Job ID = 2640697 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T09:15:56 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 ) 2019-08-24T09:15:56 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 ) 2019-08-24T09:18:04 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 ) 2019-08-24T09:19:29 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 19,307,288 reads read : 38,614,576 reads written : 19,307,288 reads 0-length : 19,307,288 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: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:06 19307288 reads; of these: 19307288 (100.00%) were unpaired; of these: 774956 (4.01%) aligned 0 times 15374115 (79.63%) aligned exactly 1 time 3158217 (16.36%) aligned >1 times 95.99% overall alignment rate Time searching: 00:14:08 Overall time: 00:14:08 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] 1295890 / 18532332 = 0.0699 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:40:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375054/SRX5375054.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375054/SRX5375054.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375054/SRX5375054.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375054/SRX5375054.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 18:40:56: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:40:56: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:41:03: 1000000 INFO @ Sat, 24 Aug 2019 18:41:09: 2000000 INFO @ Sat, 24 Aug 2019 18:41:15: 3000000 INFO @ Sat, 24 Aug 2019 18:41:21: 4000000 INFO @ Sat, 24 Aug 2019 18:41:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375054/SRX5375054.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375054/SRX5375054.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375054/SRX5375054.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375054/SRX5375054.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 18:41:26: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:41:26: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:41:28: 5000000 INFO @ Sat, 24 Aug 2019 18:41:34: 6000000 INFO @ Sat, 24 Aug 2019 18:41:34: 1000000 INFO @ Sat, 24 Aug 2019 18:41:40: 7000000 INFO @ Sat, 24 Aug 2019 18:41:41: 2000000 INFO @ Sat, 24 Aug 2019 18:41:46: 8000000 INFO @ Sat, 24 Aug 2019 18:41:49: 3000000 INFO @ Sat, 24 Aug 2019 18:41:52: 9000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:41:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375054/SRX5375054.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375054/SRX5375054.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375054/SRX5375054.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375054/SRX5375054.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 18:41:56: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:41:56: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:41:57: 4000000 INFO @ Sat, 24 Aug 2019 18:41:59: 10000000 INFO @ Sat, 24 Aug 2019 18:42:03: 1000000 INFO @ Sat, 24 Aug 2019 18:42:04: 5000000 INFO @ Sat, 24 Aug 2019 18:42:05: 11000000 INFO @ Sat, 24 Aug 2019 18:42:09: 2000000 INFO @ Sat, 24 Aug 2019 18:42:11: 12000000 INFO @ Sat, 24 Aug 2019 18:42:12: 6000000 INFO @ Sat, 24 Aug 2019 18:42:15: 3000000 INFO @ Sat, 24 Aug 2019 18:42:17: 13000000 INFO @ Sat, 24 Aug 2019 18:42:19: 7000000 INFO @ Sat, 24 Aug 2019 18:42:21: 4000000 INFO @ Sat, 24 Aug 2019 18:42:23: 14000000 INFO @ Sat, 24 Aug 2019 18:42:27: 8000000 INFO @ Sat, 24 Aug 2019 18:42:28: 5000000 INFO @ Sat, 24 Aug 2019 18:42:29: 15000000 INFO @ Sat, 24 Aug 2019 18:42:34: 6000000 INFO @ Sat, 24 Aug 2019 18:42:34: 9000000 INFO @ Sat, 24 Aug 2019 18:42:36: 16000000 INFO @ Sat, 24 Aug 2019 18:42:40: 7000000 INFO @ Sat, 24 Aug 2019 18:42:42: 10000000 INFO @ Sat, 24 Aug 2019 18:42:42: 17000000 INFO @ Sat, 24 Aug 2019 18:42:44: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:42:44: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:42:44: #1 total tags in treatment: 17236442 INFO @ Sat, 24 Aug 2019 18:42:44: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:42:44: #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 18:42:44: #1 tags after filtering in treatment: 17236213 INFO @ Sat, 24 Aug 2019 18:42:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:42:44: #1 finished! INFO @ Sat, 24 Aug 2019 18:42:44: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:42:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:42:46: 8000000 INFO @ Sat, 24 Aug 2019 18:42:49: 11000000 INFO @ Sat, 24 Aug 2019 18:42:50: #2 number of paired peaks: 85488 INFO @ Sat, 24 Aug 2019 18:42:50: start model_add_line... INFO @ Sat, 24 Aug 2019 18:42:50: start X-correlation... INFO @ Sat, 24 Aug 2019 18:42:50: end of X-cor INFO @ Sat, 24 Aug 2019 18:42:50: #2 finished! INFO @ Sat, 24 Aug 2019 18:42:50: #2 predicted fragment length is 171 bps INFO @ Sat, 24 Aug 2019 18:42:50: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 24 Aug 2019 18:42:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375054/SRX5375054.05_model.r INFO @ Sat, 24 Aug 2019 18:42:50: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:42:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:42:52: 9000000 INFO @ Sat, 24 Aug 2019 18:42:56: 12000000 INFO @ Sat, 24 Aug 2019 18:42:59: 10000000 INFO @ Sat, 24 Aug 2019 18:43:04: 13000000 INFO @ Sat, 24 Aug 2019 18:43:05: 11000000 INFO @ Sat, 24 Aug 2019 18:43:11: 14000000 INFO @ Sat, 24 Aug 2019 18:43:11: 12000000 INFO @ Sat, 24 Aug 2019 18:43:17: 13000000 INFO @ Sat, 24 Aug 2019 18:43:18: 15000000 INFO @ Sat, 24 Aug 2019 18:43:23: 14000000 INFO @ Sat, 24 Aug 2019 18:43:26: 16000000 INFO @ Sat, 24 Aug 2019 18:43:29: 15000000 INFO @ Sat, 24 Aug 2019 18:43:33: 17000000 INFO @ Sat, 24 Aug 2019 18:43:35: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:43:35: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:43:35: #1 total tags in treatment: 17236442 INFO @ Sat, 24 Aug 2019 18:43:35: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:43:35: #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 18:43:35: 16000000 INFO @ Sat, 24 Aug 2019 18:43:35: #1 tags after filtering in treatment: 17236213 INFO @ Sat, 24 Aug 2019 18:43:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:43:35: #1 finished! INFO @ Sat, 24 Aug 2019 18:43:35: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:43:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:43:41: #2 number of paired peaks: 85488 INFO @ Sat, 24 Aug 2019 18:43:41: start model_add_line... INFO @ Sat, 24 Aug 2019 18:43:41: start X-correlation... INFO @ Sat, 24 Aug 2019 18:43:41: end of X-cor INFO @ Sat, 24 Aug 2019 18:43:41: #2 finished! INFO @ Sat, 24 Aug 2019 18:43:41: #2 predicted fragment length is 171 bps INFO @ Sat, 24 Aug 2019 18:43:41: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 24 Aug 2019 18:43:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375054/SRX5375054.10_model.r INFO @ Sat, 24 Aug 2019 18:43:41: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:43:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:43:42: 17000000 INFO @ Sat, 24 Aug 2019 18:43:43: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:43:43: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:43:43: #1 total tags in treatment: 17236442 INFO @ Sat, 24 Aug 2019 18:43:43: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:43:43: #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 18:43:44: #1 tags after filtering in treatment: 17236213 INFO @ Sat, 24 Aug 2019 18:43:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:43:44: #1 finished! INFO @ Sat, 24 Aug 2019 18:43:44: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:43:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:43:46: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:43:49: #2 number of paired peaks: 85488 INFO @ Sat, 24 Aug 2019 18:43:49: start model_add_line... INFO @ Sat, 24 Aug 2019 18:43:49: start X-correlation... INFO @ Sat, 24 Aug 2019 18:43:49: end of X-cor INFO @ Sat, 24 Aug 2019 18:43:49: #2 finished! INFO @ Sat, 24 Aug 2019 18:43:49: #2 predicted fragment length is 171 bps INFO @ Sat, 24 Aug 2019 18:43:49: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 24 Aug 2019 18:43:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375054/SRX5375054.20_model.r INFO @ Sat, 24 Aug 2019 18:43:49: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:43:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:44:16: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375054/SRX5375054.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:44:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375054/SRX5375054.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:44:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375054/SRX5375054.05_summits.bed INFO @ Sat, 24 Aug 2019 18:44:16: Done! pass1 - making usageList (121 chroms): 8 millis pass2 - checking and writing primary data (35903 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:44:37: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:44:45: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:45:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375054/SRX5375054.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:45:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375054/SRX5375054.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:45:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375054/SRX5375054.10_summits.bed INFO @ Sat, 24 Aug 2019 18:45:07: Done! pass1 - making usageList (91 chroms): 5 millis pass2 - checking and writing primary data (22133 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:45:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375054/SRX5375054.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:45:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375054/SRX5375054.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:45:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375054/SRX5375054.20_summits.bed INFO @ Sat, 24 Aug 2019 18:45:15: Done! pass1 - making usageList (63 chroms): 2 millis pass2 - checking and writing primary data (10129 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。