Job ID = 1294978 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T02:01:26 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 ) 2019-06-03T02:01:26 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 ) 2019-06-03T02:01:26 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 : 18,953,572 reads read : 18,953,572 reads written : 18,953,572 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: 00:09:39 18953572 reads; of these: 18953572 (100.00%) were unpaired; of these: 973847 (5.14%) aligned 0 times 11627618 (61.35%) aligned exactly 1 time 6352107 (33.51%) aligned >1 times 94.86% overall alignment rate Time searching: 00:09:39 Overall time: 00:09:39 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] 3038855 / 17979725 = 0.1690 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 11:25:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288036/SRX288036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288036/SRX288036.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288036/SRX288036.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288036/SRX288036.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 11:25:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:25:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:25:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288036/SRX288036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288036/SRX288036.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288036/SRX288036.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288036/SRX288036.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 11:25:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:25:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:25:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288036/SRX288036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288036/SRX288036.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288036/SRX288036.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288036/SRX288036.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 11:25:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:25:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:25:29: 1000000 INFO @ Mon, 03 Jun 2019 11:25:30: 1000000 INFO @ Mon, 03 Jun 2019 11:25:30: 1000000 INFO @ Mon, 03 Jun 2019 11:25:38: 2000000 INFO @ Mon, 03 Jun 2019 11:25:39: 2000000 INFO @ Mon, 03 Jun 2019 11:25:39: 2000000 INFO @ Mon, 03 Jun 2019 11:25:46: 3000000 INFO @ Mon, 03 Jun 2019 11:25:48: 3000000 INFO @ Mon, 03 Jun 2019 11:25:48: 3000000 INFO @ Mon, 03 Jun 2019 11:25:54: 4000000 INFO @ Mon, 03 Jun 2019 11:25:57: 4000000 INFO @ Mon, 03 Jun 2019 11:25:57: 4000000 INFO @ Mon, 03 Jun 2019 11:26:02: 5000000 INFO @ Mon, 03 Jun 2019 11:26:06: 5000000 INFO @ Mon, 03 Jun 2019 11:26:06: 5000000 INFO @ Mon, 03 Jun 2019 11:26:11: 6000000 INFO @ Mon, 03 Jun 2019 11:26:16: 6000000 INFO @ Mon, 03 Jun 2019 11:26:16: 6000000 INFO @ Mon, 03 Jun 2019 11:26:19: 7000000 INFO @ Mon, 03 Jun 2019 11:26:25: 7000000 INFO @ Mon, 03 Jun 2019 11:26:25: 7000000 INFO @ Mon, 03 Jun 2019 11:26:28: 8000000 INFO @ Mon, 03 Jun 2019 11:26:34: 8000000 INFO @ Mon, 03 Jun 2019 11:26:34: 8000000 INFO @ Mon, 03 Jun 2019 11:26:36: 9000000 INFO @ Mon, 03 Jun 2019 11:26:43: 9000000 INFO @ Mon, 03 Jun 2019 11:26:43: 9000000 INFO @ Mon, 03 Jun 2019 11:26:45: 10000000 INFO @ Mon, 03 Jun 2019 11:26:52: 10000000 INFO @ Mon, 03 Jun 2019 11:26:52: 10000000 INFO @ Mon, 03 Jun 2019 11:26:53: 11000000 INFO @ Mon, 03 Jun 2019 11:27:01: 12000000 INFO @ Mon, 03 Jun 2019 11:27:02: 11000000 INFO @ Mon, 03 Jun 2019 11:27:02: 11000000 INFO @ Mon, 03 Jun 2019 11:27:10: 13000000 INFO @ Mon, 03 Jun 2019 11:27:11: 12000000 INFO @ Mon, 03 Jun 2019 11:27:11: 12000000 INFO @ Mon, 03 Jun 2019 11:27:18: 14000000 INFO @ Mon, 03 Jun 2019 11:27:20: 13000000 INFO @ Mon, 03 Jun 2019 11:27:20: 13000000 INFO @ Mon, 03 Jun 2019 11:27:26: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:27:26: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:27:26: #1 total tags in treatment: 14940870 INFO @ Mon, 03 Jun 2019 11:27:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:27:26: #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 11:27:27: #1 tags after filtering in treatment: 14940870 INFO @ Mon, 03 Jun 2019 11:27:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:27:27: #1 finished! INFO @ Mon, 03 Jun 2019 11:27:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:27:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:27:28: #2 number of paired peaks: 427 WARNING @ Mon, 03 Jun 2019 11:27:28: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Mon, 03 Jun 2019 11:27:28: start model_add_line... INFO @ Mon, 03 Jun 2019 11:27:28: start X-correlation... INFO @ Mon, 03 Jun 2019 11:27:28: end of X-cor INFO @ Mon, 03 Jun 2019 11:27:28: #2 finished! INFO @ Mon, 03 Jun 2019 11:27:28: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 11:27:28: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 03 Jun 2019 11:27:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288036/SRX288036.20_model.r WARNING @ Mon, 03 Jun 2019 11:27:28: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:27:28: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 03 Jun 2019 11:27:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 11:27:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:27:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:27:29: 14000000 INFO @ Mon, 03 Jun 2019 11:27:29: 14000000 INFO @ Mon, 03 Jun 2019 11:27:38: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:27:38: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:27:38: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:27:38: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:27:38: #1 total tags in treatment: 14940870 INFO @ Mon, 03 Jun 2019 11:27:38: #1 total tags in treatment: 14940870 INFO @ Mon, 03 Jun 2019 11:27:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:27:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:27:38: #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 11:27:38: #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 11:27:38: #1 tags after filtering in treatment: 14940870 INFO @ Mon, 03 Jun 2019 11:27:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:27:38: #1 finished! INFO @ Mon, 03 Jun 2019 11:27:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:27:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:27:38: #1 tags after filtering in treatment: 14940870 INFO @ Mon, 03 Jun 2019 11:27:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:27:38: #1 finished! INFO @ Mon, 03 Jun 2019 11:27:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:27:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:27:40: #2 number of paired peaks: 427 WARNING @ Mon, 03 Jun 2019 11:27:40: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Mon, 03 Jun 2019 11:27:40: start model_add_line... INFO @ Mon, 03 Jun 2019 11:27:40: #2 number of paired peaks: 427 WARNING @ Mon, 03 Jun 2019 11:27:40: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Mon, 03 Jun 2019 11:27:40: start model_add_line... INFO @ Mon, 03 Jun 2019 11:27:40: start X-correlation... INFO @ Mon, 03 Jun 2019 11:27:40: start X-correlation... INFO @ Mon, 03 Jun 2019 11:27:40: end of X-cor INFO @ Mon, 03 Jun 2019 11:27:40: #2 finished! INFO @ Mon, 03 Jun 2019 11:27:40: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 11:27:40: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 03 Jun 2019 11:27:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288036/SRX288036.10_model.r WARNING @ Mon, 03 Jun 2019 11:27:40: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:27:40: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 03 Jun 2019 11:27:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 11:27:40: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:27:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:27:40: end of X-cor INFO @ Mon, 03 Jun 2019 11:27:40: #2 finished! INFO @ Mon, 03 Jun 2019 11:27:40: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 11:27:40: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 03 Jun 2019 11:27:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288036/SRX288036.05_model.r WARNING @ Mon, 03 Jun 2019 11:27:40: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:27:40: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 03 Jun 2019 11:27:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 11:27:40: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:27:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:28:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:28:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:28:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:28:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288036/SRX288036.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:28:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288036/SRX288036.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:28:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288036/SRX288036.20_summits.bed INFO @ Mon, 03 Jun 2019 11:28:29: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1545 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:28:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288036/SRX288036.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:28:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288036/SRX288036.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:28:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288036/SRX288036.10_summits.bed INFO @ Mon, 03 Jun 2019 11:28:40: Done! INFO @ Mon, 03 Jun 2019 11:28:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288036/SRX288036.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:28:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288036/SRX288036.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:28:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288036/SRX288036.05_summits.bed pass1 - making usageList (13 chroms): 1 millis INFO @ Mon, 03 Jun 2019 11:28:40: Done! pass2 - checking and writing primary data (1952 records, 4 fields): 7 millis CompletedMACS2peakCalling pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2206 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。