Job ID = 2640521 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:26:38 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 : 23,459,071 reads read : 46,918,142 reads written : 23,459,071 reads 0-length : 23,459,071 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:19:13 23459071 reads; of these: 23459071 (100.00%) were unpaired; of these: 981522 (4.18%) aligned 0 times 16502677 (70.35%) aligned exactly 1 time 5974872 (25.47%) aligned >1 times 95.82% overall alignment rate Time searching: 00:19:16 Overall time: 00:19:16 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 2943258 / 22477549 = 0.1309 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:00:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375002/SRX5375002.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375002/SRX5375002.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375002/SRX5375002.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375002/SRX5375002.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 18:00:27: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:00:27: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:00:36: 1000000 INFO @ Sat, 24 Aug 2019 18:00:43: 2000000 INFO @ Sat, 24 Aug 2019 18:00:51: 3000000 INFO @ Sat, 24 Aug 2019 18:00:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375002/SRX5375002.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375002/SRX5375002.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375002/SRX5375002.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375002/SRX5375002.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 18:00:56: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:00:56: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:00:58: 4000000 INFO @ Sat, 24 Aug 2019 18:01:06: 5000000 INFO @ Sat, 24 Aug 2019 18:01:07: 1000000 INFO @ Sat, 24 Aug 2019 18:01:14: 6000000 INFO @ Sat, 24 Aug 2019 18:01:17: 2000000 INFO @ Sat, 24 Aug 2019 18:01:21: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:01:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375002/SRX5375002.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375002/SRX5375002.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375002/SRX5375002.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375002/SRX5375002.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 18:01:26: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:01:26: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:01:27: 3000000 INFO @ Sat, 24 Aug 2019 18:01:29: 8000000 INFO @ Sat, 24 Aug 2019 18:01:36: 9000000 INFO @ Sat, 24 Aug 2019 18:01:38: 1000000 INFO @ Sat, 24 Aug 2019 18:01:38: 4000000 INFO @ Sat, 24 Aug 2019 18:01:44: 10000000 INFO @ Sat, 24 Aug 2019 18:01:48: 2000000 INFO @ Sat, 24 Aug 2019 18:01:49: 5000000 INFO @ Sat, 24 Aug 2019 18:01:51: 11000000 INFO @ Sat, 24 Aug 2019 18:01:58: 12000000 INFO @ Sat, 24 Aug 2019 18:02:00: 3000000 INFO @ Sat, 24 Aug 2019 18:02:00: 6000000 INFO @ Sat, 24 Aug 2019 18:02:05: 13000000 INFO @ Sat, 24 Aug 2019 18:02:11: 4000000 INFO @ Sat, 24 Aug 2019 18:02:11: 7000000 INFO @ Sat, 24 Aug 2019 18:02:13: 14000000 INFO @ Sat, 24 Aug 2019 18:02:20: 15000000 INFO @ Sat, 24 Aug 2019 18:02:22: 5000000 INFO @ Sat, 24 Aug 2019 18:02:23: 8000000 INFO @ Sat, 24 Aug 2019 18:02:27: 16000000 INFO @ Sat, 24 Aug 2019 18:02:34: 6000000 INFO @ Sat, 24 Aug 2019 18:02:34: 17000000 INFO @ Sat, 24 Aug 2019 18:02:34: 9000000 INFO @ Sat, 24 Aug 2019 18:02:41: 18000000 INFO @ Sat, 24 Aug 2019 18:02:45: 7000000 INFO @ Sat, 24 Aug 2019 18:02:45: 10000000 INFO @ Sat, 24 Aug 2019 18:02:49: 19000000 INFO @ Sat, 24 Aug 2019 18:02:53: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:02:53: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:02:53: #1 total tags in treatment: 19534291 INFO @ Sat, 24 Aug 2019 18:02:53: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:02:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:02:53: #1 tags after filtering in treatment: 19534128 INFO @ Sat, 24 Aug 2019 18:02:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:02:53: #1 finished! INFO @ Sat, 24 Aug 2019 18:02:53: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:02:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:02:56: #2 number of paired peaks: 5252 INFO @ Sat, 24 Aug 2019 18:02:56: start model_add_line... INFO @ Sat, 24 Aug 2019 18:02:56: start X-correlation... INFO @ Sat, 24 Aug 2019 18:02:56: end of X-cor INFO @ Sat, 24 Aug 2019 18:02:56: #2 finished! INFO @ Sat, 24 Aug 2019 18:02:56: #2 predicted fragment length is 52 bps INFO @ Sat, 24 Aug 2019 18:02:56: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 24 Aug 2019 18:02:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375002/SRX5375002.05_model.r WARNING @ Sat, 24 Aug 2019 18:02:56: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 18:02:56: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 24 Aug 2019 18:02:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 18:02:56: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:02:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:02:56: 8000000 INFO @ Sat, 24 Aug 2019 18:02:57: 11000000 INFO @ Sat, 24 Aug 2019 18:03:08: 9000000 INFO @ Sat, 24 Aug 2019 18:03:08: 12000000 INFO @ Sat, 24 Aug 2019 18:03:19: 10000000 INFO @ Sat, 24 Aug 2019 18:03:19: 13000000 INFO @ Sat, 24 Aug 2019 18:03:30: 11000000 INFO @ Sat, 24 Aug 2019 18:03:31: 14000000 INFO @ Sat, 24 Aug 2019 18:03:41: 12000000 INFO @ Sat, 24 Aug 2019 18:03:42: 15000000 INFO @ Sat, 24 Aug 2019 18:03:50: 13000000 INFO @ Sat, 24 Aug 2019 18:03:52: 16000000 INFO @ Sat, 24 Aug 2019 18:03:57: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:04:00: 14000000 INFO @ Sat, 24 Aug 2019 18:04:02: 17000000 INFO @ Sat, 24 Aug 2019 18:04:09: 15000000 INFO @ Sat, 24 Aug 2019 18:04:12: 18000000 INFO @ Sat, 24 Aug 2019 18:04:18: 16000000 INFO @ Sat, 24 Aug 2019 18:04:22: 19000000 INFO @ Sat, 24 Aug 2019 18:04:26: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375002/SRX5375002.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:04:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375002/SRX5375002.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:04:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375002/SRX5375002.05_summits.bed INFO @ Sat, 24 Aug 2019 18:04:26: Done! pass1 - making usageList (56 chroms): 2 millis pass2 - checking and writing primary data (1402 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:04:27: 17000000 INFO @ Sat, 24 Aug 2019 18:04:27: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:04:27: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:04:27: #1 total tags in treatment: 19534291 INFO @ Sat, 24 Aug 2019 18:04:27: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:04:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:04:28: #1 tags after filtering in treatment: 19534128 INFO @ Sat, 24 Aug 2019 18:04:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:04:28: #1 finished! INFO @ Sat, 24 Aug 2019 18:04:28: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:04:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:04:30: #2 number of paired peaks: 5252 INFO @ Sat, 24 Aug 2019 18:04:30: start model_add_line... INFO @ Sat, 24 Aug 2019 18:04:30: start X-correlation... INFO @ Sat, 24 Aug 2019 18:04:30: end of X-cor INFO @ Sat, 24 Aug 2019 18:04:30: #2 finished! INFO @ Sat, 24 Aug 2019 18:04:30: #2 predicted fragment length is 52 bps INFO @ Sat, 24 Aug 2019 18:04:30: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 24 Aug 2019 18:04:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375002/SRX5375002.10_model.r WARNING @ Sat, 24 Aug 2019 18:04:30: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 18:04:30: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 24 Aug 2019 18:04:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 18:04:30: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:04:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:04:36: 18000000 INFO @ Sat, 24 Aug 2019 18:04:43: 19000000 INFO @ Sat, 24 Aug 2019 18:04:47: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:04:47: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:04:47: #1 total tags in treatment: 19534291 INFO @ Sat, 24 Aug 2019 18:04:47: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:04:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:04:48: #1 tags after filtering in treatment: 19534128 INFO @ Sat, 24 Aug 2019 18:04:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:04:48: #1 finished! INFO @ Sat, 24 Aug 2019 18:04:48: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:04:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:04:50: #2 number of paired peaks: 5252 INFO @ Sat, 24 Aug 2019 18:04:50: start model_add_line... INFO @ Sat, 24 Aug 2019 18:04:50: start X-correlation... INFO @ Sat, 24 Aug 2019 18:04:50: end of X-cor INFO @ Sat, 24 Aug 2019 18:04:50: #2 finished! INFO @ Sat, 24 Aug 2019 18:04:50: #2 predicted fragment length is 52 bps INFO @ Sat, 24 Aug 2019 18:04:50: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 24 Aug 2019 18:04:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375002/SRX5375002.20_model.r WARNING @ Sat, 24 Aug 2019 18:04:50: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 18:04:50: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 24 Aug 2019 18:04:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 18:04:50: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:04:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:05:31: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:05:51: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:06:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375002/SRX5375002.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:06:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375002/SRX5375002.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:06:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375002/SRX5375002.10_summits.bed INFO @ Sat, 24 Aug 2019 18:06:01: Done! pass1 - making usageList (42 chroms): 0 millis pass2 - checking and writing primary data (729 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:06:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375002/SRX5375002.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:06:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375002/SRX5375002.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:06:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375002/SRX5375002.20_summits.bed INFO @ Sat, 24 Aug 2019 18:06:21: Done! pass1 - making usageList (33 chroms): 2 millis pass2 - checking and writing primary data (354 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。