13:51:48: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:51:48: #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 13:51:48: #1 tags after filtering in treatment: 16995448 INFO @ Thu, 05 Dec 2019 13:51:48: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:51:48: #1 finished! INFO @ Thu, 05 Dec 2019 13:51:48: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:51:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:51:50: #2 number of paired peaks: 467 WARNING @ Thu, 05 Dec 2019 13:51:50: Fewer paired peaks (467) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 467 pairs to build model! INFO @ Thu, 05 Dec 2019 13:51:50: start model_add_line... INFO @ Thu, 05 Dec 2019 13:51:50: start X-correlation... INFO @ Thu, 05 Dec 2019 13:51:50: end of X-cor INFO @ Thu, 05 Dec 2019 13:51:50: #2 finished! INFO @ Thu, 05 Dec 2019 13:51:50: #2 predicted fragment length is 123 bps INFO @ Thu, 05 Dec 2019 13:51:50: #2 alternative fragment length(s) may be 4,123 bps INFO @ Thu, 05 Dec 2019 13:51:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6468479/SRX6468479.10_model.r INFO @ Thu, 05 Dec 2019 13:51:50: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:51:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:51:52: 13000000 INFO @ Thu, 05 Dec 2019 13:51:54: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:51:54: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:51:54: #1 total tags in treatment: 16995448 INFO @ Thu, 05 Dec 2019 13:51:54: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:51:54: #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 13:51:55: #1 tags after filtering in treatment: 16995448 INFO @ Thu, 05 Dec 2019 13:51:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:51:55: #1 finished! INFO @ Thu, 05 Dec 2019 13:51:55: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:51:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:51:56: #2 number of paired peaks: 467 WARNING @ Thu, 05 Dec 2019 13:51:56: Fewer paired peaks (467) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 467 pairs to build model! INFO @ Thu, 05 Dec 2019 13:51:56: start model_add_line... INFO @ Thu, 05 Dec 2019 13:51:56: start X-correlation... INFO @ Thu, 05 Dec 2019 13:51:56: end of X-cor INFO @ Thu, 05 Dec 2019 13:51:56: #2 finished! INFO @ Thu, 05 Dec 2019 13:51:56: #2 predicted fragment length is 123 bps INFO @ Thu, 05 Dec 2019 13:51:56: #2 alternative fragment length(s) may be 4,123 bps INFO @ Thu, 05 Dec 2019 13:51:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6468479/SRX6468479.05_model.r INFO @ Thu, 05 Dec 2019 13:51:56: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:51:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:52:02: 14000000 INFO @ Thu, 05 Dec 2019 13:52:11: 15000000 INFO @ Thu, 05 Dec 2019 13:52:19: 16000000 INFO @ Thu, 05 Dec 2019 13:52:29: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:52:29: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:52:29: #1 total tags in treatment: 16995448 INFO @ Thu, 05 Dec 2019 13:52:29: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:52:29: #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 13:52:29: #1 tags after filtering in treatment: 16995448 INFO @ Thu, 05 Dec 2019 13:52:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:52:29: #1 finished! INFO @ Thu, 05 Dec 2019 13:52:29: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:52:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:52:31: #2 number of paired peaks: 467 WARNING @ Thu, 05 Dec 2019 13:52:31: Fewer paired peaks (467) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 467 pairs to build model! INFO @ Thu, 05 Dec 2019 13:52:31: start model_add_line... INFO @ Thu, 05 Dec 2019 13:52:31: start X-correlation... INFO @ Thu, 05 Dec 2019 13:52:31: end of X-cor INFO @ Thu, 05 Dec 2019 13:52:31: #2 finished! INFO @ Thu, 05 Dec 2019 13:52:31: #2 predicted fragment length is 123 bps INFO @ Thu, 05 Dec 2019 13:52:31: #2 alternative fragment length(s) may be 4,123 bps INFO @ Thu, 05 Dec 2019 13:52:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6468479/SRX6468479.20_model.r INFO @ Thu, 05 Dec 2019 13:52:31: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:52:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:52:39: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:52:43: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:53:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6468479/SRX6468479.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:53:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6468479/SRX6468479.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:53:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6468479/SRX6468479.10_summits.bed INFO @ Thu, 05 Dec 2019 13:53:04: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5151 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:53:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6468479/SRX6468479.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:53:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6468479/SRX6468479.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:53:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6468479/SRX6468479.05_summits.bed INFO @ Thu, 05 Dec 2019 13:53:08: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (8044 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:53:18: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:53:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6468479/SRX6468479.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:53:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6468479/SRX6468479.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:53:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6468479/SRX6468479.20_summits.bed INFO @ Thu, 05 Dec 2019 13:53:42: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1639 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。