Job ID = 2640722 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T09:29:18 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 ) 2019-08-24T09:29:18 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 ) 2019-08-24T09:29:18 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 ) 2019-08-24T09:33:05 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 ) 2019-08-24T09:33:05 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 ) 2019-08-24T09:33:27 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 ) 2019-08-24T09:33:27 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 : 24,054,612 reads read : 24,054,612 reads written : 24,054,612 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: 00:00:00 Multiseed full-index search: 00:07:16 24054612 reads; of these: 24054612 (100.00%) were unpaired; of these: 16252394 (67.56%) aligned 0 times 5974827 (24.84%) aligned exactly 1 time 1827391 (7.60%) aligned >1 times 32.44% overall alignment rate Time searching: 00:07:19 Overall time: 00:07:19 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_rmdupse_core] 2098090 / 7802218 = 0.2689 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:50:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX555166/SRX555166.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX555166/SRX555166.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX555166/SRX555166.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX555166/SRX555166.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 18:50:17: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:50:17: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:50:25: 1000000 INFO @ Sat, 24 Aug 2019 18:50:34: 2000000 INFO @ Sat, 24 Aug 2019 18:50:43: 3000000 INFO @ Sat, 24 Aug 2019 18:50:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX555166/SRX555166.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX555166/SRX555166.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX555166/SRX555166.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX555166/SRX555166.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 18:50:46: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:50:46: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:50:52: 4000000 INFO @ Sat, 24 Aug 2019 18:50:55: 1000000 INFO @ Sat, 24 Aug 2019 18:51:01: 5000000 INFO @ Sat, 24 Aug 2019 18:51:04: 2000000 INFO @ Sat, 24 Aug 2019 18:51:07: #1 tag size is determined as 44 bps INFO @ Sat, 24 Aug 2019 18:51:07: #1 tag size = 44 INFO @ Sat, 24 Aug 2019 18:51:07: #1 total tags in treatment: 5704128 INFO @ Sat, 24 Aug 2019 18:51:07: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:51:07: #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 18:51:08: #1 tags after filtering in treatment: 5703864 INFO @ Sat, 24 Aug 2019 18:51:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:51:08: #1 finished! INFO @ Sat, 24 Aug 2019 18:51:08: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:51:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:51:10: #2 number of paired peaks: 26759 INFO @ Sat, 24 Aug 2019 18:51:10: start model_add_line... INFO @ Sat, 24 Aug 2019 18:51:10: start X-correlation... INFO @ Sat, 24 Aug 2019 18:51:10: end of X-cor INFO @ Sat, 24 Aug 2019 18:51:10: #2 finished! INFO @ Sat, 24 Aug 2019 18:51:10: #2 predicted fragment length is 121 bps INFO @ Sat, 24 Aug 2019 18:51:10: #2 alternative fragment length(s) may be 49,121 bps INFO @ Sat, 24 Aug 2019 18:51:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX555166/SRX555166.05_model.r INFO @ Sat, 24 Aug 2019 18:51:10: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:51:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:51:13: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:51:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX555166/SRX555166.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX555166/SRX555166.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX555166/SRX555166.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX555166/SRX555166.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 18:51:16: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:51:16: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:51:22: 4000000 INFO @ Sat, 24 Aug 2019 18:51:25: 1000000 INFO @ Sat, 24 Aug 2019 18:51:28: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:51:31: 5000000 INFO @ Sat, 24 Aug 2019 18:51:34: 2000000 INFO @ Sat, 24 Aug 2019 18:51:37: #1 tag size is determined as 44 bps INFO @ Sat, 24 Aug 2019 18:51:37: #1 tag size = 44 INFO @ Sat, 24 Aug 2019 18:51:37: #1 total tags in treatment: 5704128 INFO @ Sat, 24 Aug 2019 18:51:37: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:51:37: #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 18:51:37: #1 tags after filtering in treatment: 5703864 INFO @ Sat, 24 Aug 2019 18:51:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:51:37: #1 finished! INFO @ Sat, 24 Aug 2019 18:51:37: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:51:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:51:38: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX555166/SRX555166.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:51:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX555166/SRX555166.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:51:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX555166/SRX555166.05_summits.bed INFO @ Sat, 24 Aug 2019 18:51:38: Done! pass1 - making usageList (60 chroms): 2 millis pass2 - checking and writing primary data (653 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:51:40: #2 number of paired peaks: 26759 INFO @ Sat, 24 Aug 2019 18:51:40: start model_add_line... INFO @ Sat, 24 Aug 2019 18:51:40: start X-correlation... INFO @ Sat, 24 Aug 2019 18:51:40: end of X-cor INFO @ Sat, 24 Aug 2019 18:51:40: #2 finished! INFO @ Sat, 24 Aug 2019 18:51:40: #2 predicted fragment length is 121 bps INFO @ Sat, 24 Aug 2019 18:51:40: #2 alternative fragment length(s) may be 49,121 bps INFO @ Sat, 24 Aug 2019 18:51:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX555166/SRX555166.10_model.r INFO @ Sat, 24 Aug 2019 18:51:40: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:51:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:51:41: 3000000 INFO @ Sat, 24 Aug 2019 18:51:49: 4000000 INFO @ Sat, 24 Aug 2019 18:51:57: 5000000 INFO @ Sat, 24 Aug 2019 18:51:58: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:52:02: #1 tag size is determined as 44 bps INFO @ Sat, 24 Aug 2019 18:52:02: #1 tag size = 44 INFO @ Sat, 24 Aug 2019 18:52:02: #1 total tags in treatment: 5704128 INFO @ Sat, 24 Aug 2019 18:52:02: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:52:02: #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 18:52:02: #1 tags after filtering in treatment: 5703864 INFO @ Sat, 24 Aug 2019 18:52:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:52:02: #1 finished! INFO @ Sat, 24 Aug 2019 18:52:02: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:52:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:52:05: #2 number of paired peaks: 26759 INFO @ Sat, 24 Aug 2019 18:52:05: start model_add_line... INFO @ Sat, 24 Aug 2019 18:52:05: start X-correlation... INFO @ Sat, 24 Aug 2019 18:52:05: end of X-cor INFO @ Sat, 24 Aug 2019 18:52:05: #2 finished! INFO @ Sat, 24 Aug 2019 18:52:05: #2 predicted fragment length is 121 bps INFO @ Sat, 24 Aug 2019 18:52:05: #2 alternative fragment length(s) may be 49,121 bps INFO @ Sat, 24 Aug 2019 18:52:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX555166/SRX555166.20_model.r INFO @ Sat, 24 Aug 2019 18:52:05: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:52:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:52:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX555166/SRX555166.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:52:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX555166/SRX555166.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:52:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX555166/SRX555166.10_summits.bed INFO @ Sat, 24 Aug 2019 18:52:07: Done! pass1 - making usageList (53 chroms): 2 millis pass2 - checking and writing primary data (360 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:52:23: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:52:32: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX555166/SRX555166.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:52:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX555166/SRX555166.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:52:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX555166/SRX555166.20_summits.bed INFO @ Sat, 24 Aug 2019 18:52:32: Done! pass1 - making usageList (47 chroms): 1 millis pass2 - checking and writing primary data (168 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。