Job ID = 2003695 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T04:11:14 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 : 27,898,924 reads read : 27,898,924 reads written : 27,898,924 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1103818.sra.cache’: 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: 00:23:54 27898924 reads; of these: 27898924 (100.00%) were unpaired; of these: 1626252 (5.83%) aligned 0 times 18461697 (66.17%) aligned exactly 1 time 7810975 (28.00%) aligned >1 times 94.17% overall alignment rate Time searching: 00:23:54 Overall time: 00:23:54 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] 926474 / 26272672 = 0.0353 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 @ Fri, 05 Jul 2019 13:52:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX423109/SRX423109.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX423109/SRX423109.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX423109/SRX423109.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX423109/SRX423109.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 @ Fri, 05 Jul 2019 13:52:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:52:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:52:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX423109/SRX423109.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX423109/SRX423109.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX423109/SRX423109.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX423109/SRX423109.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 @ Fri, 05 Jul 2019 13:52:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:52:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:52:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX423109/SRX423109.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX423109/SRX423109.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX423109/SRX423109.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX423109/SRX423109.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 @ Fri, 05 Jul 2019 13:52:39: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:52:39: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:52:47: 1000000 INFO @ Fri, 05 Jul 2019 13:52:48: 1000000 INFO @ Fri, 05 Jul 2019 13:52:49: 1000000 INFO @ Fri, 05 Jul 2019 13:52:55: 2000000 INFO @ Fri, 05 Jul 2019 13:52:57: 2000000 INFO @ Fri, 05 Jul 2019 13:52:59: 2000000 INFO @ Fri, 05 Jul 2019 13:53:04: 3000000 INFO @ Fri, 05 Jul 2019 13:53:05: 3000000 INFO @ Fri, 05 Jul 2019 13:53:09: 3000000 INFO @ Fri, 05 Jul 2019 13:53:13: 4000000 INFO @ Fri, 05 Jul 2019 13:53:14: 4000000 INFO @ Fri, 05 Jul 2019 13:53:19: 4000000 INFO @ Fri, 05 Jul 2019 13:53:21: 5000000 INFO @ Fri, 05 Jul 2019 13:53:23: 5000000 INFO @ Fri, 05 Jul 2019 13:53:30: 5000000 INFO @ Fri, 05 Jul 2019 13:53:30: 6000000 INFO @ Fri, 05 Jul 2019 13:53:31: 6000000 INFO @ Fri, 05 Jul 2019 13:53:39: 7000000 INFO @ Fri, 05 Jul 2019 13:53:40: 7000000 INFO @ Fri, 05 Jul 2019 13:53:40: 6000000 INFO @ Fri, 05 Jul 2019 13:53:48: 8000000 INFO @ Fri, 05 Jul 2019 13:53:49: 8000000 INFO @ Fri, 05 Jul 2019 13:53:51: 7000000 INFO @ Fri, 05 Jul 2019 13:53:57: 9000000 INFO @ Fri, 05 Jul 2019 13:53:58: 9000000 INFO @ Fri, 05 Jul 2019 13:54:01: 8000000 INFO @ Fri, 05 Jul 2019 13:54:05: 10000000 INFO @ Fri, 05 Jul 2019 13:54:06: 10000000 INFO @ Fri, 05 Jul 2019 13:54:11: 9000000 INFO @ Fri, 05 Jul 2019 13:54:14: 11000000 INFO @ Fri, 05 Jul 2019 13:54:15: 11000000 INFO @ Fri, 05 Jul 2019 13:54:21: 10000000 INFO @ Fri, 05 Jul 2019 13:54:22: 12000000 INFO @ Fri, 05 Jul 2019 13:54:23: 12000000 INFO @ Fri, 05 Jul 2019 13:54:31: 11000000 INFO @ Fri, 05 Jul 2019 13:54:31: 13000000 INFO @ Fri, 05 Jul 2019 13:54:32: 13000000 INFO @ Fri, 05 Jul 2019 13:54:39: 14000000 INFO @ Fri, 05 Jul 2019 13:54:40: 14000000 INFO @ Fri, 05 Jul 2019 13:54:41: 12000000 INFO @ Fri, 05 Jul 2019 13:54:48: 15000000 INFO @ Fri, 05 Jul 2019 13:54:49: 15000000 INFO @ Fri, 05 Jul 2019 13:54:52: 13000000 INFO @ Fri, 05 Jul 2019 13:54:56: 16000000 INFO @ Fri, 05 Jul 2019 13:54:57: 16000000 INFO @ Fri, 05 Jul 2019 13:55:02: 14000000 INFO @ Fri, 05 Jul 2019 13:55:05: 17000000 INFO @ Fri, 05 Jul 2019 13:55:06: 17000000 INFO @ Fri, 05 Jul 2019 13:55:13: 15000000 INFO @ Fri, 05 Jul 2019 13:55:13: 18000000 INFO @ Fri, 05 Jul 2019 13:55:14: 18000000 INFO @ Fri, 05 Jul 2019 13:55:22: 19000000 INFO @ Fri, 05 Jul 2019 13:55:23: 19000000 INFO @ Fri, 05 Jul 2019 13:55:23: 16000000 INFO @ Fri, 05 Jul 2019 13:55:31: 20000000 INFO @ Fri, 05 Jul 2019 13:55:31: 20000000 INFO @ Fri, 05 Jul 2019 13:55:33: 17000000 INFO @ Fri, 05 Jul 2019 13:55:39: 21000000 INFO @ Fri, 05 Jul 2019 13:55:40: 21000000 INFO @ Fri, 05 Jul 2019 13:55:44: 18000000 INFO @ Fri, 05 Jul 2019 13:55:48: 22000000 INFO @ Fri, 05 Jul 2019 13:55:48: 22000000 INFO @ Fri, 05 Jul 2019 13:55:55: 19000000 INFO @ Fri, 05 Jul 2019 13:55:56: 23000000 INFO @ Fri, 05 Jul 2019 13:55:57: 23000000 INFO @ Fri, 05 Jul 2019 13:56:05: 24000000 INFO @ Fri, 05 Jul 2019 13:56:05: 24000000 INFO @ Fri, 05 Jul 2019 13:56:06: 20000000 INFO @ Fri, 05 Jul 2019 13:56:13: 25000000 INFO @ Fri, 05 Jul 2019 13:56:14: 25000000 INFO @ Fri, 05 Jul 2019 13:56:17: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 13:56:17: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 13:56:17: #1 total tags in treatment: 25346198 INFO @ Fri, 05 Jul 2019 13:56:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:56:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 13:56:17: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 13:56:17: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 13:56:17: 21000000 INFO @ Fri, 05 Jul 2019 13:56:17: #1 total tags in treatment: 25346198 INFO @ Fri, 05 Jul 2019 13:56:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:56:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 13:56:17: #1 tags after filtering in treatment: 25346093 INFO @ Fri, 05 Jul 2019 13:56:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:56:17: #1 finished! INFO @ Fri, 05 Jul 2019 13:56:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:56:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:56:18: #1 tags after filtering in treatment: 25346093 INFO @ Fri, 05 Jul 2019 13:56:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:56:18: #1 finished! INFO @ Fri, 05 Jul 2019 13:56:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:56:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:56:20: #2 number of paired peaks: 6516 INFO @ Fri, 05 Jul 2019 13:56:20: start model_add_line... INFO @ Fri, 05 Jul 2019 13:56:20: start X-correlation... INFO @ Fri, 05 Jul 2019 13:56:20: end of X-cor INFO @ Fri, 05 Jul 2019 13:56:20: #2 finished! INFO @ Fri, 05 Jul 2019 13:56:20: #2 predicted fragment length is 92 bps INFO @ Fri, 05 Jul 2019 13:56:20: #2 alternative fragment length(s) may be 92 bps INFO @ Fri, 05 Jul 2019 13:56:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX423109/SRX423109.20_model.r WARNING @ Fri, 05 Jul 2019 13:56:20: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 13:56:20: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Fri, 05 Jul 2019 13:56:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 13:56:20: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:56:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:56:21: #2 number of paired peaks: 6516 INFO @ Fri, 05 Jul 2019 13:56:21: start model_add_line... INFO @ Fri, 05 Jul 2019 13:56:21: start X-correlation... INFO @ Fri, 05 Jul 2019 13:56:21: end of X-cor INFO @ Fri, 05 Jul 2019 13:56:21: #2 finished! INFO @ Fri, 05 Jul 2019 13:56:21: #2 predicted fragment length is 92 bps INFO @ Fri, 05 Jul 2019 13:56:21: #2 alternative fragment length(s) may be 92 bps INFO @ Fri, 05 Jul 2019 13:56:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX423109/SRX423109.10_model.r WARNING @ Fri, 05 Jul 2019 13:56:21: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 13:56:21: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Fri, 05 Jul 2019 13:56:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 13:56:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:56:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:56:28: 22000000 INFO @ Fri, 05 Jul 2019 13:56:37: 23000000 INFO @ Fri, 05 Jul 2019 13:56:47: 24000000 INFO @ Fri, 05 Jul 2019 13:56:57: 25000000 INFO @ Fri, 05 Jul 2019 13:57:01: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 13:57:01: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 13:57:01: #1 total tags in treatment: 25346198 INFO @ Fri, 05 Jul 2019 13:57:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:57:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 13:57:01: #1 tags after filtering in treatment: 25346093 INFO @ Fri, 05 Jul 2019 13:57:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:57:01: #1 finished! INFO @ Fri, 05 Jul 2019 13:57:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:57:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:57:04: #2 number of paired peaks: 6516 INFO @ Fri, 05 Jul 2019 13:57:04: start model_add_line... INFO @ Fri, 05 Jul 2019 13:57:05: start X-correlation... INFO @ Fri, 05 Jul 2019 13:57:05: end of X-cor INFO @ Fri, 05 Jul 2019 13:57:05: #2 finished! INFO @ Fri, 05 Jul 2019 13:57:05: #2 predicted fragment length is 92 bps INFO @ Fri, 05 Jul 2019 13:57:05: #2 alternative fragment length(s) may be 92 bps INFO @ Fri, 05 Jul 2019 13:57:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX423109/SRX423109.05_model.r WARNING @ Fri, 05 Jul 2019 13:57:05: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 13:57:05: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Fri, 05 Jul 2019 13:57:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 13:57:05: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:57:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:57:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:57:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:58:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX423109/SRX423109.10_peaks.xls INFO @ Fri, 05 Jul 2019 13:58:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX423109/SRX423109.20_peaks.xls INFO @ Fri, 05 Jul 2019 13:58:25: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:58:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX423109/SRX423109.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:58:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX423109/SRX423109.20_summits.bed INFO @ Fri, 05 Jul 2019 13:58:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX423109/SRX423109.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:58:26: Done! INFO @ Fri, 05 Jul 2019 13:58:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX423109/SRX423109.10_summits.bed INFO @ Fri, 05 Jul 2019 13:58:26: Done! pass1 - making usageList (37 chroms): 2 millis pass1 - making usageList (23 chroms): 2 millis pass2 - checking and writing primary data (222 records, 4 fields): 23 millis pass2 - checking and writing primary data (647 records, 4 fields): 26 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 13:59:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX423109/SRX423109.05_peaks.xls INFO @ Fri, 05 Jul 2019 13:59:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX423109/SRX423109.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:59:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX423109/SRX423109.05_summits.bed INFO @ Fri, 05 Jul 2019 13:59:05: Done! pass1 - making usageList (46 chroms): 2 millis pass2 - checking and writing primary data (1608 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。