Job ID = 2640568 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:41:46 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 ) 2019-08-24T08:41:46 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 ) 2019-08-24T08:41:46 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 ) 2019-08-24T08:41:46 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 : 25,068,885 reads read : 50,137,770 reads written : 25,068,885 reads 0-length : 25,068,885 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: 00:16:33 25068885 reads; of these: 25068885 (100.00%) were unpaired; of these: 547091 (2.18%) aligned 0 times 19959337 (79.62%) aligned exactly 1 time 4562457 (18.20%) aligned >1 times 97.82% overall alignment rate Time searching: 00:16:36 Overall time: 00:16:36 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] 5225279 / 24521794 = 0.2131 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:09:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375014/SRX5375014.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375014/SRX5375014.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375014/SRX5375014.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375014/SRX5375014.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 18:09:15: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:09:15: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:09:25: 1000000 INFO @ Sat, 24 Aug 2019 18:09:35: 2000000 INFO @ Sat, 24 Aug 2019 18:09:44: 3000000 INFO @ Sat, 24 Aug 2019 18:09:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375014/SRX5375014.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375014/SRX5375014.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375014/SRX5375014.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375014/SRX5375014.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 18:09:45: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:09:45: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:09:54: 4000000 INFO @ Sat, 24 Aug 2019 18:09:55: 1000000 INFO @ Sat, 24 Aug 2019 18:10:04: 5000000 INFO @ Sat, 24 Aug 2019 18:10:05: 2000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:10:14: 6000000 INFO @ Sat, 24 Aug 2019 18:10:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375014/SRX5375014.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375014/SRX5375014.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375014/SRX5375014.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375014/SRX5375014.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 18:10:15: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:10:15: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:10:15: 3000000 INFO @ Sat, 24 Aug 2019 18:10:24: 7000000 INFO @ Sat, 24 Aug 2019 18:10:25: 1000000 INFO @ Sat, 24 Aug 2019 18:10:25: 4000000 INFO @ Sat, 24 Aug 2019 18:10:35: 8000000 INFO @ Sat, 24 Aug 2019 18:10:35: 2000000 INFO @ Sat, 24 Aug 2019 18:10:36: 5000000 INFO @ Sat, 24 Aug 2019 18:10:45: 3000000 INFO @ Sat, 24 Aug 2019 18:10:45: 9000000 INFO @ Sat, 24 Aug 2019 18:10:46: 6000000 INFO @ Sat, 24 Aug 2019 18:10:55: 4000000 INFO @ Sat, 24 Aug 2019 18:10:55: 10000000 INFO @ Sat, 24 Aug 2019 18:10:56: 7000000 INFO @ Sat, 24 Aug 2019 18:11:05: 5000000 INFO @ Sat, 24 Aug 2019 18:11:05: 11000000 INFO @ Sat, 24 Aug 2019 18:11:06: 8000000 INFO @ Sat, 24 Aug 2019 18:11:14: 6000000 INFO @ Sat, 24 Aug 2019 18:11:15: 12000000 INFO @ Sat, 24 Aug 2019 18:11:16: 9000000 INFO @ Sat, 24 Aug 2019 18:11:24: 7000000 INFO @ Sat, 24 Aug 2019 18:11:25: 13000000 INFO @ Sat, 24 Aug 2019 18:11:27: 10000000 INFO @ Sat, 24 Aug 2019 18:11:34: 8000000 INFO @ Sat, 24 Aug 2019 18:11:35: 14000000 INFO @ Sat, 24 Aug 2019 18:11:37: 11000000 INFO @ Sat, 24 Aug 2019 18:11:44: 9000000 INFO @ Sat, 24 Aug 2019 18:11:45: 15000000 INFO @ Sat, 24 Aug 2019 18:11:46: 12000000 INFO @ Sat, 24 Aug 2019 18:11:54: 10000000 INFO @ Sat, 24 Aug 2019 18:11:55: 16000000 INFO @ Sat, 24 Aug 2019 18:11:56: 13000000 INFO @ Sat, 24 Aug 2019 18:12:03: 11000000 INFO @ Sat, 24 Aug 2019 18:12:06: 17000000 INFO @ Sat, 24 Aug 2019 18:12:06: 14000000 INFO @ Sat, 24 Aug 2019 18:12:13: 12000000 INFO @ Sat, 24 Aug 2019 18:12:16: 15000000 INFO @ Sat, 24 Aug 2019 18:12:16: 18000000 INFO @ Sat, 24 Aug 2019 18:12:23: 13000000 INFO @ Sat, 24 Aug 2019 18:12:26: 16000000 INFO @ Sat, 24 Aug 2019 18:12:27: 19000000 INFO @ Sat, 24 Aug 2019 18:12:30: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:12:30: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:12:30: #1 total tags in treatment: 19296515 INFO @ Sat, 24 Aug 2019 18:12:30: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:12:30: #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 18:12:31: #1 tags after filtering in treatment: 19296334 INFO @ Sat, 24 Aug 2019 18:12:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:12:31: #1 finished! INFO @ Sat, 24 Aug 2019 18:12:31: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:12:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:12:32: 14000000 INFO @ Sat, 24 Aug 2019 18:12:36: #2 number of paired peaks: 60814 INFO @ Sat, 24 Aug 2019 18:12:36: start model_add_line... INFO @ Sat, 24 Aug 2019 18:12:36: start X-correlation... INFO @ Sat, 24 Aug 2019 18:12:36: end of X-cor INFO @ Sat, 24 Aug 2019 18:12:36: #2 finished! INFO @ Sat, 24 Aug 2019 18:12:36: #2 predicted fragment length is 171 bps INFO @ Sat, 24 Aug 2019 18:12:36: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 24 Aug 2019 18:12:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375014/SRX5375014.05_model.r INFO @ Sat, 24 Aug 2019 18:12:36: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:12:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:12:37: 17000000 INFO @ Sat, 24 Aug 2019 18:12:42: 15000000 INFO @ Sat, 24 Aug 2019 18:12:47: 18000000 INFO @ Sat, 24 Aug 2019 18:12:52: 16000000 INFO @ Sat, 24 Aug 2019 18:12:57: 19000000 INFO @ Sat, 24 Aug 2019 18:13:00: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:13:00: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:13:00: #1 total tags in treatment: 19296515 INFO @ Sat, 24 Aug 2019 18:13:00: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:13:00: #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 18:13:00: #1 tags after filtering in treatment: 19296334 INFO @ Sat, 24 Aug 2019 18:13:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:13:00: #1 finished! INFO @ Sat, 24 Aug 2019 18:13:00: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:13:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:13:02: 17000000 INFO @ Sat, 24 Aug 2019 18:13:05: #2 number of paired peaks: 60814 INFO @ Sat, 24 Aug 2019 18:13:05: start model_add_line... INFO @ Sat, 24 Aug 2019 18:13:05: start X-correlation... INFO @ Sat, 24 Aug 2019 18:13:05: end of X-cor INFO @ Sat, 24 Aug 2019 18:13:05: #2 finished! INFO @ Sat, 24 Aug 2019 18:13:05: #2 predicted fragment length is 171 bps INFO @ Sat, 24 Aug 2019 18:13:05: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 24 Aug 2019 18:13:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375014/SRX5375014.10_model.r INFO @ Sat, 24 Aug 2019 18:13:05: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:13:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:13:12: 18000000 INFO @ Sat, 24 Aug 2019 18:13:22: 19000000 INFO @ Sat, 24 Aug 2019 18:13:25: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:13:25: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:13:25: #1 total tags in treatment: 19296515 INFO @ Sat, 24 Aug 2019 18:13:25: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:13:25: #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 18:13:25: #1 tags after filtering in treatment: 19296334 INFO @ Sat, 24 Aug 2019 18:13:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:13:25: #1 finished! INFO @ Sat, 24 Aug 2019 18:13:25: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:13:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:13:30: #2 number of paired peaks: 60814 INFO @ Sat, 24 Aug 2019 18:13:30: start model_add_line... INFO @ Sat, 24 Aug 2019 18:13:30: start X-correlation... INFO @ Sat, 24 Aug 2019 18:13:30: end of X-cor INFO @ Sat, 24 Aug 2019 18:13:30: #2 finished! INFO @ Sat, 24 Aug 2019 18:13:30: #2 predicted fragment length is 171 bps INFO @ Sat, 24 Aug 2019 18:13:30: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 24 Aug 2019 18:13:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375014/SRX5375014.20_model.r INFO @ Sat, 24 Aug 2019 18:13:30: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:13:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:13:38: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:14:07: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:14:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375014/SRX5375014.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:14:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375014/SRX5375014.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:14:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375014/SRX5375014.05_summits.bed INFO @ Sat, 24 Aug 2019 18:14:12: Done! pass1 - making usageList (103 chroms): 8 millis pass2 - checking and writing primary data (23619 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:14:33: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:14:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375014/SRX5375014.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:14:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375014/SRX5375014.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:14:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375014/SRX5375014.10_summits.bed INFO @ Sat, 24 Aug 2019 18:14:41: Done! pass1 - making usageList (89 chroms): 4 millis pass2 - checking and writing primary data (18064 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:15:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375014/SRX5375014.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:15:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375014/SRX5375014.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:15:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375014/SRX5375014.20_summits.bed INFO @ Sat, 24 Aug 2019 18:15:06: Done! pass1 - making usageList (62 chroms): 5 millis pass2 - checking and writing primary data (12077 records, 4 fields): 24 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。