Job ID = 2640459 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T07:59:03 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 ) 2019-08-24T07:59:03 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 ) 2019-08-24T07:59:03 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 ) 2019-08-24T07:59:03 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 ) 2019-08-24T07:59:03 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 ) 2019-08-24T08:00:49 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 ) 2019-08-24T08:00:49 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 ) 2019-08-24T08:00:49 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 ) 2019-08-24T08:00:49 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 : 12,795,435 reads read : 25,590,870 reads written : 12,795,435 reads 0-length : 12,795,435 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: 00:11:26 12795435 reads; of these: 12795435 (100.00%) were unpaired; of these: 474564 (3.71%) aligned 0 times 9095485 (71.08%) aligned exactly 1 time 3225386 (25.21%) aligned >1 times 96.29% overall alignment rate Time searching: 00:11:29 Overall time: 00:11:29 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] 866017 / 12320871 = 0.0703 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:19:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374980/SRX5374980.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374980/SRX5374980.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374980/SRX5374980.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374980/SRX5374980.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 17:19:19: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:19:19: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:19:27: 1000000 INFO @ Sat, 24 Aug 2019 17:19:34: 2000000 INFO @ Sat, 24 Aug 2019 17:19:41: 3000000 INFO @ Sat, 24 Aug 2019 17:19:48: 4000000 INFO @ Sat, 24 Aug 2019 17:19:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374980/SRX5374980.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374980/SRX5374980.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374980/SRX5374980.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374980/SRX5374980.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 17:19:49: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:19:49: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:19:55: 5000000 INFO @ Sat, 24 Aug 2019 17:19:55: 1000000 INFO @ Sat, 24 Aug 2019 17:20:02: 2000000 INFO @ Sat, 24 Aug 2019 17:20:02: 6000000 INFO @ Sat, 24 Aug 2019 17:20:09: 3000000 INFO @ Sat, 24 Aug 2019 17:20:09: 7000000 INFO @ Sat, 24 Aug 2019 17:20:15: 4000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:20:16: 8000000 INFO @ Sat, 24 Aug 2019 17:20:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374980/SRX5374980.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374980/SRX5374980.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374980/SRX5374980.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374980/SRX5374980.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 17:20:19: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:20:19: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:20:22: 5000000 INFO @ Sat, 24 Aug 2019 17:20:23: 9000000 INFO @ Sat, 24 Aug 2019 17:20:26: 1000000 INFO @ Sat, 24 Aug 2019 17:20:28: 6000000 INFO @ Sat, 24 Aug 2019 17:20:30: 10000000 INFO @ Sat, 24 Aug 2019 17:20:33: 2000000 INFO @ Sat, 24 Aug 2019 17:20:35: 7000000 INFO @ Sat, 24 Aug 2019 17:20:38: 11000000 INFO @ Sat, 24 Aug 2019 17:20:41: 3000000 INFO @ Sat, 24 Aug 2019 17:20:41: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:20:41: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:20:41: #1 total tags in treatment: 11454854 INFO @ Sat, 24 Aug 2019 17:20:41: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:20:41: #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 17:20:41: #1 tags after filtering in treatment: 11454651 INFO @ Sat, 24 Aug 2019 17:20:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:20:41: #1 finished! INFO @ Sat, 24 Aug 2019 17:20:41: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:20:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:20:42: 8000000 INFO @ Sat, 24 Aug 2019 17:20:43: #2 number of paired peaks: 9096 INFO @ Sat, 24 Aug 2019 17:20:43: start model_add_line... INFO @ Sat, 24 Aug 2019 17:20:43: start X-correlation... INFO @ Sat, 24 Aug 2019 17:20:43: end of X-cor INFO @ Sat, 24 Aug 2019 17:20:43: #2 finished! INFO @ Sat, 24 Aug 2019 17:20:43: #2 predicted fragment length is 110 bps INFO @ Sat, 24 Aug 2019 17:20:43: #2 alternative fragment length(s) may be 110 bps INFO @ Sat, 24 Aug 2019 17:20:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374980/SRX5374980.05_model.r INFO @ Sat, 24 Aug 2019 17:20:43: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:20:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:20:48: 4000000 INFO @ Sat, 24 Aug 2019 17:20:48: 9000000 INFO @ Sat, 24 Aug 2019 17:20:55: 10000000 INFO @ Sat, 24 Aug 2019 17:20:55: 5000000 INFO @ Sat, 24 Aug 2019 17:21:02: 11000000 INFO @ Sat, 24 Aug 2019 17:21:02: 6000000 INFO @ Sat, 24 Aug 2019 17:21:05: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:21:05: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:21:05: #1 total tags in treatment: 11454854 INFO @ Sat, 24 Aug 2019 17:21:05: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:21:05: #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 17:21:05: #1 tags after filtering in treatment: 11454651 INFO @ Sat, 24 Aug 2019 17:21:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:21:05: #1 finished! INFO @ Sat, 24 Aug 2019 17:21:05: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:21:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:21:07: #2 number of paired peaks: 9096 INFO @ Sat, 24 Aug 2019 17:21:07: start model_add_line... INFO @ Sat, 24 Aug 2019 17:21:07: start X-correlation... INFO @ Sat, 24 Aug 2019 17:21:07: end of X-cor INFO @ Sat, 24 Aug 2019 17:21:07: #2 finished! INFO @ Sat, 24 Aug 2019 17:21:07: #2 predicted fragment length is 110 bps INFO @ Sat, 24 Aug 2019 17:21:07: #2 alternative fragment length(s) may be 110 bps INFO @ Sat, 24 Aug 2019 17:21:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374980/SRX5374980.10_model.r INFO @ Sat, 24 Aug 2019 17:21:07: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:21:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:21:09: 7000000 INFO @ Sat, 24 Aug 2019 17:21:16: 8000000 INFO @ Sat, 24 Aug 2019 17:21:20: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:21:23: 9000000 INFO @ Sat, 24 Aug 2019 17:21:30: 10000000 INFO @ Sat, 24 Aug 2019 17:21:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374980/SRX5374980.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:21:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374980/SRX5374980.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:21:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374980/SRX5374980.05_summits.bed INFO @ Sat, 24 Aug 2019 17:21:37: Done! pass1 - making usageList (45 chroms): 2 millis pass2 - checking and writing primary data (2069 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:21:38: 11000000 INFO @ Sat, 24 Aug 2019 17:21:41: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:21:41: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:21:41: #1 total tags in treatment: 11454854 INFO @ Sat, 24 Aug 2019 17:21:41: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:21:41: #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 17:21:41: #1 tags after filtering in treatment: 11454651 INFO @ Sat, 24 Aug 2019 17:21:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:21:41: #1 finished! INFO @ Sat, 24 Aug 2019 17:21:41: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:21:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:21:43: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:21:43: #2 number of paired peaks: 9096 INFO @ Sat, 24 Aug 2019 17:21:43: start model_add_line... INFO @ Sat, 24 Aug 2019 17:21:43: start X-correlation... INFO @ Sat, 24 Aug 2019 17:21:43: end of X-cor INFO @ Sat, 24 Aug 2019 17:21:43: #2 finished! INFO @ Sat, 24 Aug 2019 17:21:43: #2 predicted fragment length is 110 bps INFO @ Sat, 24 Aug 2019 17:21:43: #2 alternative fragment length(s) may be 110 bps INFO @ Sat, 24 Aug 2019 17:21:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374980/SRX5374980.20_model.r INFO @ Sat, 24 Aug 2019 17:21:43: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:21:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:22:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374980/SRX5374980.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:22:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374980/SRX5374980.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:22:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374980/SRX5374980.10_summits.bed INFO @ Sat, 24 Aug 2019 17:22:01: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (1053 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:22:20: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:22:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374980/SRX5374980.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:22:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374980/SRX5374980.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:22:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374980/SRX5374980.20_summits.bed INFO @ Sat, 24 Aug 2019 17:22:37: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (441 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。