Job ID = 1299963 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T09:53:42 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 ) 2019-06-03T09:53:42 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 ) 2019-06-03T09:53:42 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 : 33,068,527 reads read : 33,068,527 reads written : 33,068,527 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: 00:16:13 33068527 reads; of these: 33068527 (100.00%) were unpaired; of these: 863332 (2.61%) aligned 0 times 22207648 (67.16%) aligned exactly 1 time 9997547 (30.23%) aligned >1 times 97.39% overall alignment rate Time searching: 00:16:13 Overall time: 00:16:13 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] 4210881 / 32205195 = 0.1308 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 19:31:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801799/SRX4801799.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801799/SRX4801799.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801799/SRX4801799.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801799/SRX4801799.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 19:31:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:31:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:31:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801799/SRX4801799.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801799/SRX4801799.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801799/SRX4801799.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801799/SRX4801799.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 19:31:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:31:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:31:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801799/SRX4801799.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801799/SRX4801799.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801799/SRX4801799.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801799/SRX4801799.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 19:31:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:31:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:31:10: 1000000 INFO @ Mon, 03 Jun 2019 19:31:12: 1000000 INFO @ Mon, 03 Jun 2019 19:31:12: 1000000 INFO @ Mon, 03 Jun 2019 19:31:17: 2000000 INFO @ Mon, 03 Jun 2019 19:31:21: 2000000 INFO @ Mon, 03 Jun 2019 19:31:22: 2000000 INFO @ Mon, 03 Jun 2019 19:31:25: 3000000 INFO @ Mon, 03 Jun 2019 19:31:30: 3000000 INFO @ Mon, 03 Jun 2019 19:31:31: 3000000 INFO @ Mon, 03 Jun 2019 19:31:32: 4000000 INFO @ Mon, 03 Jun 2019 19:31:38: 4000000 INFO @ Mon, 03 Jun 2019 19:31:39: 5000000 INFO @ Mon, 03 Jun 2019 19:31:40: 4000000 INFO @ Mon, 03 Jun 2019 19:31:46: 6000000 INFO @ Mon, 03 Jun 2019 19:31:47: 5000000 INFO @ Mon, 03 Jun 2019 19:31:49: 5000000 INFO @ Mon, 03 Jun 2019 19:31:53: 7000000 INFO @ Mon, 03 Jun 2019 19:31:56: 6000000 INFO @ Mon, 03 Jun 2019 19:31:58: 6000000 INFO @ Mon, 03 Jun 2019 19:32:02: 8000000 INFO @ Mon, 03 Jun 2019 19:32:04: 7000000 INFO @ Mon, 03 Jun 2019 19:32:07: 7000000 INFO @ Mon, 03 Jun 2019 19:32:09: 9000000 INFO @ Mon, 03 Jun 2019 19:32:13: 8000000 INFO @ Mon, 03 Jun 2019 19:32:16: 10000000 INFO @ Mon, 03 Jun 2019 19:32:16: 8000000 INFO @ Mon, 03 Jun 2019 19:32:21: 9000000 INFO @ Mon, 03 Jun 2019 19:32:23: 11000000 INFO @ Mon, 03 Jun 2019 19:32:25: 9000000 INFO @ Mon, 03 Jun 2019 19:32:30: 10000000 INFO @ Mon, 03 Jun 2019 19:32:30: 12000000 INFO @ Mon, 03 Jun 2019 19:32:34: 10000000 INFO @ Mon, 03 Jun 2019 19:32:37: 13000000 INFO @ Mon, 03 Jun 2019 19:32:39: 11000000 INFO @ Mon, 03 Jun 2019 19:32:44: 11000000 INFO @ Mon, 03 Jun 2019 19:32:45: 14000000 INFO @ Mon, 03 Jun 2019 19:32:48: 12000000 INFO @ Mon, 03 Jun 2019 19:32:52: 15000000 INFO @ Mon, 03 Jun 2019 19:32:52: 12000000 INFO @ Mon, 03 Jun 2019 19:32:56: 13000000 INFO @ Mon, 03 Jun 2019 19:32:58: 16000000 INFO @ Mon, 03 Jun 2019 19:33:01: 13000000 INFO @ Mon, 03 Jun 2019 19:33:04: 14000000 INFO @ Mon, 03 Jun 2019 19:33:05: 17000000 INFO @ Mon, 03 Jun 2019 19:33:10: 14000000 INFO @ Mon, 03 Jun 2019 19:33:13: 15000000 INFO @ Mon, 03 Jun 2019 19:33:13: 18000000 INFO @ Mon, 03 Jun 2019 19:33:19: 15000000 INFO @ Mon, 03 Jun 2019 19:33:21: 16000000 INFO @ Mon, 03 Jun 2019 19:33:21: 19000000 INFO @ Mon, 03 Jun 2019 19:33:27: 16000000 INFO @ Mon, 03 Jun 2019 19:33:29: 20000000 INFO @ Mon, 03 Jun 2019 19:33:30: 17000000 INFO @ Mon, 03 Jun 2019 19:33:36: 21000000 INFO @ Mon, 03 Jun 2019 19:33:36: 17000000 INFO @ Mon, 03 Jun 2019 19:33:38: 18000000 INFO @ Mon, 03 Jun 2019 19:33:43: 22000000 INFO @ Mon, 03 Jun 2019 19:33:45: 18000000 INFO @ Mon, 03 Jun 2019 19:33:46: 19000000 INFO @ Mon, 03 Jun 2019 19:33:51: 23000000 INFO @ Mon, 03 Jun 2019 19:33:53: 19000000 INFO @ Mon, 03 Jun 2019 19:33:55: 20000000 INFO @ Mon, 03 Jun 2019 19:33:58: 24000000 INFO @ Mon, 03 Jun 2019 19:34:03: 20000000 INFO @ Mon, 03 Jun 2019 19:34:04: 21000000 INFO @ Mon, 03 Jun 2019 19:34:05: 25000000 INFO @ Mon, 03 Jun 2019 19:34:12: 21000000 INFO @ Mon, 03 Jun 2019 19:34:12: 26000000 INFO @ Mon, 03 Jun 2019 19:34:13: 22000000 INFO @ Mon, 03 Jun 2019 19:34:19: 27000000 INFO @ Mon, 03 Jun 2019 19:34:21: 22000000 INFO @ Mon, 03 Jun 2019 19:34:22: 23000000 INFO @ Mon, 03 Jun 2019 19:34:27: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:34:27: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:34:27: #1 total tags in treatment: 27994314 INFO @ Mon, 03 Jun 2019 19:34:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:34:27: #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 19:34:27: #1 tags after filtering in treatment: 27994314 INFO @ Mon, 03 Jun 2019 19:34:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:34:27: #1 finished! INFO @ Mon, 03 Jun 2019 19:34:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:34:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:34:29: #2 number of paired peaks: 395 WARNING @ Mon, 03 Jun 2019 19:34:29: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Mon, 03 Jun 2019 19:34:29: start model_add_line... INFO @ Mon, 03 Jun 2019 19:34:30: start X-correlation... INFO @ Mon, 03 Jun 2019 19:34:30: end of X-cor INFO @ Mon, 03 Jun 2019 19:34:30: #2 finished! INFO @ Mon, 03 Jun 2019 19:34:30: #2 predicted fragment length is 51 bps INFO @ Mon, 03 Jun 2019 19:34:30: #2 alternative fragment length(s) may be 2,51,588 bps INFO @ Mon, 03 Jun 2019 19:34:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801799/SRX4801799.10_model.r WARNING @ Mon, 03 Jun 2019 19:34:30: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:34:30: #2 You may need to consider one of the other alternative d(s): 2,51,588 WARNING @ Mon, 03 Jun 2019 19:34:30: #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 19:34:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:34:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:34:30: 23000000 INFO @ Mon, 03 Jun 2019 19:34:30: 24000000 INFO @ Mon, 03 Jun 2019 19:34:39: 25000000 INFO @ Mon, 03 Jun 2019 19:34:39: 24000000 INFO @ Mon, 03 Jun 2019 19:34:48: 26000000 INFO @ Mon, 03 Jun 2019 19:34:48: 25000000 INFO @ Mon, 03 Jun 2019 19:34:56: 27000000 INFO @ Mon, 03 Jun 2019 19:34:57: 26000000 INFO @ Mon, 03 Jun 2019 19:35:05: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:35:05: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:35:05: #1 total tags in treatment: 27994314 INFO @ Mon, 03 Jun 2019 19:35:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:35:05: #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 19:35:05: #1 tags after filtering in treatment: 27994314 INFO @ Mon, 03 Jun 2019 19:35:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:35:05: #1 finished! INFO @ Mon, 03 Jun 2019 19:35:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:35:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:35:06: 27000000 INFO @ Mon, 03 Jun 2019 19:35:08: #2 number of paired peaks: 395 WARNING @ Mon, 03 Jun 2019 19:35:08: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Mon, 03 Jun 2019 19:35:08: start model_add_line... INFO @ Mon, 03 Jun 2019 19:35:08: start X-correlation... INFO @ Mon, 03 Jun 2019 19:35:08: end of X-cor INFO @ Mon, 03 Jun 2019 19:35:08: #2 finished! INFO @ Mon, 03 Jun 2019 19:35:08: #2 predicted fragment length is 51 bps INFO @ Mon, 03 Jun 2019 19:35:08: #2 alternative fragment length(s) may be 2,51,588 bps INFO @ Mon, 03 Jun 2019 19:35:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801799/SRX4801799.05_model.r WARNING @ Mon, 03 Jun 2019 19:35:08: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:35:08: #2 You may need to consider one of the other alternative d(s): 2,51,588 WARNING @ Mon, 03 Jun 2019 19:35:08: #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 19:35:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:35:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:35:15: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:35:15: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:35:15: #1 total tags in treatment: 27994314 INFO @ Mon, 03 Jun 2019 19:35:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:35:15: #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 19:35:15: #1 tags after filtering in treatment: 27994314 INFO @ Mon, 03 Jun 2019 19:35:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:35:15: #1 finished! INFO @ Mon, 03 Jun 2019 19:35:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:35:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:35:18: #2 number of paired peaks: 395 WARNING @ Mon, 03 Jun 2019 19:35:18: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Mon, 03 Jun 2019 19:35:18: start model_add_line... INFO @ Mon, 03 Jun 2019 19:35:18: start X-correlation... INFO @ Mon, 03 Jun 2019 19:35:18: end of X-cor INFO @ Mon, 03 Jun 2019 19:35:18: #2 finished! INFO @ Mon, 03 Jun 2019 19:35:18: #2 predicted fragment length is 51 bps INFO @ Mon, 03 Jun 2019 19:35:18: #2 alternative fragment length(s) may be 2,51,588 bps INFO @ Mon, 03 Jun 2019 19:35:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801799/SRX4801799.20_model.r WARNING @ Mon, 03 Jun 2019 19:35:18: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:35:18: #2 You may need to consider one of the other alternative d(s): 2,51,588 WARNING @ Mon, 03 Jun 2019 19:35:18: #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 19:35:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:35:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:35:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:36:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801799/SRX4801799.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:36:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801799/SRX4801799.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:36:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801799/SRX4801799.10_summits.bed INFO @ Mon, 03 Jun 2019 19:36:08: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2029 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:36:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:36:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:36:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801799/SRX4801799.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:36:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801799/SRX4801799.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:36:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801799/SRX4801799.05_summits.bed INFO @ Mon, 03 Jun 2019 19:36:50: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3869 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:36:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801799/SRX4801799.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:36:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801799/SRX4801799.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:36:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801799/SRX4801799.20_summits.bed INFO @ Mon, 03 Jun 2019 19:36:57: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (901 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。