Job ID = 1299721 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T09:26:15 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 ) 2019-06-03T09:26:15 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 ) 2019-06-03T09:41:07 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 : 16,316,387 reads read : 32,632,774 reads written : 32,632,774 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: 00:48:20 16316387 reads; of these: 16316387 (100.00%) were paired; of these: 796236 (4.88%) aligned concordantly 0 times 10566906 (64.76%) aligned concordantly exactly 1 time 4953245 (30.36%) aligned concordantly >1 times ---- 796236 pairs aligned concordantly 0 times; of these: 30477 (3.83%) aligned discordantly 1 time ---- 765759 pairs aligned 0 times concordantly or discordantly; of these: 1531518 mates make up the pairs; of these: 1160118 (75.75%) aligned 0 times 267383 (17.46%) aligned exactly 1 time 104017 (6.79%) aligned >1 times 96.44% overall alignment rate Time searching: 00:48:20 Overall time: 00:48:20 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 2362970 / 15518718 = 0.1523 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 19:41:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474600/SRX474600.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474600/SRX474600.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474600/SRX474600.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474600/SRX474600.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 19:41:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:41:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:41:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474600/SRX474600.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474600/SRX474600.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474600/SRX474600.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474600/SRX474600.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 19:41:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:41:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:41:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474600/SRX474600.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474600/SRX474600.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474600/SRX474600.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474600/SRX474600.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 19:41:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:41:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:41:44: 1000000 INFO @ Mon, 03 Jun 2019 19:41:44: 1000000 INFO @ Mon, 03 Jun 2019 19:41:45: 1000000 INFO @ Mon, 03 Jun 2019 19:41:52: 2000000 INFO @ Mon, 03 Jun 2019 19:41:53: 2000000 INFO @ Mon, 03 Jun 2019 19:41:55: 2000000 INFO @ Mon, 03 Jun 2019 19:42:00: 3000000 INFO @ Mon, 03 Jun 2019 19:42:01: 3000000 INFO @ Mon, 03 Jun 2019 19:42:04: 3000000 INFO @ Mon, 03 Jun 2019 19:42:08: 4000000 INFO @ Mon, 03 Jun 2019 19:42:09: 4000000 INFO @ Mon, 03 Jun 2019 19:42:13: 4000000 INFO @ Mon, 03 Jun 2019 19:42:16: 5000000 INFO @ Mon, 03 Jun 2019 19:42:18: 5000000 INFO @ Mon, 03 Jun 2019 19:42:23: 5000000 INFO @ Mon, 03 Jun 2019 19:42:24: 6000000 INFO @ Mon, 03 Jun 2019 19:42:26: 6000000 INFO @ Mon, 03 Jun 2019 19:42:31: 7000000 INFO @ Mon, 03 Jun 2019 19:42:32: 6000000 INFO @ Mon, 03 Jun 2019 19:42:34: 7000000 INFO @ Mon, 03 Jun 2019 19:42:39: 8000000 INFO @ Mon, 03 Jun 2019 19:42:42: 7000000 INFO @ Mon, 03 Jun 2019 19:42:42: 8000000 INFO @ Mon, 03 Jun 2019 19:42:47: 9000000 INFO @ Mon, 03 Jun 2019 19:42:50: 9000000 INFO @ Mon, 03 Jun 2019 19:42:51: 8000000 INFO @ Mon, 03 Jun 2019 19:42:55: 10000000 INFO @ Mon, 03 Jun 2019 19:42:59: 10000000 INFO @ Mon, 03 Jun 2019 19:43:00: 9000000 INFO @ Mon, 03 Jun 2019 19:43:03: 11000000 INFO @ Mon, 03 Jun 2019 19:43:07: 11000000 INFO @ Mon, 03 Jun 2019 19:43:09: 10000000 INFO @ Mon, 03 Jun 2019 19:43:11: 12000000 INFO @ Mon, 03 Jun 2019 19:43:15: 12000000 INFO @ Mon, 03 Jun 2019 19:43:18: 13000000 INFO @ Mon, 03 Jun 2019 19:43:19: 11000000 INFO @ Mon, 03 Jun 2019 19:43:23: 13000000 INFO @ Mon, 03 Jun 2019 19:43:26: 14000000 INFO @ Mon, 03 Jun 2019 19:43:28: 12000000 INFO @ Mon, 03 Jun 2019 19:43:31: 14000000 INFO @ Mon, 03 Jun 2019 19:43:34: 15000000 INFO @ Mon, 03 Jun 2019 19:43:38: 13000000 INFO @ Mon, 03 Jun 2019 19:43:39: 15000000 INFO @ Mon, 03 Jun 2019 19:43:42: 16000000 INFO @ Mon, 03 Jun 2019 19:43:47: 14000000 INFO @ Mon, 03 Jun 2019 19:43:47: 16000000 INFO @ Mon, 03 Jun 2019 19:43:49: 17000000 INFO @ Mon, 03 Jun 2019 19:43:56: 17000000 INFO @ Mon, 03 Jun 2019 19:43:56: 15000000 INFO @ Mon, 03 Jun 2019 19:43:57: 18000000 INFO @ Mon, 03 Jun 2019 19:44:04: 18000000 INFO @ Mon, 03 Jun 2019 19:44:05: 19000000 INFO @ Mon, 03 Jun 2019 19:44:06: 16000000 INFO @ Mon, 03 Jun 2019 19:44:12: 19000000 INFO @ Mon, 03 Jun 2019 19:44:13: 20000000 INFO @ Mon, 03 Jun 2019 19:44:15: 17000000 INFO @ Mon, 03 Jun 2019 19:44:20: 20000000 INFO @ Mon, 03 Jun 2019 19:44:21: 21000000 INFO @ Mon, 03 Jun 2019 19:44:25: 18000000 INFO @ Mon, 03 Jun 2019 19:44:28: 21000000 INFO @ Mon, 03 Jun 2019 19:44:29: 22000000 INFO @ Mon, 03 Jun 2019 19:44:35: 19000000 INFO @ Mon, 03 Jun 2019 19:44:36: 23000000 INFO @ Mon, 03 Jun 2019 19:44:37: 22000000 INFO @ Mon, 03 Jun 2019 19:44:44: 24000000 INFO @ Mon, 03 Jun 2019 19:44:44: 20000000 INFO @ Mon, 03 Jun 2019 19:44:45: 23000000 INFO @ Mon, 03 Jun 2019 19:44:52: 25000000 INFO @ Mon, 03 Jun 2019 19:44:53: 24000000 INFO @ Mon, 03 Jun 2019 19:44:54: 21000000 INFO @ Mon, 03 Jun 2019 19:45:00: 26000000 INFO @ Mon, 03 Jun 2019 19:45:01: 25000000 INFO @ Mon, 03 Jun 2019 19:45:03: 22000000 INFO @ Mon, 03 Jun 2019 19:45:06: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:45:06: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:45:06: #1 total tags in treatment: 13158792 INFO @ Mon, 03 Jun 2019 19:45:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:45:06: #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 19:45:06: #1 tags after filtering in treatment: 11529595 INFO @ Mon, 03 Jun 2019 19:45:06: #1 Redundant rate of treatment: 0.12 INFO @ Mon, 03 Jun 2019 19:45:06: #1 finished! INFO @ Mon, 03 Jun 2019 19:45:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:45:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:45:07: #2 number of paired peaks: 131 WARNING @ Mon, 03 Jun 2019 19:45:07: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Mon, 03 Jun 2019 19:45:07: start model_add_line... INFO @ Mon, 03 Jun 2019 19:45:07: start X-correlation... INFO @ Mon, 03 Jun 2019 19:45:07: end of X-cor INFO @ Mon, 03 Jun 2019 19:45:07: #2 finished! INFO @ Mon, 03 Jun 2019 19:45:07: #2 predicted fragment length is 95 bps INFO @ Mon, 03 Jun 2019 19:45:07: #2 alternative fragment length(s) may be 95 bps INFO @ Mon, 03 Jun 2019 19:45:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474600/SRX474600.05_model.r WARNING @ Mon, 03 Jun 2019 19:45:07: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:45:07: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Mon, 03 Jun 2019 19:45:07: #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 19:45:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:45:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:45:09: 26000000 INFO @ Mon, 03 Jun 2019 19:45:13: 23000000 INFO @ Mon, 03 Jun 2019 19:45:15: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:45:15: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:45:15: #1 total tags in treatment: 13158792 INFO @ Mon, 03 Jun 2019 19:45:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:45:15: #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 19:45:15: #1 tags after filtering in treatment: 11529595 INFO @ Mon, 03 Jun 2019 19:45:15: #1 Redundant rate of treatment: 0.12 INFO @ Mon, 03 Jun 2019 19:45:15: #1 finished! INFO @ Mon, 03 Jun 2019 19:45:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:45:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:45:16: #2 number of paired peaks: 131 WARNING @ Mon, 03 Jun 2019 19:45:16: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Mon, 03 Jun 2019 19:45:16: start model_add_line... INFO @ Mon, 03 Jun 2019 19:45:16: start X-correlation... INFO @ Mon, 03 Jun 2019 19:45:16: end of X-cor INFO @ Mon, 03 Jun 2019 19:45:16: #2 finished! INFO @ Mon, 03 Jun 2019 19:45:16: #2 predicted fragment length is 95 bps INFO @ Mon, 03 Jun 2019 19:45:16: #2 alternative fragment length(s) may be 95 bps INFO @ Mon, 03 Jun 2019 19:45:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474600/SRX474600.10_model.r WARNING @ Mon, 03 Jun 2019 19:45:16: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:45:16: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Mon, 03 Jun 2019 19:45:16: #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 19:45:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:45:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:45:21: 24000000 INFO @ Mon, 03 Jun 2019 19:45:30: 25000000 INFO @ Mon, 03 Jun 2019 19:45:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:45:39: 26000000 INFO @ Mon, 03 Jun 2019 19:45:46: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:45:46: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:45:46: #1 total tags in treatment: 13158792 INFO @ Mon, 03 Jun 2019 19:45:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:45:46: #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 19:45:46: #1 tags after filtering in treatment: 11529595 INFO @ Mon, 03 Jun 2019 19:45:46: #1 Redundant rate of treatment: 0.12 INFO @ Mon, 03 Jun 2019 19:45:46: #1 finished! INFO @ Mon, 03 Jun 2019 19:45:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:45:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:45:47: #2 number of paired peaks: 131 WARNING @ Mon, 03 Jun 2019 19:45:47: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Mon, 03 Jun 2019 19:45:47: start model_add_line... INFO @ Mon, 03 Jun 2019 19:45:47: start X-correlation... INFO @ Mon, 03 Jun 2019 19:45:47: end of X-cor INFO @ Mon, 03 Jun 2019 19:45:47: #2 finished! INFO @ Mon, 03 Jun 2019 19:45:47: #2 predicted fragment length is 95 bps INFO @ Mon, 03 Jun 2019 19:45:47: #2 alternative fragment length(s) may be 95 bps INFO @ Mon, 03 Jun 2019 19:45:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474600/SRX474600.20_model.r WARNING @ Mon, 03 Jun 2019 19:45:47: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:45:47: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Mon, 03 Jun 2019 19:45:47: #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 19:45:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:45:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:45:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:45:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474600/SRX474600.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:45:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474600/SRX474600.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:45:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474600/SRX474600.05_summits.bed INFO @ Mon, 03 Jun 2019 19:45:54: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1219 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:46:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474600/SRX474600.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:46:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474600/SRX474600.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:46:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474600/SRX474600.10_summits.bed INFO @ Mon, 03 Jun 2019 19:46:03: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (918 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:46:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:46:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474600/SRX474600.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:46:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474600/SRX474600.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:46:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474600/SRX474600.20_summits.bed INFO @ Mon, 03 Jun 2019 19:46:34: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (644 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。