Job ID = 2640573 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:42:20 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 ) 2019-08-24T08:46:20 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 ) 2019-08-24T08:46:20 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 ) 2019-08-24T08:46:20 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 : 19,571,142 reads read : 39,142,284 reads written : 19,571,142 reads 0-length : 19,571,142 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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:12:27 19571142 reads; of these: 19571142 (100.00%) were unpaired; of these: 2014132 (10.29%) aligned 0 times 14179100 (72.45%) aligned exactly 1 time 3377910 (17.26%) aligned >1 times 89.71% overall alignment rate Time searching: 00:12:29 Overall time: 00:12:29 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] 1991036 / 17557010 = 0.1134 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:05:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375017/SRX5375017.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375017/SRX5375017.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375017/SRX5375017.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375017/SRX5375017.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 18:05:39: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:05:39: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:05:46: 1000000 INFO @ Sat, 24 Aug 2019 18:05:53: 2000000 INFO @ Sat, 24 Aug 2019 18:06:00: 3000000 INFO @ Sat, 24 Aug 2019 18:06:06: 4000000 INFO @ Sat, 24 Aug 2019 18:06:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375017/SRX5375017.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375017/SRX5375017.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375017/SRX5375017.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375017/SRX5375017.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 18:06:09: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:06:09: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:06:13: 5000000 INFO @ Sat, 24 Aug 2019 18:06:17: 1000000 INFO @ Sat, 24 Aug 2019 18:06:20: 6000000 INFO @ Sat, 24 Aug 2019 18:06:25: 2000000 INFO @ Sat, 24 Aug 2019 18:06:27: 7000000 INFO @ Sat, 24 Aug 2019 18:06:32: 3000000 INFO @ Sat, 24 Aug 2019 18:06:34: 8000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:06:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375017/SRX5375017.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375017/SRX5375017.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375017/SRX5375017.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375017/SRX5375017.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 18:06:39: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:06:39: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:06:40: 4000000 INFO @ Sat, 24 Aug 2019 18:06:41: 9000000 INFO @ Sat, 24 Aug 2019 18:06:47: 5000000 INFO @ Sat, 24 Aug 2019 18:06:48: 10000000 INFO @ Sat, 24 Aug 2019 18:06:48: 1000000 INFO @ Sat, 24 Aug 2019 18:06:55: 11000000 INFO @ Sat, 24 Aug 2019 18:06:55: 6000000 INFO @ Sat, 24 Aug 2019 18:06:57: 2000000 INFO @ Sat, 24 Aug 2019 18:07:02: 12000000 INFO @ Sat, 24 Aug 2019 18:07:03: 7000000 INFO @ Sat, 24 Aug 2019 18:07:06: 3000000 INFO @ Sat, 24 Aug 2019 18:07:09: 13000000 INFO @ Sat, 24 Aug 2019 18:07:11: 8000000 INFO @ Sat, 24 Aug 2019 18:07:14: 4000000 INFO @ Sat, 24 Aug 2019 18:07:16: 14000000 INFO @ Sat, 24 Aug 2019 18:07:18: 9000000 INFO @ Sat, 24 Aug 2019 18:07:23: 15000000 INFO @ Sat, 24 Aug 2019 18:07:23: 5000000 INFO @ Sat, 24 Aug 2019 18:07:26: 10000000 INFO @ Sat, 24 Aug 2019 18:07:27: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:07:27: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:07:27: #1 total tags in treatment: 15565974 INFO @ Sat, 24 Aug 2019 18:07:27: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:07:27: #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 18:07:28: #1 tags after filtering in treatment: 15565762 INFO @ Sat, 24 Aug 2019 18:07:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:07:28: #1 finished! INFO @ Sat, 24 Aug 2019 18:07:28: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:07:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:07:32: 6000000 INFO @ Sat, 24 Aug 2019 18:07:32: #2 number of paired peaks: 82919 INFO @ Sat, 24 Aug 2019 18:07:32: start model_add_line... INFO @ Sat, 24 Aug 2019 18:07:33: start X-correlation... INFO @ Sat, 24 Aug 2019 18:07:33: end of X-cor INFO @ Sat, 24 Aug 2019 18:07:33: #2 finished! INFO @ Sat, 24 Aug 2019 18:07:33: #2 predicted fragment length is 229 bps INFO @ Sat, 24 Aug 2019 18:07:33: #2 alternative fragment length(s) may be 4,229,242 bps INFO @ Sat, 24 Aug 2019 18:07:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375017/SRX5375017.05_model.r INFO @ Sat, 24 Aug 2019 18:07:33: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:07:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:07:34: 11000000 INFO @ Sat, 24 Aug 2019 18:07:41: 7000000 INFO @ Sat, 24 Aug 2019 18:07:42: 12000000 INFO @ Sat, 24 Aug 2019 18:07:49: 13000000 INFO @ Sat, 24 Aug 2019 18:07:49: 8000000 INFO @ Sat, 24 Aug 2019 18:07:57: 14000000 INFO @ Sat, 24 Aug 2019 18:07:58: 9000000 INFO @ Sat, 24 Aug 2019 18:08:05: 15000000 INFO @ Sat, 24 Aug 2019 18:08:07: 10000000 INFO @ Sat, 24 Aug 2019 18:08:09: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:08:09: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:08:09: #1 total tags in treatment: 15565974 INFO @ Sat, 24 Aug 2019 18:08:09: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:08:09: #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 18:08:10: #1 tags after filtering in treatment: 15565762 INFO @ Sat, 24 Aug 2019 18:08:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:08:10: #1 finished! INFO @ Sat, 24 Aug 2019 18:08:10: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:08:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:08:15: #2 number of paired peaks: 82919 INFO @ Sat, 24 Aug 2019 18:08:15: start model_add_line... INFO @ Sat, 24 Aug 2019 18:08:15: start X-correlation... INFO @ Sat, 24 Aug 2019 18:08:15: end of X-cor INFO @ Sat, 24 Aug 2019 18:08:15: #2 finished! INFO @ Sat, 24 Aug 2019 18:08:15: #2 predicted fragment length is 229 bps INFO @ Sat, 24 Aug 2019 18:08:15: #2 alternative fragment length(s) may be 4,229,242 bps INFO @ Sat, 24 Aug 2019 18:08:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375017/SRX5375017.10_model.r INFO @ Sat, 24 Aug 2019 18:08:15: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:08:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:08:16: 11000000 INFO @ Sat, 24 Aug 2019 18:08:25: 12000000 INFO @ Sat, 24 Aug 2019 18:08:32: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:08:34: 13000000 INFO @ Sat, 24 Aug 2019 18:08:43: 14000000 INFO @ Sat, 24 Aug 2019 18:08:52: 15000000 INFO @ Sat, 24 Aug 2019 18:08:57: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:08:57: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:08:57: #1 total tags in treatment: 15565974 INFO @ Sat, 24 Aug 2019 18:08:57: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:08:57: #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 18:08:57: #1 tags after filtering in treatment: 15565762 INFO @ Sat, 24 Aug 2019 18:08:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:08:57: #1 finished! INFO @ Sat, 24 Aug 2019 18:08:57: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:08:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:09:02: #2 number of paired peaks: 82919 INFO @ Sat, 24 Aug 2019 18:09:02: start model_add_line... INFO @ Sat, 24 Aug 2019 18:09:02: start X-correlation... INFO @ Sat, 24 Aug 2019 18:09:02: end of X-cor INFO @ Sat, 24 Aug 2019 18:09:02: #2 finished! INFO @ Sat, 24 Aug 2019 18:09:02: #2 predicted fragment length is 229 bps INFO @ Sat, 24 Aug 2019 18:09:02: #2 alternative fragment length(s) may be 4,229,242 bps INFO @ Sat, 24 Aug 2019 18:09:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375017/SRX5375017.20_model.r INFO @ Sat, 24 Aug 2019 18:09:02: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:09:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:09:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375017/SRX5375017.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:09:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375017/SRX5375017.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:09:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375017/SRX5375017.05_summits.bed INFO @ Sat, 24 Aug 2019 18:09:05: Done! pass1 - making usageList (64 chroms): 3 millis pass2 - checking and writing primary data (4608 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:09:08: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:09:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375017/SRX5375017.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:09:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375017/SRX5375017.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:09:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375017/SRX5375017.10_summits.bed INFO @ Sat, 24 Aug 2019 18:09:33: Done! pass1 - making usageList (38 chroms): 2 millis pass2 - checking and writing primary data (1745 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:09:55: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:10:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375017/SRX5375017.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:10:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375017/SRX5375017.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:10:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375017/SRX5375017.20_summits.bed INFO @ Sat, 24 Aug 2019 18:10:21: Done! pass1 - making usageList (30 chroms): 2 millis pass2 - checking and writing primary data (599 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。