Job ID = 1294587 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:05:19 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 ) 2019-06-03T00:05:19 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 ) 2019-06-03T00:05:19 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 ) 2019-06-03T00:05:19 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 : 15,680,982 reads read : 15,680,982 reads written : 15,680,982 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: 00:04:36 15680982 reads; of these: 15680982 (100.00%) were unpaired; of these: 2441188 (15.57%) aligned 0 times 10188487 (64.97%) aligned exactly 1 time 3051307 (19.46%) aligned >1 times 84.43% overall alignment rate Time searching: 00:04:36 Overall time: 00:04:36 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] 897257 / 13239794 = 0.0678 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 09:23:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287761/SRX287761.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287761/SRX287761.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287761/SRX287761.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287761/SRX287761.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 09:23:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287761/SRX287761.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287761/SRX287761.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287761/SRX287761.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287761/SRX287761.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 09:23:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:23:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:23:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:23:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:23:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287761/SRX287761.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287761/SRX287761.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287761/SRX287761.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287761/SRX287761.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 09:23:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:23:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:23:29: 1000000 INFO @ Mon, 03 Jun 2019 09:23:29: 1000000 INFO @ Mon, 03 Jun 2019 09:23:29: 1000000 INFO @ Mon, 03 Jun 2019 09:23:37: 2000000 INFO @ Mon, 03 Jun 2019 09:23:37: 2000000 INFO @ Mon, 03 Jun 2019 09:23:38: 2000000 INFO @ Mon, 03 Jun 2019 09:23:46: 3000000 INFO @ Mon, 03 Jun 2019 09:23:46: 3000000 INFO @ Mon, 03 Jun 2019 09:23:47: 3000000 INFO @ Mon, 03 Jun 2019 09:23:54: 4000000 INFO @ Mon, 03 Jun 2019 09:23:54: 4000000 INFO @ Mon, 03 Jun 2019 09:23:56: 4000000 INFO @ Mon, 03 Jun 2019 09:24:02: 5000000 INFO @ Mon, 03 Jun 2019 09:24:02: 5000000 INFO @ Mon, 03 Jun 2019 09:24:05: 5000000 INFO @ Mon, 03 Jun 2019 09:24:11: 6000000 INFO @ Mon, 03 Jun 2019 09:24:11: 6000000 INFO @ Mon, 03 Jun 2019 09:24:13: 6000000 INFO @ Mon, 03 Jun 2019 09:24:19: 7000000 INFO @ Mon, 03 Jun 2019 09:24:19: 7000000 INFO @ Mon, 03 Jun 2019 09:24:22: 7000000 INFO @ Mon, 03 Jun 2019 09:24:27: 8000000 INFO @ Mon, 03 Jun 2019 09:24:27: 8000000 INFO @ Mon, 03 Jun 2019 09:24:30: 8000000 INFO @ Mon, 03 Jun 2019 09:24:36: 9000000 INFO @ Mon, 03 Jun 2019 09:24:36: 9000000 INFO @ Mon, 03 Jun 2019 09:24:39: 9000000 INFO @ Mon, 03 Jun 2019 09:24:44: 10000000 INFO @ Mon, 03 Jun 2019 09:24:44: 10000000 INFO @ Mon, 03 Jun 2019 09:24:48: 10000000 INFO @ Mon, 03 Jun 2019 09:24:52: 11000000 INFO @ Mon, 03 Jun 2019 09:24:52: 11000000 INFO @ Mon, 03 Jun 2019 09:24:57: 11000000 INFO @ Mon, 03 Jun 2019 09:25:00: 12000000 INFO @ Mon, 03 Jun 2019 09:25:00: 12000000 INFO @ Mon, 03 Jun 2019 09:25:03: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:25:03: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:25:03: #1 total tags in treatment: 12342537 INFO @ Mon, 03 Jun 2019 09:25:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:25:03: #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 09:25:03: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:25:03: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:25:03: #1 total tags in treatment: 12342537 INFO @ Mon, 03 Jun 2019 09:25:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:25:03: #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 09:25:03: #1 tags after filtering in treatment: 12342537 INFO @ Mon, 03 Jun 2019 09:25:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:25:03: #1 finished! INFO @ Mon, 03 Jun 2019 09:25:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:25:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:25:03: #1 tags after filtering in treatment: 12342537 INFO @ Mon, 03 Jun 2019 09:25:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:25:03: #1 finished! INFO @ Mon, 03 Jun 2019 09:25:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:25:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:25:04: #2 number of paired peaks: 179 WARNING @ Mon, 03 Jun 2019 09:25:04: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Mon, 03 Jun 2019 09:25:04: start model_add_line... INFO @ Mon, 03 Jun 2019 09:25:04: #2 number of paired peaks: 179 WARNING @ Mon, 03 Jun 2019 09:25:04: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Mon, 03 Jun 2019 09:25:04: start model_add_line... INFO @ Mon, 03 Jun 2019 09:25:04: start X-correlation... INFO @ Mon, 03 Jun 2019 09:25:04: start X-correlation... INFO @ Mon, 03 Jun 2019 09:25:04: end of X-cor INFO @ Mon, 03 Jun 2019 09:25:04: #2 finished! INFO @ Mon, 03 Jun 2019 09:25:04: #2 predicted fragment length is 149 bps INFO @ Mon, 03 Jun 2019 09:25:04: #2 alternative fragment length(s) may be 149 bps INFO @ Mon, 03 Jun 2019 09:25:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287761/SRX287761.10_model.r INFO @ Mon, 03 Jun 2019 09:25:04: end of X-cor INFO @ Mon, 03 Jun 2019 09:25:04: #2 finished! INFO @ Mon, 03 Jun 2019 09:25:04: #2 predicted fragment length is 149 bps INFO @ Mon, 03 Jun 2019 09:25:04: #2 alternative fragment length(s) may be 149 bps INFO @ Mon, 03 Jun 2019 09:25:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287761/SRX287761.20_model.r INFO @ Mon, 03 Jun 2019 09:25:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:25:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:25:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:25:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:25:05: 12000000 INFO @ Mon, 03 Jun 2019 09:25:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:25:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:25:08: #1 total tags in treatment: 12342537 INFO @ Mon, 03 Jun 2019 09:25:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:25:08: #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 09:25:08: #1 tags after filtering in treatment: 12342537 INFO @ Mon, 03 Jun 2019 09:25:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:25:08: #1 finished! INFO @ Mon, 03 Jun 2019 09:25:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:25:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:25:09: #2 number of paired peaks: 179 WARNING @ Mon, 03 Jun 2019 09:25:09: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Mon, 03 Jun 2019 09:25:09: start model_add_line... INFO @ Mon, 03 Jun 2019 09:25:09: start X-correlation... INFO @ Mon, 03 Jun 2019 09:25:09: end of X-cor INFO @ Mon, 03 Jun 2019 09:25:09: #2 finished! INFO @ Mon, 03 Jun 2019 09:25:09: #2 predicted fragment length is 149 bps INFO @ Mon, 03 Jun 2019 09:25:09: #2 alternative fragment length(s) may be 149 bps INFO @ Mon, 03 Jun 2019 09:25:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287761/SRX287761.05_model.r INFO @ Mon, 03 Jun 2019 09:25:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:25:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:25:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:25:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:25:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:25:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287761/SRX287761.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:25:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287761/SRX287761.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:25:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287761/SRX287761.20_summits.bed INFO @ Mon, 03 Jun 2019 09:25:57: Done! pass1 - making usageList (12 chroms): 1 millis INFO @ Mon, 03 Jun 2019 09:25:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287761/SRX287761.10_peaks.xls pass2 - checking and writing primary data (588 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:25:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287761/SRX287761.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:25:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287761/SRX287761.10_summits.bed INFO @ Mon, 03 Jun 2019 09:25:57: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2509 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:26:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287761/SRX287761.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:26:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287761/SRX287761.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:26:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287761/SRX287761.05_summits.bed INFO @ Mon, 03 Jun 2019 09:26:02: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5993 records, 4 fields): 90 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。