Job ID = 1294707 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:41:50 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 ) 2019-06-03T00:41:50 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 ) 2019-06-03T00:47:03 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 ) 2019-06-03T00:47:03 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 : 16,333,147 reads read : 16,333,147 reads written : 16,333,147 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: 00:04:35 16333147 reads; of these: 16333147 (100.00%) were unpaired; of these: 669066 (4.10%) aligned 0 times 13812824 (84.57%) aligned exactly 1 time 1851257 (11.33%) aligned >1 times 95.90% overall alignment rate Time searching: 00:04:35 Overall time: 00:04:35 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] 1535003 / 15664081 = 0.0980 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 09:58:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287835/SRX287835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287835/SRX287835.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287835/SRX287835.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287835/SRX287835.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 09:58:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:58:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:58:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287835/SRX287835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287835/SRX287835.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287835/SRX287835.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287835/SRX287835.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 09:58:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:58:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:58:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287835/SRX287835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287835/SRX287835.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287835/SRX287835.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287835/SRX287835.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 09:58:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:58:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:59:03: 1000000 INFO @ Mon, 03 Jun 2019 09:59:03: 1000000 INFO @ Mon, 03 Jun 2019 09:59:03: 1000000 INFO @ Mon, 03 Jun 2019 09:59:11: 2000000 INFO @ Mon, 03 Jun 2019 09:59:12: 2000000 INFO @ Mon, 03 Jun 2019 09:59:13: 2000000 INFO @ Mon, 03 Jun 2019 09:59:19: 3000000 INFO @ Mon, 03 Jun 2019 09:59:20: 3000000 INFO @ Mon, 03 Jun 2019 09:59:21: 3000000 INFO @ Mon, 03 Jun 2019 09:59:27: 4000000 INFO @ Mon, 03 Jun 2019 09:59:29: 4000000 INFO @ Mon, 03 Jun 2019 09:59:30: 4000000 INFO @ Mon, 03 Jun 2019 09:59:34: 5000000 INFO @ Mon, 03 Jun 2019 09:59:37: 5000000 INFO @ Mon, 03 Jun 2019 09:59:38: 5000000 INFO @ Mon, 03 Jun 2019 09:59:42: 6000000 INFO @ Mon, 03 Jun 2019 09:59:46: 6000000 INFO @ Mon, 03 Jun 2019 09:59:46: 6000000 INFO @ Mon, 03 Jun 2019 09:59:50: 7000000 INFO @ Mon, 03 Jun 2019 09:59:54: 7000000 INFO @ Mon, 03 Jun 2019 09:59:55: 7000000 INFO @ Mon, 03 Jun 2019 09:59:58: 8000000 INFO @ Mon, 03 Jun 2019 10:00:02: 8000000 INFO @ Mon, 03 Jun 2019 10:00:03: 8000000 INFO @ Mon, 03 Jun 2019 10:00:06: 9000000 INFO @ Mon, 03 Jun 2019 10:00:11: 9000000 INFO @ Mon, 03 Jun 2019 10:00:11: 9000000 INFO @ Mon, 03 Jun 2019 10:00:14: 10000000 INFO @ Mon, 03 Jun 2019 10:00:19: 10000000 INFO @ Mon, 03 Jun 2019 10:00:20: 10000000 INFO @ Mon, 03 Jun 2019 10:00:22: 11000000 INFO @ Mon, 03 Jun 2019 10:00:29: 11000000 INFO @ Mon, 03 Jun 2019 10:00:29: 11000000 INFO @ Mon, 03 Jun 2019 10:00:30: 12000000 INFO @ Mon, 03 Jun 2019 10:00:37: 12000000 INFO @ Mon, 03 Jun 2019 10:00:37: 12000000 INFO @ Mon, 03 Jun 2019 10:00:38: 13000000 INFO @ Mon, 03 Jun 2019 10:00:45: 14000000 INFO @ Mon, 03 Jun 2019 10:00:45: 13000000 INFO @ Mon, 03 Jun 2019 10:00:46: 13000000 INFO @ Mon, 03 Jun 2019 10:00:46: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:00:46: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:00:46: #1 total tags in treatment: 14129078 INFO @ Mon, 03 Jun 2019 10:00:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:00:46: #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 10:00:46: #1 tags after filtering in treatment: 14129078 INFO @ Mon, 03 Jun 2019 10:00:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:00:46: #1 finished! INFO @ Mon, 03 Jun 2019 10:00:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:00:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:00:48: #2 number of paired peaks: 604 WARNING @ Mon, 03 Jun 2019 10:00:48: Fewer paired peaks (604) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 604 pairs to build model! INFO @ Mon, 03 Jun 2019 10:00:48: start model_add_line... INFO @ Mon, 03 Jun 2019 10:00:48: start X-correlation... INFO @ Mon, 03 Jun 2019 10:00:48: end of X-cor INFO @ Mon, 03 Jun 2019 10:00:48: #2 finished! INFO @ Mon, 03 Jun 2019 10:00:48: #2 predicted fragment length is 210 bps INFO @ Mon, 03 Jun 2019 10:00:48: #2 alternative fragment length(s) may be 210 bps INFO @ Mon, 03 Jun 2019 10:00:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287835/SRX287835.10_model.r INFO @ Mon, 03 Jun 2019 10:00:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:00:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:00:53: 14000000 INFO @ Mon, 03 Jun 2019 10:00:54: 14000000 INFO @ Mon, 03 Jun 2019 10:00:54: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:00:54: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:00:54: #1 total tags in treatment: 14129078 INFO @ Mon, 03 Jun 2019 10:00:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:00:54: #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 10:00:55: #1 tags after filtering in treatment: 14129078 INFO @ Mon, 03 Jun 2019 10:00:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:00:55: #1 finished! INFO @ Mon, 03 Jun 2019 10:00:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:00:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:00:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:00:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:00:55: #1 total tags in treatment: 14129078 INFO @ Mon, 03 Jun 2019 10:00:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:00:55: #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 10:00:55: #1 tags after filtering in treatment: 14129078 INFO @ Mon, 03 Jun 2019 10:00:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:00:55: #1 finished! INFO @ Mon, 03 Jun 2019 10:00:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:00:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:00:56: #2 number of paired peaks: 604 WARNING @ Mon, 03 Jun 2019 10:00:56: Fewer paired peaks (604) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 604 pairs to build model! INFO @ Mon, 03 Jun 2019 10:00:56: start model_add_line... INFO @ Mon, 03 Jun 2019 10:00:56: start X-correlation... INFO @ Mon, 03 Jun 2019 10:00:56: end of X-cor INFO @ Mon, 03 Jun 2019 10:00:56: #2 finished! INFO @ Mon, 03 Jun 2019 10:00:56: #2 predicted fragment length is 210 bps INFO @ Mon, 03 Jun 2019 10:00:56: #2 alternative fragment length(s) may be 210 bps INFO @ Mon, 03 Jun 2019 10:00:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287835/SRX287835.20_model.r INFO @ Mon, 03 Jun 2019 10:00:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:00:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:00:57: #2 number of paired peaks: 604 WARNING @ Mon, 03 Jun 2019 10:00:57: Fewer paired peaks (604) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 604 pairs to build model! INFO @ Mon, 03 Jun 2019 10:00:57: start model_add_line... INFO @ Mon, 03 Jun 2019 10:00:57: start X-correlation... INFO @ Mon, 03 Jun 2019 10:00:57: end of X-cor INFO @ Mon, 03 Jun 2019 10:00:57: #2 finished! INFO @ Mon, 03 Jun 2019 10:00:57: #2 predicted fragment length is 210 bps INFO @ Mon, 03 Jun 2019 10:00:57: #2 alternative fragment length(s) may be 210 bps INFO @ Mon, 03 Jun 2019 10:00:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287835/SRX287835.05_model.r INFO @ Mon, 03 Jun 2019 10:00:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:00:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:01:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:01:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:01:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:01:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287835/SRX287835.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:01:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287835/SRX287835.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:01:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287835/SRX287835.10_summits.bed INFO @ Mon, 03 Jun 2019 10:01:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4730 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:01:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287835/SRX287835.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:01:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287835/SRX287835.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:01:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287835/SRX287835.20_summits.bed INFO @ Mon, 03 Jun 2019 10:01:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2895 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:01:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287835/SRX287835.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:01:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287835/SRX287835.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:01:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287835/SRX287835.05_summits.bed INFO @ Mon, 03 Jun 2019 10:01:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6612 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。