Job ID = 2640587 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:58:20 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 ) 2019-08-24T08:58:20 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 ) 2019-08-24T08:58:20 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 ) 2019-08-24T08:58:20 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 : 17,134,078 reads read : 34,268,156 reads written : 17,134,078 reads 0-length : 17,134,078 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: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:36 17134078 reads; of these: 17134078 (100.00%) were unpaired; of these: 1068204 (6.23%) aligned 0 times 13476760 (78.65%) aligned exactly 1 time 2589114 (15.11%) aligned >1 times 93.77% overall alignment rate Time searching: 00:09:37 Overall time: 00:09:37 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] 1020316 / 16065874 = 0.0635 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:15:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375025/SRX5375025.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375025/SRX5375025.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375025/SRX5375025.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375025/SRX5375025.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 18:15:33: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:15:33: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:15:42: 1000000 INFO @ Sat, 24 Aug 2019 18:15:50: 2000000 INFO @ Sat, 24 Aug 2019 18:15:59: 3000000 INFO @ Sat, 24 Aug 2019 18:16:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375025/SRX5375025.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375025/SRX5375025.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375025/SRX5375025.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375025/SRX5375025.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 18:16:03: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:16:03: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:16:07: 4000000 INFO @ Sat, 24 Aug 2019 18:16:11: 1000000 INFO @ Sat, 24 Aug 2019 18:16:16: 5000000 INFO @ Sat, 24 Aug 2019 18:16:19: 2000000 INFO @ Sat, 24 Aug 2019 18:16:25: 6000000 INFO @ Sat, 24 Aug 2019 18:16:27: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:16:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375025/SRX5375025.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375025/SRX5375025.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375025/SRX5375025.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375025/SRX5375025.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 18:16:33: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:16:33: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:16:33: 7000000 INFO @ Sat, 24 Aug 2019 18:16:34: 4000000 INFO @ Sat, 24 Aug 2019 18:16:42: 8000000 INFO @ Sat, 24 Aug 2019 18:16:42: 5000000 INFO @ Sat, 24 Aug 2019 18:16:44: 1000000 INFO @ Sat, 24 Aug 2019 18:16:50: 6000000 INFO @ Sat, 24 Aug 2019 18:16:51: 9000000 INFO @ Sat, 24 Aug 2019 18:16:55: 2000000 INFO @ Sat, 24 Aug 2019 18:16:58: 7000000 INFO @ Sat, 24 Aug 2019 18:17:00: 10000000 INFO @ Sat, 24 Aug 2019 18:17:06: 3000000 INFO @ Sat, 24 Aug 2019 18:17:06: 8000000 INFO @ Sat, 24 Aug 2019 18:17:08: 11000000 INFO @ Sat, 24 Aug 2019 18:17:14: 9000000 INFO @ Sat, 24 Aug 2019 18:17:16: 4000000 INFO @ Sat, 24 Aug 2019 18:17:17: 12000000 INFO @ Sat, 24 Aug 2019 18:17:22: 10000000 INFO @ Sat, 24 Aug 2019 18:17:26: 13000000 INFO @ Sat, 24 Aug 2019 18:17:27: 5000000 INFO @ Sat, 24 Aug 2019 18:17:30: 11000000 INFO @ Sat, 24 Aug 2019 18:17:35: 14000000 INFO @ Sat, 24 Aug 2019 18:17:37: 12000000 INFO @ Sat, 24 Aug 2019 18:17:38: 6000000 INFO @ Sat, 24 Aug 2019 18:17:44: 15000000 INFO @ Sat, 24 Aug 2019 18:17:44: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:17:44: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:17:44: #1 total tags in treatment: 15045558 INFO @ Sat, 24 Aug 2019 18:17:44: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:17:44: #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 18:17:45: #1 tags after filtering in treatment: 15045326 INFO @ Sat, 24 Aug 2019 18:17:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:17:45: #1 finished! INFO @ Sat, 24 Aug 2019 18:17:45: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:17:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:17:45: 13000000 INFO @ Sat, 24 Aug 2019 18:17:48: 7000000 INFO @ Sat, 24 Aug 2019 18:17:49: #2 number of paired peaks: 75430 INFO @ Sat, 24 Aug 2019 18:17:49: start model_add_line... INFO @ Sat, 24 Aug 2019 18:17:50: start X-correlation... INFO @ Sat, 24 Aug 2019 18:17:50: end of X-cor INFO @ Sat, 24 Aug 2019 18:17:50: #2 finished! INFO @ Sat, 24 Aug 2019 18:17:50: #2 predicted fragment length is 177 bps INFO @ Sat, 24 Aug 2019 18:17:50: #2 alternative fragment length(s) may be 177 bps INFO @ Sat, 24 Aug 2019 18:17:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375025/SRX5375025.05_model.r INFO @ Sat, 24 Aug 2019 18:17:50: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:17:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:17:53: 14000000 INFO @ Sat, 24 Aug 2019 18:17:59: 8000000 INFO @ Sat, 24 Aug 2019 18:18:01: 15000000 INFO @ Sat, 24 Aug 2019 18:18:02: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:18:02: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:18:02: #1 total tags in treatment: 15045558 INFO @ Sat, 24 Aug 2019 18:18:02: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:18:02: #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 18:18:02: #1 tags after filtering in treatment: 15045326 INFO @ Sat, 24 Aug 2019 18:18:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:18:02: #1 finished! INFO @ Sat, 24 Aug 2019 18:18:02: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:18:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:18:07: #2 number of paired peaks: 75430 INFO @ Sat, 24 Aug 2019 18:18:07: start model_add_line... INFO @ Sat, 24 Aug 2019 18:18:07: start X-correlation... INFO @ Sat, 24 Aug 2019 18:18:07: end of X-cor INFO @ Sat, 24 Aug 2019 18:18:07: #2 finished! INFO @ Sat, 24 Aug 2019 18:18:07: #2 predicted fragment length is 177 bps INFO @ Sat, 24 Aug 2019 18:18:07: #2 alternative fragment length(s) may be 177 bps INFO @ Sat, 24 Aug 2019 18:18:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375025/SRX5375025.10_model.r INFO @ Sat, 24 Aug 2019 18:18:07: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:18:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:18:09: 9000000 INFO @ Sat, 24 Aug 2019 18:18:19: 10000000 INFO @ Sat, 24 Aug 2019 18:18:29: 11000000 INFO @ Sat, 24 Aug 2019 18:18:40: 12000000 INFO @ Sat, 24 Aug 2019 18:18:40: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:18:50: 13000000 INFO @ Sat, 24 Aug 2019 18:18:57: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:19:00: 14000000 INFO @ Sat, 24 Aug 2019 18:19:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375025/SRX5375025.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:19:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375025/SRX5375025.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:19:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375025/SRX5375025.05_summits.bed INFO @ Sat, 24 Aug 2019 18:19:06: Done! pass1 - making usageList (109 chroms): 11 millis pass2 - checking and writing primary data (34957 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:19:10: 15000000 INFO @ Sat, 24 Aug 2019 18:19:11: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:19:11: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:19:11: #1 total tags in treatment: 15045558 INFO @ Sat, 24 Aug 2019 18:19:11: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:19:11: #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 18:19:11: #1 tags after filtering in treatment: 15045326 INFO @ Sat, 24 Aug 2019 18:19:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:19:11: #1 finished! INFO @ Sat, 24 Aug 2019 18:19:11: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:19:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:19:16: #2 number of paired peaks: 75430 INFO @ Sat, 24 Aug 2019 18:19:16: start model_add_line... INFO @ Sat, 24 Aug 2019 18:19:16: start X-correlation... INFO @ Sat, 24 Aug 2019 18:19:16: end of X-cor INFO @ Sat, 24 Aug 2019 18:19:16: #2 finished! INFO @ Sat, 24 Aug 2019 18:19:16: #2 predicted fragment length is 177 bps INFO @ Sat, 24 Aug 2019 18:19:16: #2 alternative fragment length(s) may be 177 bps INFO @ Sat, 24 Aug 2019 18:19:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375025/SRX5375025.20_model.r INFO @ Sat, 24 Aug 2019 18:19:16: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:19:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:19:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375025/SRX5375025.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:19:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375025/SRX5375025.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:19:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375025/SRX5375025.10_summits.bed INFO @ Sat, 24 Aug 2019 18:19:23: Done! pass1 - making usageList (92 chroms): 6 millis pass2 - checking and writing primary data (23542 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:20:06: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:20:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375025/SRX5375025.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:20:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375025/SRX5375025.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:20:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375025/SRX5375025.20_summits.bed INFO @ Sat, 24 Aug 2019 18:20:31: Done! pass1 - making usageList (62 chroms): 3 millis pass2 - checking and writing primary data (12589 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。