Job ID = 2640471 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:05:49 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 ) 2019-08-24T08:05:49 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 ) 2019-08-24T08:05:49 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 ) 2019-08-24T08:05:49 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 ) 2019-08-24T08:05:49 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 ) 2019-08-24T08:05:49 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 ) 2019-08-24T08:12:31 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 ) 2019-08-24T08:13:40 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 : 23,426,048 reads read : 46,852,096 reads written : 23,426,048 reads 0-length : 23,426,048 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: 00:17:18 23426048 reads; of these: 23426048 (100.00%) were unpaired; of these: 1767066 (7.54%) aligned 0 times 16187188 (69.10%) aligned exactly 1 time 5471794 (23.36%) aligned >1 times 92.46% overall alignment rate Time searching: 00:17:21 Overall time: 00:17:21 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] 1452545 / 21658982 = 0.0671 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:38:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374986/SRX5374986.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374986/SRX5374986.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374986/SRX5374986.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374986/SRX5374986.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 17:38:24: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:38:24: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:38:31: 1000000 INFO @ Sat, 24 Aug 2019 17:38:37: 2000000 INFO @ Sat, 24 Aug 2019 17:38:43: 3000000 INFO @ Sat, 24 Aug 2019 17:38:50: 4000000 INFO @ Sat, 24 Aug 2019 17:38:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374986/SRX5374986.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374986/SRX5374986.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374986/SRX5374986.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374986/SRX5374986.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 17:38:53: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:38:53: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:38:56: 5000000 INFO @ Sat, 24 Aug 2019 17:39:01: 1000000 INFO @ Sat, 24 Aug 2019 17:39:03: 6000000 INFO @ Sat, 24 Aug 2019 17:39:07: 2000000 INFO @ Sat, 24 Aug 2019 17:39:09: 7000000 INFO @ Sat, 24 Aug 2019 17:39:14: 3000000 INFO @ Sat, 24 Aug 2019 17:39:16: 8000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:39:21: 4000000 INFO @ Sat, 24 Aug 2019 17:39:23: 9000000 INFO @ Sat, 24 Aug 2019 17:39:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374986/SRX5374986.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374986/SRX5374986.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374986/SRX5374986.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374986/SRX5374986.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 17:39:23: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:39:23: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:39:28: 5000000 INFO @ Sat, 24 Aug 2019 17:39:29: 10000000 INFO @ Sat, 24 Aug 2019 17:39:30: 1000000 INFO @ Sat, 24 Aug 2019 17:39:35: 6000000 INFO @ Sat, 24 Aug 2019 17:39:36: 11000000 INFO @ Sat, 24 Aug 2019 17:39:36: 2000000 INFO @ Sat, 24 Aug 2019 17:39:42: 12000000 INFO @ Sat, 24 Aug 2019 17:39:42: 7000000 INFO @ Sat, 24 Aug 2019 17:39:43: 3000000 INFO @ Sat, 24 Aug 2019 17:39:49: 13000000 INFO @ Sat, 24 Aug 2019 17:39:49: 4000000 INFO @ Sat, 24 Aug 2019 17:39:50: 8000000 INFO @ Sat, 24 Aug 2019 17:39:55: 14000000 INFO @ Sat, 24 Aug 2019 17:39:56: 5000000 INFO @ Sat, 24 Aug 2019 17:39:57: 9000000 INFO @ Sat, 24 Aug 2019 17:40:02: 15000000 INFO @ Sat, 24 Aug 2019 17:40:02: 6000000 INFO @ Sat, 24 Aug 2019 17:40:04: 10000000 INFO @ Sat, 24 Aug 2019 17:40:08: 16000000 INFO @ Sat, 24 Aug 2019 17:40:09: 7000000 INFO @ Sat, 24 Aug 2019 17:40:11: 11000000 INFO @ Sat, 24 Aug 2019 17:40:15: 17000000 INFO @ Sat, 24 Aug 2019 17:40:15: 8000000 INFO @ Sat, 24 Aug 2019 17:40:18: 12000000 INFO @ Sat, 24 Aug 2019 17:40:21: 18000000 INFO @ Sat, 24 Aug 2019 17:40:22: 9000000 INFO @ Sat, 24 Aug 2019 17:40:25: 13000000 INFO @ Sat, 24 Aug 2019 17:40:28: 19000000 INFO @ Sat, 24 Aug 2019 17:40:29: 10000000 INFO @ Sat, 24 Aug 2019 17:40:32: 14000000 INFO @ Sat, 24 Aug 2019 17:40:35: 20000000 INFO @ Sat, 24 Aug 2019 17:40:35: 11000000 INFO @ Sat, 24 Aug 2019 17:40:36: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:40:36: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:40:36: #1 total tags in treatment: 20206437 INFO @ Sat, 24 Aug 2019 17:40:36: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:40:36: #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 17:40:37: #1 tags after filtering in treatment: 20206277 INFO @ Sat, 24 Aug 2019 17:40:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:40:37: #1 finished! INFO @ Sat, 24 Aug 2019 17:40:37: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:40:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:40:39: 15000000 INFO @ Sat, 24 Aug 2019 17:40:40: #2 number of paired peaks: 17021 INFO @ Sat, 24 Aug 2019 17:40:40: start model_add_line... INFO @ Sat, 24 Aug 2019 17:40:40: start X-correlation... INFO @ Sat, 24 Aug 2019 17:40:40: end of X-cor INFO @ Sat, 24 Aug 2019 17:40:40: #2 finished! INFO @ Sat, 24 Aug 2019 17:40:40: #2 predicted fragment length is 127 bps INFO @ Sat, 24 Aug 2019 17:40:40: #2 alternative fragment length(s) may be 127 bps INFO @ Sat, 24 Aug 2019 17:40:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374986/SRX5374986.05_model.r INFO @ Sat, 24 Aug 2019 17:40:40: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:40:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:40:42: 12000000 INFO @ Sat, 24 Aug 2019 17:40:46: 16000000 INFO @ Sat, 24 Aug 2019 17:40:48: 13000000 INFO @ Sat, 24 Aug 2019 17:40:53: 17000000 INFO @ Sat, 24 Aug 2019 17:40:55: 14000000 INFO @ Sat, 24 Aug 2019 17:41:00: 18000000 INFO @ Sat, 24 Aug 2019 17:41:01: 15000000 INFO @ Sat, 24 Aug 2019 17:41:07: 19000000 INFO @ Sat, 24 Aug 2019 17:41:08: 16000000 INFO @ Sat, 24 Aug 2019 17:41:15: 17000000 INFO @ Sat, 24 Aug 2019 17:41:15: 20000000 INFO @ Sat, 24 Aug 2019 17:41:17: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:41:17: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:41:17: #1 total tags in treatment: 20206437 INFO @ Sat, 24 Aug 2019 17:41:17: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:41:17: #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 17:41:17: #1 tags after filtering in treatment: 20206277 INFO @ Sat, 24 Aug 2019 17:41:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:41:17: #1 finished! INFO @ Sat, 24 Aug 2019 17:41:17: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:41:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:41:20: #2 number of paired peaks: 17021 INFO @ Sat, 24 Aug 2019 17:41:20: start model_add_line... INFO @ Sat, 24 Aug 2019 17:41:20: start X-correlation... INFO @ Sat, 24 Aug 2019 17:41:20: end of X-cor INFO @ Sat, 24 Aug 2019 17:41:20: #2 finished! INFO @ Sat, 24 Aug 2019 17:41:20: #2 predicted fragment length is 127 bps INFO @ Sat, 24 Aug 2019 17:41:20: #2 alternative fragment length(s) may be 127 bps INFO @ Sat, 24 Aug 2019 17:41:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374986/SRX5374986.10_model.r INFO @ Sat, 24 Aug 2019 17:41:20: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:41:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:41:21: 18000000 INFO @ Sat, 24 Aug 2019 17:41:28: 19000000 INFO @ Sat, 24 Aug 2019 17:41:34: 20000000 INFO @ Sat, 24 Aug 2019 17:41:36: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:41:36: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:41:36: #1 total tags in treatment: 20206437 INFO @ Sat, 24 Aug 2019 17:41:36: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:41:36: #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 17:41:36: #1 tags after filtering in treatment: 20206277 INFO @ Sat, 24 Aug 2019 17:41:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:41:36: #1 finished! INFO @ Sat, 24 Aug 2019 17:41:36: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:41:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:41:39: #2 number of paired peaks: 17021 INFO @ Sat, 24 Aug 2019 17:41:39: start model_add_line... INFO @ Sat, 24 Aug 2019 17:41:39: start X-correlation... INFO @ Sat, 24 Aug 2019 17:41:39: end of X-cor INFO @ Sat, 24 Aug 2019 17:41:39: #2 finished! INFO @ Sat, 24 Aug 2019 17:41:39: #2 predicted fragment length is 127 bps INFO @ Sat, 24 Aug 2019 17:41:39: #2 alternative fragment length(s) may be 127 bps INFO @ Sat, 24 Aug 2019 17:41:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374986/SRX5374986.20_model.r INFO @ Sat, 24 Aug 2019 17:41:39: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:41:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:41:44: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:42:17: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374986/SRX5374986.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:42:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374986/SRX5374986.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:42:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374986/SRX5374986.05_summits.bed INFO @ Sat, 24 Aug 2019 17:42:18: Done! pass1 - making usageList (77 chroms): 4 millis pass2 - checking and writing primary data (9977 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:42:24: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:42:43: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:42:58: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374986/SRX5374986.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:42:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374986/SRX5374986.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:42:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374986/SRX5374986.10_summits.bed INFO @ Sat, 24 Aug 2019 17:42:58: Done! pass1 - making usageList (54 chroms): 3 millis pass2 - checking and writing primary data (6134 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:43:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374986/SRX5374986.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:43:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374986/SRX5374986.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:43:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374986/SRX5374986.20_summits.bed INFO @ Sat, 24 Aug 2019 17:43:31: Done! pass1 - making usageList (44 chroms): 3 millis pass2 - checking and writing primary data (3303 records, 4 fields): 36 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。