Job ID = 1294060 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T19:32:58 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 : 66,964,552 reads read : 66,964,552 reads written : 66,964,552 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: 00:24:08 66964552 reads; of these: 66964552 (100.00%) were unpaired; of these: 20618300 (30.79%) aligned 0 times 24693045 (36.87%) aligned exactly 1 time 21653207 (32.34%) aligned >1 times 69.21% overall alignment rate Time searching: 00:24:08 Overall time: 00:24:08 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 20 files... [bam_rmdupse_core] 10767718 / 46346252 = 0.2323 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 05:42:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX177657/SRX177657.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX177657/SRX177657.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX177657/SRX177657.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX177657/SRX177657.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 05:42:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:42:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:42:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX177657/SRX177657.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX177657/SRX177657.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX177657/SRX177657.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX177657/SRX177657.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 05:42:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX177657/SRX177657.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX177657/SRX177657.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX177657/SRX177657.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX177657/SRX177657.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 05:42:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:42:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:42:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:42:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:42:15: 1000000 INFO @ Mon, 03 Jun 2019 05:42:16: 1000000 INFO @ Mon, 03 Jun 2019 05:42:16: 1000000 INFO @ Mon, 03 Jun 2019 05:42:23: 2000000 INFO @ Mon, 03 Jun 2019 05:42:24: 2000000 INFO @ Mon, 03 Jun 2019 05:42:24: 2000000 INFO @ Mon, 03 Jun 2019 05:42:31: 3000000 INFO @ Mon, 03 Jun 2019 05:42:31: 3000000 INFO @ Mon, 03 Jun 2019 05:42:32: 3000000 INFO @ Mon, 03 Jun 2019 05:42:38: 4000000 INFO @ Mon, 03 Jun 2019 05:42:39: 4000000 INFO @ Mon, 03 Jun 2019 05:42:39: 4000000 INFO @ Mon, 03 Jun 2019 05:42:45: 5000000 INFO @ Mon, 03 Jun 2019 05:42:47: 5000000 INFO @ Mon, 03 Jun 2019 05:42:47: 5000000 INFO @ Mon, 03 Jun 2019 05:42:54: 6000000 INFO @ Mon, 03 Jun 2019 05:42:55: 6000000 INFO @ Mon, 03 Jun 2019 05:42:56: 6000000 INFO @ Mon, 03 Jun 2019 05:43:02: 7000000 INFO @ Mon, 03 Jun 2019 05:43:03: 7000000 INFO @ Mon, 03 Jun 2019 05:43:04: 7000000 INFO @ Mon, 03 Jun 2019 05:43:10: 8000000 INFO @ Mon, 03 Jun 2019 05:43:11: 8000000 INFO @ Mon, 03 Jun 2019 05:43:12: 8000000 INFO @ Mon, 03 Jun 2019 05:43:17: 9000000 INFO @ Mon, 03 Jun 2019 05:43:20: 9000000 INFO @ Mon, 03 Jun 2019 05:43:20: 9000000 INFO @ Mon, 03 Jun 2019 05:43:25: 10000000 INFO @ Mon, 03 Jun 2019 05:43:28: 10000000 INFO @ Mon, 03 Jun 2019 05:43:28: 10000000 INFO @ Mon, 03 Jun 2019 05:43:33: 11000000 INFO @ Mon, 03 Jun 2019 05:43:36: 11000000 INFO @ Mon, 03 Jun 2019 05:43:36: 11000000 INFO @ Mon, 03 Jun 2019 05:43:40: 12000000 INFO @ Mon, 03 Jun 2019 05:43:44: 12000000 INFO @ Mon, 03 Jun 2019 05:43:44: 12000000 INFO @ Mon, 03 Jun 2019 05:43:48: 13000000 INFO @ Mon, 03 Jun 2019 05:43:51: 13000000 INFO @ Mon, 03 Jun 2019 05:43:52: 13000000 INFO @ Mon, 03 Jun 2019 05:43:55: 14000000 INFO @ Mon, 03 Jun 2019 05:44:00: 14000000 INFO @ Mon, 03 Jun 2019 05:44:00: 14000000 INFO @ Mon, 03 Jun 2019 05:44:04: 15000000 INFO @ Mon, 03 Jun 2019 05:44:08: 15000000 INFO @ Mon, 03 Jun 2019 05:44:08: 15000000 INFO @ Mon, 03 Jun 2019 05:44:12: 16000000 INFO @ Mon, 03 Jun 2019 05:44:15: 16000000 INFO @ Mon, 03 Jun 2019 05:44:16: 16000000 INFO @ Mon, 03 Jun 2019 05:44:19: 17000000 INFO @ Mon, 03 Jun 2019 05:44:23: 17000000 INFO @ Mon, 03 Jun 2019 05:44:23: 17000000 INFO @ Mon, 03 Jun 2019 05:44:26: 18000000 INFO @ Mon, 03 Jun 2019 05:44:30: 18000000 INFO @ Mon, 03 Jun 2019 05:44:31: 18000000 INFO @ Mon, 03 Jun 2019 05:44:34: 19000000 INFO @ Mon, 03 Jun 2019 05:44:38: 19000000 INFO @ Mon, 03 Jun 2019 05:44:39: 19000000 INFO @ Mon, 03 Jun 2019 05:44:41: 20000000 INFO @ Mon, 03 Jun 2019 05:44:46: 20000000 INFO @ Mon, 03 Jun 2019 05:44:46: 20000000 INFO @ Mon, 03 Jun 2019 05:44:48: 21000000 INFO @ Mon, 03 Jun 2019 05:44:53: 21000000 INFO @ Mon, 03 Jun 2019 05:44:54: 21000000 INFO @ Mon, 03 Jun 2019 05:44:55: 22000000 INFO @ Mon, 03 Jun 2019 05:45:01: 22000000 INFO @ Mon, 03 Jun 2019 05:45:02: 22000000 INFO @ Mon, 03 Jun 2019 05:45:03: 23000000 INFO @ Mon, 03 Jun 2019 05:45:09: 23000000 INFO @ Mon, 03 Jun 2019 05:45:10: 23000000 INFO @ Mon, 03 Jun 2019 05:45:12: 24000000 INFO @ Mon, 03 Jun 2019 05:45:17: 24000000 INFO @ Mon, 03 Jun 2019 05:45:18: 24000000 INFO @ Mon, 03 Jun 2019 05:45:19: 25000000 INFO @ Mon, 03 Jun 2019 05:45:25: 25000000 INFO @ Mon, 03 Jun 2019 05:45:25: 25000000 INFO @ Mon, 03 Jun 2019 05:45:26: 26000000 INFO @ Mon, 03 Jun 2019 05:45:32: 26000000 INFO @ Mon, 03 Jun 2019 05:45:33: 26000000 INFO @ Mon, 03 Jun 2019 05:45:34: 27000000 INFO @ Mon, 03 Jun 2019 05:45:40: 27000000 INFO @ Mon, 03 Jun 2019 05:45:40: 27000000 INFO @ Mon, 03 Jun 2019 05:45:41: 28000000 INFO @ Mon, 03 Jun 2019 05:45:47: 28000000 INFO @ Mon, 03 Jun 2019 05:45:48: 28000000 INFO @ Mon, 03 Jun 2019 05:45:49: 29000000 INFO @ Mon, 03 Jun 2019 05:45:55: 29000000 INFO @ Mon, 03 Jun 2019 05:45:56: 29000000 INFO @ Mon, 03 Jun 2019 05:45:56: 30000000 INFO @ Mon, 03 Jun 2019 05:46:02: 30000000 INFO @ Mon, 03 Jun 2019 05:46:03: 31000000 INFO @ Mon, 03 Jun 2019 05:46:03: 30000000 INFO @ Mon, 03 Jun 2019 05:46:10: 32000000 INFO @ Mon, 03 Jun 2019 05:46:10: 31000000 INFO @ Mon, 03 Jun 2019 05:46:11: 31000000 INFO @ Mon, 03 Jun 2019 05:46:19: 33000000 INFO @ Mon, 03 Jun 2019 05:46:19: 32000000 INFO @ Mon, 03 Jun 2019 05:46:20: 32000000 INFO @ Mon, 03 Jun 2019 05:46:27: 34000000 INFO @ Mon, 03 Jun 2019 05:46:27: 33000000 INFO @ Mon, 03 Jun 2019 05:46:28: 33000000 INFO @ Mon, 03 Jun 2019 05:46:34: 35000000 INFO @ Mon, 03 Jun 2019 05:46:35: 34000000 INFO @ Mon, 03 Jun 2019 05:46:35: 34000000 INFO @ Mon, 03 Jun 2019 05:46:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:46:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:46:39: #1 total tags in treatment: 35578534 INFO @ Mon, 03 Jun 2019 05:46:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:46:39: #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 05:46:40: #1 tags after filtering in treatment: 35578534 INFO @ Mon, 03 Jun 2019 05:46:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:46:40: #1 finished! INFO @ Mon, 03 Jun 2019 05:46:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:46:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:46:43: 35000000 INFO @ Mon, 03 Jun 2019 05:46:43: #2 number of paired peaks: 315 WARNING @ Mon, 03 Jun 2019 05:46:43: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Mon, 03 Jun 2019 05:46:43: start model_add_line... INFO @ Mon, 03 Jun 2019 05:46:43: start X-correlation... INFO @ Mon, 03 Jun 2019 05:46:43: end of X-cor INFO @ Mon, 03 Jun 2019 05:46:43: #2 finished! INFO @ Mon, 03 Jun 2019 05:46:43: #2 predicted fragment length is 3 bps INFO @ Mon, 03 Jun 2019 05:46:43: #2 alternative fragment length(s) may be 3,24,597 bps INFO @ Mon, 03 Jun 2019 05:46:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX177657/SRX177657.20_model.r WARNING @ Mon, 03 Jun 2019 05:46:43: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:46:43: #2 You may need to consider one of the other alternative d(s): 3,24,597 WARNING @ Mon, 03 Jun 2019 05:46:43: #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 05:46:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:46:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:46:43: 35000000 INFO @ Mon, 03 Jun 2019 05:46:47: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:46:47: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:46:47: #1 total tags in treatment: 35578534 INFO @ Mon, 03 Jun 2019 05:46:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:46:47: #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 05:46:48: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:46:48: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:46:48: #1 total tags in treatment: 35578534 INFO @ Mon, 03 Jun 2019 05:46:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:46:48: #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 05:46:48: #1 tags after filtering in treatment: 35578534 INFO @ Mon, 03 Jun 2019 05:46:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:46:48: #1 finished! INFO @ Mon, 03 Jun 2019 05:46:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:46:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:46:49: #1 tags after filtering in treatment: 35578534 INFO @ Mon, 03 Jun 2019 05:46:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:46:49: #1 finished! INFO @ Mon, 03 Jun 2019 05:46:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:46:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:46:51: #2 number of paired peaks: 315 WARNING @ Mon, 03 Jun 2019 05:46:51: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Mon, 03 Jun 2019 05:46:51: start model_add_line... INFO @ Mon, 03 Jun 2019 05:46:51: start X-correlation... INFO @ Mon, 03 Jun 2019 05:46:51: end of X-cor INFO @ Mon, 03 Jun 2019 05:46:51: #2 finished! INFO @ Mon, 03 Jun 2019 05:46:51: #2 predicted fragment length is 3 bps INFO @ Mon, 03 Jun 2019 05:46:51: #2 alternative fragment length(s) may be 3,24,597 bps INFO @ Mon, 03 Jun 2019 05:46:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX177657/SRX177657.05_model.r WARNING @ Mon, 03 Jun 2019 05:46:51: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:46:51: #2 You may need to consider one of the other alternative d(s): 3,24,597 WARNING @ Mon, 03 Jun 2019 05:46:51: #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 05:46:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:46:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:46:52: #2 number of paired peaks: 315 WARNING @ Mon, 03 Jun 2019 05:46:52: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Mon, 03 Jun 2019 05:46:52: start model_add_line... INFO @ Mon, 03 Jun 2019 05:46:52: start X-correlation... INFO @ Mon, 03 Jun 2019 05:46:52: end of X-cor INFO @ Mon, 03 Jun 2019 05:46:52: #2 finished! INFO @ Mon, 03 Jun 2019 05:46:52: #2 predicted fragment length is 3 bps INFO @ Mon, 03 Jun 2019 05:46:52: #2 alternative fragment length(s) may be 3,24,597 bps INFO @ Mon, 03 Jun 2019 05:46:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX177657/SRX177657.10_model.r WARNING @ Mon, 03 Jun 2019 05:46:52: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:46:52: #2 You may need to consider one of the other alternative d(s): 3,24,597 WARNING @ Mon, 03 Jun 2019 05:46:52: #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 05:46:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:46:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:47:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:47:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:47:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:48:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX177657/SRX177657.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:48:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX177657/SRX177657.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:48:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX177657/SRX177657.20_summits.bed INFO @ Mon, 03 Jun 2019 05:48:23: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:48:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX177657/SRX177657.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:48:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX177657/SRX177657.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:48:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX177657/SRX177657.05_summits.bed INFO @ Mon, 03 Jun 2019 05:48:30: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:48:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX177657/SRX177657.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:48:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX177657/SRX177657.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:48:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX177657/SRX177657.10_summits.bed INFO @ Mon, 03 Jun 2019 05:48:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。