Job ID = 4288956 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T03:49:06 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 : 25,859,777 reads read : 51,719,554 reads written : 25,859,777 reads 0-length : 25,859,777 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: 00:34:55 25859777 reads; of these: 25859777 (100.00%) were unpaired; of these: 1030702 (3.99%) aligned 0 times 18715154 (72.37%) aligned exactly 1 time 6113921 (23.64%) aligned >1 times 96.01% overall alignment rate Time searching: 00:34:58 Overall time: 00:34:58 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] 1924860 / 24829075 = 0.0775 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:47:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460579/SRX5460579.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460579/SRX5460579.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460579/SRX5460579.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460579/SRX5460579.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 @ Tue, 10 Dec 2019 13:47:53: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:47:53: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:48:03: 1000000 INFO @ Tue, 10 Dec 2019 13:48:14: 2000000 INFO @ Tue, 10 Dec 2019 13:48:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460579/SRX5460579.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460579/SRX5460579.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460579/SRX5460579.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460579/SRX5460579.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 @ Tue, 10 Dec 2019 13:48:22: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:48:22: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:48:24: 3000000 INFO @ Tue, 10 Dec 2019 13:48:35: 4000000 INFO @ Tue, 10 Dec 2019 13:48:36: 1000000 INFO @ Tue, 10 Dec 2019 13:48:45: 5000000 INFO @ Tue, 10 Dec 2019 13:48:49: 2000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:48:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460579/SRX5460579.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460579/SRX5460579.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460579/SRX5460579.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460579/SRX5460579.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 @ Tue, 10 Dec 2019 13:48:52: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:48:52: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:48:57: 6000000 INFO @ Tue, 10 Dec 2019 13:49:04: 3000000 INFO @ Tue, 10 Dec 2019 13:49:07: 1000000 INFO @ Tue, 10 Dec 2019 13:49:08: 7000000 INFO @ Tue, 10 Dec 2019 13:49:18: 4000000 INFO @ Tue, 10 Dec 2019 13:49:19: 8000000 INFO @ Tue, 10 Dec 2019 13:49:21: 2000000 INFO @ Tue, 10 Dec 2019 13:49:30: 9000000 INFO @ Tue, 10 Dec 2019 13:49:33: 5000000 INFO @ Tue, 10 Dec 2019 13:49:35: 3000000 INFO @ Tue, 10 Dec 2019 13:49:41: 10000000 INFO @ Tue, 10 Dec 2019 13:49:48: 6000000 INFO @ Tue, 10 Dec 2019 13:49:49: 4000000 INFO @ Tue, 10 Dec 2019 13:49:52: 11000000 INFO @ Tue, 10 Dec 2019 13:50:02: 7000000 INFO @ Tue, 10 Dec 2019 13:50:03: 5000000 INFO @ Tue, 10 Dec 2019 13:50:03: 12000000 INFO @ Tue, 10 Dec 2019 13:50:15: 13000000 INFO @ Tue, 10 Dec 2019 13:50:17: 6000000 INFO @ Tue, 10 Dec 2019 13:50:17: 8000000 INFO @ Tue, 10 Dec 2019 13:50:25: 14000000 INFO @ Tue, 10 Dec 2019 13:50:31: 7000000 INFO @ Tue, 10 Dec 2019 13:50:32: 9000000 INFO @ Tue, 10 Dec 2019 13:50:36: 15000000 INFO @ Tue, 10 Dec 2019 13:50:45: 8000000 INFO @ Tue, 10 Dec 2019 13:50:46: 16000000 INFO @ Tue, 10 Dec 2019 13:50:46: 10000000 INFO @ Tue, 10 Dec 2019 13:50:57: 17000000 INFO @ Tue, 10 Dec 2019 13:50:59: 9000000 INFO @ Tue, 10 Dec 2019 13:51:01: 11000000 INFO @ Tue, 10 Dec 2019 13:51:08: 18000000 INFO @ Tue, 10 Dec 2019 13:51:13: 10000000 INFO @ Tue, 10 Dec 2019 13:51:16: 12000000 INFO @ Tue, 10 Dec 2019 13:51:18: 19000000 INFO @ Tue, 10 Dec 2019 13:51:27: 11000000 INFO @ Tue, 10 Dec 2019 13:51:29: 20000000 INFO @ Tue, 10 Dec 2019 13:51:30: 13000000 INFO @ Tue, 10 Dec 2019 13:51:39: 21000000 INFO @ Tue, 10 Dec 2019 13:51:41: 12000000 INFO @ Tue, 10 Dec 2019 13:51:45: 14000000 INFO @ Tue, 10 Dec 2019 13:51:50: 22000000 INFO @ Tue, 10 Dec 2019 13:51:55: 13000000 INFO @ Tue, 10 Dec 2019 13:51:59: 15000000 INFO @ Tue, 10 Dec 2019 13:51:59: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:51:59: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:51:59: #1 total tags in treatment: 22904215 INFO @ Tue, 10 Dec 2019 13:51:59: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:51:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:52:00: #1 tags after filtering in treatment: 22904071 INFO @ Tue, 10 Dec 2019 13:52:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:52:00: #1 finished! INFO @ Tue, 10 Dec 2019 13:52:00: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:52:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:52:03: #2 number of paired peaks: 4953 INFO @ Tue, 10 Dec 2019 13:52:03: start model_add_line... INFO @ Tue, 10 Dec 2019 13:52:03: start X-correlation... INFO @ Tue, 10 Dec 2019 13:52:03: end of X-cor INFO @ Tue, 10 Dec 2019 13:52:03: #2 finished! INFO @ Tue, 10 Dec 2019 13:52:03: #2 predicted fragment length is 84 bps INFO @ Tue, 10 Dec 2019 13:52:03: #2 alternative fragment length(s) may be 84,564 bps INFO @ Tue, 10 Dec 2019 13:52:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460579/SRX5460579.05_model.r WARNING @ Tue, 10 Dec 2019 13:52:03: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:52:03: #2 You may need to consider one of the other alternative d(s): 84,564 WARNING @ Tue, 10 Dec 2019 13:52:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:52:03: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:52:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:52:08: 14000000 INFO @ Tue, 10 Dec 2019 13:52:12: 16000000 INFO @ Tue, 10 Dec 2019 13:52:22: 15000000 INFO @ Tue, 10 Dec 2019 13:52:26: 17000000 INFO @ Tue, 10 Dec 2019 13:52:35: 16000000 INFO @ Tue, 10 Dec 2019 13:52:39: 18000000 INFO @ Tue, 10 Dec 2019 13:52:48: 17000000 INFO @ Tue, 10 Dec 2019 13:52:53: 19000000 INFO @ Tue, 10 Dec 2019 13:53:01: 18000000 INFO @ Tue, 10 Dec 2019 13:53:07: 20000000 INFO @ Tue, 10 Dec 2019 13:53:14: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:53:14: 19000000 INFO @ Tue, 10 Dec 2019 13:53:20: 21000000 INFO @ Tue, 10 Dec 2019 13:53:28: 20000000 INFO @ Tue, 10 Dec 2019 13:53:34: 22000000 INFO @ Tue, 10 Dec 2019 13:53:41: 21000000 INFO @ Tue, 10 Dec 2019 13:53:47: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:53:47: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:53:47: #1 total tags in treatment: 22904215 INFO @ Tue, 10 Dec 2019 13:53:47: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:53:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:53:47: #1 tags after filtering in treatment: 22904071 INFO @ Tue, 10 Dec 2019 13:53:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:53:47: #1 finished! INFO @ Tue, 10 Dec 2019 13:53:47: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:53:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:53:50: #2 number of paired peaks: 4953 INFO @ Tue, 10 Dec 2019 13:53:50: start model_add_line... INFO @ Tue, 10 Dec 2019 13:53:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460579/SRX5460579.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:53:50: start X-correlation... INFO @ Tue, 10 Dec 2019 13:53:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460579/SRX5460579.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:53:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460579/SRX5460579.05_summits.bed INFO @ Tue, 10 Dec 2019 13:53:50: end of X-cor INFO @ Tue, 10 Dec 2019 13:53:50: #2 finished! INFO @ Tue, 10 Dec 2019 13:53:50: #2 predicted fragment length is 84 bps INFO @ Tue, 10 Dec 2019 13:53:50: #2 alternative fragment length(s) may be 84,564 bps INFO @ Tue, 10 Dec 2019 13:53:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460579/SRX5460579.10_model.r INFO @ Tue, 10 Dec 2019 13:53:50: Done! WARNING @ Tue, 10 Dec 2019 13:53:50: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:53:50: #2 You may need to consider one of the other alternative d(s): 84,564 WARNING @ Tue, 10 Dec 2019 13:53:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:53:50: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:53:50: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (45 chroms): 2 millis pass2 - checking and writing primary data (1209 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:53:53: 22000000 INFO @ Tue, 10 Dec 2019 13:54:04: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:54:04: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:54:04: #1 total tags in treatment: 22904215 INFO @ Tue, 10 Dec 2019 13:54:04: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:54:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:54:05: #1 tags after filtering in treatment: 22904071 INFO @ Tue, 10 Dec 2019 13:54:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:54:05: #1 finished! INFO @ Tue, 10 Dec 2019 13:54:05: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:54:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:54:08: #2 number of paired peaks: 4953 INFO @ Tue, 10 Dec 2019 13:54:08: start model_add_line... INFO @ Tue, 10 Dec 2019 13:54:08: start X-correlation... INFO @ Tue, 10 Dec 2019 13:54:08: end of X-cor INFO @ Tue, 10 Dec 2019 13:54:08: #2 finished! INFO @ Tue, 10 Dec 2019 13:54:08: #2 predicted fragment length is 84 bps INFO @ Tue, 10 Dec 2019 13:54:08: #2 alternative fragment length(s) may be 84,564 bps INFO @ Tue, 10 Dec 2019 13:54:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460579/SRX5460579.20_model.r WARNING @ Tue, 10 Dec 2019 13:54:08: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:54:08: #2 You may need to consider one of the other alternative d(s): 84,564 WARNING @ Tue, 10 Dec 2019 13:54:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:54:08: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:54:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:55:02: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:55:19: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:55:38: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460579/SRX5460579.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:55:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460579/SRX5460579.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:55:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460579/SRX5460579.10_summits.bed INFO @ Tue, 10 Dec 2019 13:55:38: Done! pass1 - making usageList (39 chroms): 2 millis pass2 - checking and writing primary data (686 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:55:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460579/SRX5460579.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:55:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460579/SRX5460579.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:55:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460579/SRX5460579.20_summits.bed INFO @ Tue, 10 Dec 2019 13:55:55: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (392 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。