Job ID = 1294160 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T20:10:13 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 : 48,356,671 reads read : 48,356,671 reads written : 48,356,671 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: 00:14:17 48356671 reads; of these: 48356671 (100.00%) were unpaired; of these: 1692317 (3.50%) aligned 0 times 39304691 (81.28%) aligned exactly 1 time 7359663 (15.22%) aligned >1 times 96.50% overall alignment rate Time searching: 00:14:17 Overall time: 00:14:17 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] 13707283 / 46664354 = 0.2937 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 05:40:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193336/SRX193336.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193336/SRX193336.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193336/SRX193336.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193336/SRX193336.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 05:40:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:40:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:40:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193336/SRX193336.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193336/SRX193336.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193336/SRX193336.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193336/SRX193336.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 05:40:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:40:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:40:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193336/SRX193336.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193336/SRX193336.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193336/SRX193336.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193336/SRX193336.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 05:40:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:40:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:40:51: 1000000 INFO @ Mon, 03 Jun 2019 05:40:51: 1000000 INFO @ Mon, 03 Jun 2019 05:40:53: 1000000 INFO @ Mon, 03 Jun 2019 05:40:59: 2000000 INFO @ Mon, 03 Jun 2019 05:40:59: 2000000 INFO @ Mon, 03 Jun 2019 05:41:04: 2000000 INFO @ Mon, 03 Jun 2019 05:41:07: 3000000 INFO @ Mon, 03 Jun 2019 05:41:07: 3000000 INFO @ Mon, 03 Jun 2019 05:41:14: 3000000 INFO @ Mon, 03 Jun 2019 05:41:15: 4000000 INFO @ Mon, 03 Jun 2019 05:41:15: 4000000 INFO @ Mon, 03 Jun 2019 05:41:23: 5000000 INFO @ Mon, 03 Jun 2019 05:41:23: 5000000 INFO @ Mon, 03 Jun 2019 05:41:25: 4000000 INFO @ Mon, 03 Jun 2019 05:41:31: 6000000 INFO @ Mon, 03 Jun 2019 05:41:31: 6000000 INFO @ Mon, 03 Jun 2019 05:41:35: 5000000 INFO @ Mon, 03 Jun 2019 05:41:39: 7000000 INFO @ Mon, 03 Jun 2019 05:41:39: 7000000 INFO @ Mon, 03 Jun 2019 05:41:46: 6000000 INFO @ Mon, 03 Jun 2019 05:41:47: 8000000 INFO @ Mon, 03 Jun 2019 05:41:47: 8000000 INFO @ Mon, 03 Jun 2019 05:41:55: 9000000 INFO @ Mon, 03 Jun 2019 05:41:55: 9000000 INFO @ Mon, 03 Jun 2019 05:41:56: 7000000 INFO @ Mon, 03 Jun 2019 05:42:03: 10000000 INFO @ Mon, 03 Jun 2019 05:42:03: 10000000 INFO @ Mon, 03 Jun 2019 05:42:07: 8000000 INFO @ Mon, 03 Jun 2019 05:42:11: 11000000 INFO @ Mon, 03 Jun 2019 05:42:11: 11000000 INFO @ Mon, 03 Jun 2019 05:42:17: 9000000 INFO @ Mon, 03 Jun 2019 05:42:18: 12000000 INFO @ Mon, 03 Jun 2019 05:42:19: 12000000 INFO @ Mon, 03 Jun 2019 05:42:26: 13000000 INFO @ Mon, 03 Jun 2019 05:42:27: 13000000 INFO @ Mon, 03 Jun 2019 05:42:28: 10000000 INFO @ Mon, 03 Jun 2019 05:42:34: 14000000 INFO @ Mon, 03 Jun 2019 05:42:35: 14000000 INFO @ Mon, 03 Jun 2019 05:42:38: 11000000 INFO @ Mon, 03 Jun 2019 05:42:42: 15000000 INFO @ Mon, 03 Jun 2019 05:42:43: 15000000 INFO @ Mon, 03 Jun 2019 05:42:49: 12000000 INFO @ Mon, 03 Jun 2019 05:42:50: 16000000 INFO @ Mon, 03 Jun 2019 05:42:51: 16000000 INFO @ Mon, 03 Jun 2019 05:42:58: 17000000 INFO @ Mon, 03 Jun 2019 05:42:59: 13000000 INFO @ Mon, 03 Jun 2019 05:42:59: 17000000 INFO @ Mon, 03 Jun 2019 05:43:07: 18000000 INFO @ Mon, 03 Jun 2019 05:43:08: 18000000 INFO @ Mon, 03 Jun 2019 05:43:10: 14000000 INFO @ Mon, 03 Jun 2019 05:43:15: 19000000 INFO @ Mon, 03 Jun 2019 05:43:16: 19000000 INFO @ Mon, 03 Jun 2019 05:43:20: 15000000 INFO @ Mon, 03 Jun 2019 05:43:23: 20000000 INFO @ Mon, 03 Jun 2019 05:43:24: 20000000 INFO @ Mon, 03 Jun 2019 05:43:30: 16000000 INFO @ Mon, 03 Jun 2019 05:43:31: 21000000 INFO @ Mon, 03 Jun 2019 05:43:32: 21000000 INFO @ Mon, 03 Jun 2019 05:43:39: 22000000 INFO @ Mon, 03 Jun 2019 05:43:40: 22000000 INFO @ Mon, 03 Jun 2019 05:43:41: 17000000 INFO @ Mon, 03 Jun 2019 05:43:47: 23000000 INFO @ Mon, 03 Jun 2019 05:43:48: 23000000 INFO @ Mon, 03 Jun 2019 05:43:51: 18000000 INFO @ Mon, 03 Jun 2019 05:43:55: 24000000 INFO @ Mon, 03 Jun 2019 05:43:56: 24000000 INFO @ Mon, 03 Jun 2019 05:44:02: 19000000 INFO @ Mon, 03 Jun 2019 05:44:03: 25000000 INFO @ Mon, 03 Jun 2019 05:44:04: 25000000 INFO @ Mon, 03 Jun 2019 05:44:10: 26000000 INFO @ Mon, 03 Jun 2019 05:44:12: 26000000 INFO @ Mon, 03 Jun 2019 05:44:12: 20000000 INFO @ Mon, 03 Jun 2019 05:44:18: 27000000 INFO @ Mon, 03 Jun 2019 05:44:20: 27000000 INFO @ Mon, 03 Jun 2019 05:44:23: 21000000 INFO @ Mon, 03 Jun 2019 05:44:26: 28000000 INFO @ Mon, 03 Jun 2019 05:44:28: 28000000 INFO @ Mon, 03 Jun 2019 05:44:33: 22000000 INFO @ Mon, 03 Jun 2019 05:44:34: 29000000 INFO @ Mon, 03 Jun 2019 05:44:35: 29000000 INFO @ Mon, 03 Jun 2019 05:44:42: 30000000 INFO @ Mon, 03 Jun 2019 05:44:43: 30000000 INFO @ Mon, 03 Jun 2019 05:44:44: 23000000 INFO @ Mon, 03 Jun 2019 05:44:50: 31000000 INFO @ Mon, 03 Jun 2019 05:44:51: 31000000 INFO @ Mon, 03 Jun 2019 05:44:54: 24000000 INFO @ Mon, 03 Jun 2019 05:44:58: 32000000 INFO @ Mon, 03 Jun 2019 05:44:59: 32000000 INFO @ Mon, 03 Jun 2019 05:45:05: 25000000 INFO @ Mon, 03 Jun 2019 05:45:05: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:45:05: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:45:05: #1 total tags in treatment: 32957071 INFO @ Mon, 03 Jun 2019 05:45:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:45:05: #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 05:45:06: #1 tags after filtering in treatment: 32957071 INFO @ Mon, 03 Jun 2019 05:45:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:45:06: #1 finished! INFO @ Mon, 03 Jun 2019 05:45:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:45:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:45:07: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:45:07: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:45:07: #1 total tags in treatment: 32957071 INFO @ Mon, 03 Jun 2019 05:45:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:45:07: #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 05:45:08: #1 tags after filtering in treatment: 32957071 INFO @ Mon, 03 Jun 2019 05:45:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:45:08: #1 finished! INFO @ Mon, 03 Jun 2019 05:45:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:45:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:45:09: #2 number of paired peaks: 1974 INFO @ Mon, 03 Jun 2019 05:45:09: start model_add_line... INFO @ Mon, 03 Jun 2019 05:45:10: start X-correlation... INFO @ Mon, 03 Jun 2019 05:45:10: end of X-cor INFO @ Mon, 03 Jun 2019 05:45:10: #2 finished! INFO @ Mon, 03 Jun 2019 05:45:10: #2 predicted fragment length is 98 bps INFO @ Mon, 03 Jun 2019 05:45:10: #2 alternative fragment length(s) may be 3,98 bps INFO @ Mon, 03 Jun 2019 05:45:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193336/SRX193336.10_model.r WARNING @ Mon, 03 Jun 2019 05:45:10: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:45:10: #2 You may need to consider one of the other alternative d(s): 3,98 WARNING @ Mon, 03 Jun 2019 05:45:10: #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 05:45:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:45:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:45:11: #2 number of paired peaks: 1974 INFO @ Mon, 03 Jun 2019 05:45:11: start model_add_line... INFO @ Mon, 03 Jun 2019 05:45:11: start X-correlation... INFO @ Mon, 03 Jun 2019 05:45:11: end of X-cor INFO @ Mon, 03 Jun 2019 05:45:11: #2 finished! INFO @ Mon, 03 Jun 2019 05:45:11: #2 predicted fragment length is 98 bps INFO @ Mon, 03 Jun 2019 05:45:11: #2 alternative fragment length(s) may be 3,98 bps INFO @ Mon, 03 Jun 2019 05:45:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193336/SRX193336.20_model.r WARNING @ Mon, 03 Jun 2019 05:45:11: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:45:11: #2 You may need to consider one of the other alternative d(s): 3,98 WARNING @ Mon, 03 Jun 2019 05:45:11: #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 05:45:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:45:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:45:15: 26000000 INFO @ Mon, 03 Jun 2019 05:45:25: 27000000 INFO @ Mon, 03 Jun 2019 05:45:35: 28000000 INFO @ Mon, 03 Jun 2019 05:45:44: 29000000 INFO @ Mon, 03 Jun 2019 05:45:55: 30000000 INFO @ Mon, 03 Jun 2019 05:46:05: 31000000 INFO @ Mon, 03 Jun 2019 05:46:15: 32000000 INFO @ Mon, 03 Jun 2019 05:46:25: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:46:25: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:46:25: #1 total tags in treatment: 32957071 INFO @ Mon, 03 Jun 2019 05:46:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:46:25: #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 05:46:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:46:26: #1 tags after filtering in treatment: 32957071 INFO @ Mon, 03 Jun 2019 05:46:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:46:26: #1 finished! INFO @ Mon, 03 Jun 2019 05:46:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:46:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:46:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:46:29: #2 number of paired peaks: 1974 INFO @ Mon, 03 Jun 2019 05:46:29: start model_add_line... INFO @ Mon, 03 Jun 2019 05:46:29: start X-correlation... INFO @ Mon, 03 Jun 2019 05:46:29: end of X-cor INFO @ Mon, 03 Jun 2019 05:46:29: #2 finished! INFO @ Mon, 03 Jun 2019 05:46:29: #2 predicted fragment length is 98 bps INFO @ Mon, 03 Jun 2019 05:46:29: #2 alternative fragment length(s) may be 3,98 bps INFO @ Mon, 03 Jun 2019 05:46:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193336/SRX193336.05_model.r WARNING @ Mon, 03 Jun 2019 05:46:29: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:46:29: #2 You may need to consider one of the other alternative d(s): 3,98 WARNING @ Mon, 03 Jun 2019 05:46:29: #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 05:46:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:46:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:46:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193336/SRX193336.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:46:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193336/SRX193336.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:46:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193336/SRX193336.10_summits.bed INFO @ Mon, 03 Jun 2019 05:46:59: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (11908 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:47:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193336/SRX193336.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:47:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193336/SRX193336.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:47:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193336/SRX193336.20_summits.bed INFO @ Mon, 03 Jun 2019 05:47:00: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4288 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:47:45: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 05:48:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193336/SRX193336.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:48:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193336/SRX193336.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:48:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193336/SRX193336.05_summits.bed INFO @ Mon, 03 Jun 2019 05:48:19: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (19436 records, 4 fields): 24 millis CompletedMACS2peakCalling BigWig に変換しました。