Job ID = 4287331 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T02:56:47 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 ) 2019-12-10T03:00:41 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 ) 2019-12-10T03:00:41 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 : 15,898,601 reads read : 31,797,202 reads written : 15,898,601 reads 0-length : 15,898,601 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:13:42 15898601 reads; of these: 15898601 (100.00%) were unpaired; of these: 401615 (2.53%) aligned 0 times 10666237 (67.09%) aligned exactly 1 time 4830749 (30.38%) aligned >1 times 97.47% overall alignment rate Time searching: 00:13:46 Overall time: 00:13:46 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 8 files... [bam_rmdupse_core] 655692 / 15496986 = 0.0423 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 12:19:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654060/SRX4654060.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654060/SRX4654060.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654060/SRX4654060.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654060/SRX4654060.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 12:19:51: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:19:51: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:20:01: 1000000 INFO @ Tue, 10 Dec 2019 12:20:12: 2000000 INFO @ Tue, 10 Dec 2019 12:20:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654060/SRX4654060.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654060/SRX4654060.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654060/SRX4654060.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654060/SRX4654060.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 12:20:19: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:20:19: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:20:22: 3000000 INFO @ Tue, 10 Dec 2019 12:20:28: 1000000 INFO @ Tue, 10 Dec 2019 12:20:33: 4000000 INFO @ Tue, 10 Dec 2019 12:20:36: 2000000 INFO @ Tue, 10 Dec 2019 12:20:43: 5000000 INFO @ Tue, 10 Dec 2019 12:20:44: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 12:20:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654060/SRX4654060.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654060/SRX4654060.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654060/SRX4654060.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654060/SRX4654060.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 12:20:49: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:20:49: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:20:52: 4000000 INFO @ Tue, 10 Dec 2019 12:20:54: 6000000 INFO @ Tue, 10 Dec 2019 12:20:59: 1000000 INFO @ Tue, 10 Dec 2019 12:21:00: 5000000 INFO @ Tue, 10 Dec 2019 12:21:06: 7000000 INFO @ Tue, 10 Dec 2019 12:21:09: 6000000 INFO @ Tue, 10 Dec 2019 12:21:09: 2000000 INFO @ Tue, 10 Dec 2019 12:21:17: 8000000 INFO @ Tue, 10 Dec 2019 12:21:17: 7000000 INFO @ Tue, 10 Dec 2019 12:21:19: 3000000 INFO @ Tue, 10 Dec 2019 12:21:25: 8000000 INFO @ Tue, 10 Dec 2019 12:21:28: 9000000 INFO @ Tue, 10 Dec 2019 12:21:29: 4000000 INFO @ Tue, 10 Dec 2019 12:21:34: 9000000 INFO @ Tue, 10 Dec 2019 12:21:38: 10000000 INFO @ Tue, 10 Dec 2019 12:21:39: 5000000 INFO @ Tue, 10 Dec 2019 12:21:42: 10000000 INFO @ Tue, 10 Dec 2019 12:21:49: 6000000 INFO @ Tue, 10 Dec 2019 12:21:49: 11000000 INFO @ Tue, 10 Dec 2019 12:21:50: 11000000 INFO @ Tue, 10 Dec 2019 12:21:58: 7000000 INFO @ Tue, 10 Dec 2019 12:21:58: 12000000 INFO @ Tue, 10 Dec 2019 12:21:59: 12000000 INFO @ Tue, 10 Dec 2019 12:22:07: 13000000 INFO @ Tue, 10 Dec 2019 12:22:08: 8000000 INFO @ Tue, 10 Dec 2019 12:22:09: 13000000 INFO @ Tue, 10 Dec 2019 12:22:15: 14000000 INFO @ Tue, 10 Dec 2019 12:22:18: 9000000 INFO @ Tue, 10 Dec 2019 12:22:19: 14000000 INFO @ Tue, 10 Dec 2019 12:22:22: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:22:22: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:22:22: #1 total tags in treatment: 14841294 INFO @ Tue, 10 Dec 2019 12:22:22: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:22:22: #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 12:22:22: #1 tags after filtering in treatment: 14841146 INFO @ Tue, 10 Dec 2019 12:22:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:22:22: #1 finished! INFO @ Tue, 10 Dec 2019 12:22:22: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:22:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:22:24: #2 number of paired peaks: 6024 INFO @ Tue, 10 Dec 2019 12:22:24: start model_add_line... INFO @ Tue, 10 Dec 2019 12:22:24: start X-correlation... INFO @ Tue, 10 Dec 2019 12:22:24: end of X-cor INFO @ Tue, 10 Dec 2019 12:22:24: #2 finished! INFO @ Tue, 10 Dec 2019 12:22:24: #2 predicted fragment length is 50 bps INFO @ Tue, 10 Dec 2019 12:22:24: #2 alternative fragment length(s) may be 50,213,413 bps INFO @ Tue, 10 Dec 2019 12:22:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654060/SRX4654060.10_model.r WARNING @ Tue, 10 Dec 2019 12:22:25: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:22:25: #2 You may need to consider one of the other alternative d(s): 50,213,413 WARNING @ Tue, 10 Dec 2019 12:22:25: #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 12:22:25: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:22:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:22:28: 10000000 INFO @ Tue, 10 Dec 2019 12:22:28: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:22:28: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:22:28: #1 total tags in treatment: 14841294 INFO @ Tue, 10 Dec 2019 12:22:28: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:22:28: #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 12:22:29: #1 tags after filtering in treatment: 14841146 INFO @ Tue, 10 Dec 2019 12:22:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:22:29: #1 finished! INFO @ Tue, 10 Dec 2019 12:22:29: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:22:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:22:31: #2 number of paired peaks: 6024 INFO @ Tue, 10 Dec 2019 12:22:31: start model_add_line... INFO @ Tue, 10 Dec 2019 12:22:31: start X-correlation... INFO @ Tue, 10 Dec 2019 12:22:31: end of X-cor INFO @ Tue, 10 Dec 2019 12:22:31: #2 finished! INFO @ Tue, 10 Dec 2019 12:22:31: #2 predicted fragment length is 50 bps INFO @ Tue, 10 Dec 2019 12:22:31: #2 alternative fragment length(s) may be 50,213,413 bps INFO @ Tue, 10 Dec 2019 12:22:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654060/SRX4654060.05_model.r WARNING @ Tue, 10 Dec 2019 12:22:31: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:22:31: #2 You may need to consider one of the other alternative d(s): 50,213,413 WARNING @ Tue, 10 Dec 2019 12:22:31: #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 12:22:31: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:22:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:22:37: 11000000 INFO @ Tue, 10 Dec 2019 12:22:47: 12000000 INFO @ Tue, 10 Dec 2019 12:22:56: 13000000 INFO @ Tue, 10 Dec 2019 12:23:06: 14000000 INFO @ Tue, 10 Dec 2019 12:23:12: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:23:14: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:23:14: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:23:14: #1 total tags in treatment: 14841294 INFO @ Tue, 10 Dec 2019 12:23:14: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:23:14: #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 12:23:14: #1 tags after filtering in treatment: 14841146 INFO @ Tue, 10 Dec 2019 12:23:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:23:14: #1 finished! INFO @ Tue, 10 Dec 2019 12:23:14: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:23:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:23:16: #2 number of paired peaks: 6024 INFO @ Tue, 10 Dec 2019 12:23:16: start model_add_line... INFO @ Tue, 10 Dec 2019 12:23:16: start X-correlation... INFO @ Tue, 10 Dec 2019 12:23:16: end of X-cor INFO @ Tue, 10 Dec 2019 12:23:16: #2 finished! INFO @ Tue, 10 Dec 2019 12:23:16: #2 predicted fragment length is 50 bps INFO @ Tue, 10 Dec 2019 12:23:16: #2 alternative fragment length(s) may be 50,213,413 bps INFO @ Tue, 10 Dec 2019 12:23:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654060/SRX4654060.20_model.r WARNING @ Tue, 10 Dec 2019 12:23:16: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:23:16: #2 You may need to consider one of the other alternative d(s): 50,213,413 WARNING @ Tue, 10 Dec 2019 12:23:16: #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 12:23:16: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:23:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:23:19: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:23:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654060/SRX4654060.10_peaks.xls INFO @ Tue, 10 Dec 2019 12:23:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654060/SRX4654060.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:23:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654060/SRX4654060.10_summits.bed INFO @ Tue, 10 Dec 2019 12:23:34: Done! pass1 - making usageList (39 chroms): 1 millis pass2 - checking and writing primary data (698 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:23:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654060/SRX4654060.05_peaks.xls INFO @ Tue, 10 Dec 2019 12:23:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654060/SRX4654060.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:23:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654060/SRX4654060.05_summits.bed INFO @ Tue, 10 Dec 2019 12:23:42: Done! pass1 - making usageList (51 chroms): 2 millis pass2 - checking and writing primary data (1226 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:24:03: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:24:25: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654060/SRX4654060.20_peaks.xls INFO @ Tue, 10 Dec 2019 12:24:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654060/SRX4654060.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:24:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654060/SRX4654060.20_summits.bed INFO @ Tue, 10 Dec 2019 12:24:25: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (321 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。