Job ID = 1294247 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T20:49:04 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 ) 2019-06-02T20:49:04 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 : 25,625,486 reads read : 51,250,972 reads written : 25,625,486 reads 0-length : 25,625,486 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: 00:14:03 25625486 reads; of these: 25625486 (100.00%) were unpaired; of these: 982988 (3.84%) aligned 0 times 19025099 (74.24%) aligned exactly 1 time 5617399 (21.92%) aligned >1 times 96.16% overall alignment rate Time searching: 00:14:03 Overall time: 00:14:03 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 12 files... [bam_rmdupse_core] 5321952 / 24642498 = 0.2160 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 06:18:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2035278/SRX2035278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2035278/SRX2035278.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2035278/SRX2035278.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2035278/SRX2035278.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 06:18:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:18:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:18:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2035278/SRX2035278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2035278/SRX2035278.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2035278/SRX2035278.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2035278/SRX2035278.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 06:18:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:18:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:18:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2035278/SRX2035278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2035278/SRX2035278.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2035278/SRX2035278.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2035278/SRX2035278.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 06:18:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:18:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:18:23: 1000000 INFO @ Mon, 03 Jun 2019 06:18:23: 1000000 INFO @ Mon, 03 Jun 2019 06:18:26: 1000000 INFO @ Mon, 03 Jun 2019 06:18:32: 2000000 INFO @ Mon, 03 Jun 2019 06:18:33: 2000000 INFO @ Mon, 03 Jun 2019 06:18:38: 2000000 INFO @ Mon, 03 Jun 2019 06:18:41: 3000000 INFO @ Mon, 03 Jun 2019 06:18:43: 3000000 INFO @ Mon, 03 Jun 2019 06:18:50: 4000000 INFO @ Mon, 03 Jun 2019 06:18:50: 3000000 INFO @ Mon, 03 Jun 2019 06:18:52: 4000000 INFO @ Mon, 03 Jun 2019 06:18:59: 5000000 INFO @ Mon, 03 Jun 2019 06:19:01: 5000000 INFO @ Mon, 03 Jun 2019 06:19:02: 4000000 INFO @ Mon, 03 Jun 2019 06:19:07: 6000000 INFO @ Mon, 03 Jun 2019 06:19:11: 6000000 INFO @ Mon, 03 Jun 2019 06:19:14: 5000000 INFO @ Mon, 03 Jun 2019 06:19:16: 7000000 INFO @ Mon, 03 Jun 2019 06:19:20: 7000000 INFO @ Mon, 03 Jun 2019 06:19:25: 8000000 INFO @ Mon, 03 Jun 2019 06:19:26: 6000000 INFO @ Mon, 03 Jun 2019 06:19:29: 8000000 INFO @ Mon, 03 Jun 2019 06:19:33: 9000000 INFO @ Mon, 03 Jun 2019 06:19:37: 7000000 INFO @ Mon, 03 Jun 2019 06:19:38: 9000000 INFO @ Mon, 03 Jun 2019 06:19:42: 10000000 INFO @ Mon, 03 Jun 2019 06:19:47: 10000000 INFO @ Mon, 03 Jun 2019 06:19:48: 8000000 INFO @ Mon, 03 Jun 2019 06:19:50: 11000000 INFO @ Mon, 03 Jun 2019 06:19:56: 11000000 INFO @ Mon, 03 Jun 2019 06:19:59: 12000000 INFO @ Mon, 03 Jun 2019 06:19:59: 9000000 INFO @ Mon, 03 Jun 2019 06:20:06: 12000000 INFO @ Mon, 03 Jun 2019 06:20:08: 13000000 INFO @ Mon, 03 Jun 2019 06:20:11: 10000000 INFO @ Mon, 03 Jun 2019 06:20:15: 13000000 INFO @ Mon, 03 Jun 2019 06:20:16: 14000000 INFO @ Mon, 03 Jun 2019 06:20:22: 11000000 INFO @ Mon, 03 Jun 2019 06:20:24: 14000000 INFO @ Mon, 03 Jun 2019 06:20:25: 15000000 INFO @ Mon, 03 Jun 2019 06:20:33: 12000000 INFO @ Mon, 03 Jun 2019 06:20:33: 15000000 INFO @ Mon, 03 Jun 2019 06:20:34: 16000000 INFO @ Mon, 03 Jun 2019 06:20:43: 16000000 INFO @ Mon, 03 Jun 2019 06:20:43: 17000000 INFO @ Mon, 03 Jun 2019 06:20:44: 13000000 INFO @ Mon, 03 Jun 2019 06:20:51: 18000000 INFO @ Mon, 03 Jun 2019 06:20:52: 17000000 INFO @ Mon, 03 Jun 2019 06:20:56: 14000000 INFO @ Mon, 03 Jun 2019 06:21:00: 19000000 INFO @ Mon, 03 Jun 2019 06:21:01: 18000000 INFO @ Mon, 03 Jun 2019 06:21:02: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 06:21:02: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 06:21:02: #1 total tags in treatment: 19320546 INFO @ Mon, 03 Jun 2019 06:21:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:21:02: #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 06:21:03: #1 tags after filtering in treatment: 19320546 INFO @ Mon, 03 Jun 2019 06:21:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:21:03: #1 finished! INFO @ Mon, 03 Jun 2019 06:21:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:21:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:21:05: #2 number of paired peaks: 1375 INFO @ Mon, 03 Jun 2019 06:21:05: start model_add_line... INFO @ Mon, 03 Jun 2019 06:21:05: start X-correlation... INFO @ Mon, 03 Jun 2019 06:21:05: end of X-cor INFO @ Mon, 03 Jun 2019 06:21:05: #2 finished! INFO @ Mon, 03 Jun 2019 06:21:05: #2 predicted fragment length is 133 bps INFO @ Mon, 03 Jun 2019 06:21:05: #2 alternative fragment length(s) may be 133 bps INFO @ Mon, 03 Jun 2019 06:21:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2035278/SRX2035278.20_model.r WARNING @ Mon, 03 Jun 2019 06:21:05: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:21:05: #2 You may need to consider one of the other alternative d(s): 133 WARNING @ Mon, 03 Jun 2019 06:21:05: #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 06:21:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:21:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:21:07: 15000000 INFO @ Mon, 03 Jun 2019 06:21:10: 19000000 INFO @ Mon, 03 Jun 2019 06:21:13: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 06:21:13: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 06:21:13: #1 total tags in treatment: 19320546 INFO @ Mon, 03 Jun 2019 06:21:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:21:13: #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 06:21:13: #1 tags after filtering in treatment: 19320546 INFO @ Mon, 03 Jun 2019 06:21:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:21:13: #1 finished! INFO @ Mon, 03 Jun 2019 06:21:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:21:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:21:15: #2 number of paired peaks: 1375 INFO @ Mon, 03 Jun 2019 06:21:15: start model_add_line... INFO @ Mon, 03 Jun 2019 06:21:15: start X-correlation... INFO @ Mon, 03 Jun 2019 06:21:15: end of X-cor INFO @ Mon, 03 Jun 2019 06:21:15: #2 finished! INFO @ Mon, 03 Jun 2019 06:21:15: #2 predicted fragment length is 133 bps INFO @ Mon, 03 Jun 2019 06:21:15: #2 alternative fragment length(s) may be 133 bps INFO @ Mon, 03 Jun 2019 06:21:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2035278/SRX2035278.10_model.r WARNING @ Mon, 03 Jun 2019 06:21:15: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:21:15: #2 You may need to consider one of the other alternative d(s): 133 WARNING @ Mon, 03 Jun 2019 06:21:15: #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 06:21:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:21:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:21:18: 16000000 INFO @ Mon, 03 Jun 2019 06:21:29: 17000000 INFO @ Mon, 03 Jun 2019 06:21:39: 18000000 INFO @ Mon, 03 Jun 2019 06:21:50: 19000000 INFO @ Mon, 03 Jun 2019 06:21:54: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 06:21:54: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 06:21:54: #1 total tags in treatment: 19320546 INFO @ Mon, 03 Jun 2019 06:21:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:21:54: #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 06:21:54: #1 tags after filtering in treatment: 19320546 INFO @ Mon, 03 Jun 2019 06:21:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:21:54: #1 finished! INFO @ Mon, 03 Jun 2019 06:21:54: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:21:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:21:56: #2 number of paired peaks: 1375 INFO @ Mon, 03 Jun 2019 06:21:56: start model_add_line... INFO @ Mon, 03 Jun 2019 06:21:56: start X-correlation... INFO @ Mon, 03 Jun 2019 06:21:56: end of X-cor INFO @ Mon, 03 Jun 2019 06:21:56: #2 finished! INFO @ Mon, 03 Jun 2019 06:21:56: #2 predicted fragment length is 133 bps INFO @ Mon, 03 Jun 2019 06:21:56: #2 alternative fragment length(s) may be 133 bps INFO @ Mon, 03 Jun 2019 06:21:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2035278/SRX2035278.05_model.r WARNING @ Mon, 03 Jun 2019 06:21:56: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:21:56: #2 You may need to consider one of the other alternative d(s): 133 WARNING @ Mon, 03 Jun 2019 06:21:56: #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 06:21:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:21:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:22:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:22:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:22:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2035278/SRX2035278.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:22:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2035278/SRX2035278.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:22:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2035278/SRX2035278.20_summits.bed INFO @ Mon, 03 Jun 2019 06:22:27: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (7245 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:22:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2035278/SRX2035278.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:22:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2035278/SRX2035278.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:22:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2035278/SRX2035278.10_summits.bed INFO @ Mon, 03 Jun 2019 06:22:36: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10737 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:22:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:23:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2035278/SRX2035278.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:23:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2035278/SRX2035278.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:23:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2035278/SRX2035278.05_summits.bed INFO @ Mon, 03 Jun 2019 06:23:17: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (14659 records, 4 fields): 40 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。