Job ID = 2640442 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T07:43:31 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 ) 2019-08-24T07:43:31 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 ) 2019-08-24T07:43:31 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 ) 2019-08-24T07:54:51 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 ) 2019-08-24T07:54:51 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 ) 2019-08-24T07:54:51 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 ) 2019-08-24T07:58:23 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 ) 2019-08-24T07:59:18 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 ) 2019-08-24T07:59:18 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 ) 2019-08-24T08:00:43 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 ) 2019-08-24T08:00:43 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 : 38,240,996 reads read : 76,481,992 reads written : 38,240,996 reads 0-length : 38,240,996 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: 00:30:19 38240996 reads; of these: 38240996 (100.00%) were unpaired; of these: 4779743 (12.50%) aligned 0 times 26810408 (70.11%) aligned exactly 1 time 6650845 (17.39%) aligned >1 times 87.50% overall alignment rate Time searching: 00:30:22 Overall time: 00:30:22 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 16 files... [bam_rmdupse_core] 6420669 / 33461253 = 0.1919 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:00:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4320108/SRX4320108.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4320108/SRX4320108.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4320108/SRX4320108.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4320108/SRX4320108.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 18:00:13: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:00:13: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:00:22: 1000000 INFO @ Sat, 24 Aug 2019 18:00:30: 2000000 INFO @ Sat, 24 Aug 2019 18:00:38: 3000000 INFO @ Sat, 24 Aug 2019 18:00:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4320108/SRX4320108.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4320108/SRX4320108.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4320108/SRX4320108.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4320108/SRX4320108.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 18:00:42: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:00:42: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:00:46: 4000000 INFO @ Sat, 24 Aug 2019 18:00:51: 1000000 INFO @ Sat, 24 Aug 2019 18:00:55: 5000000 INFO @ Sat, 24 Aug 2019 18:00:59: 2000000 INFO @ Sat, 24 Aug 2019 18:01:03: 6000000 INFO @ Sat, 24 Aug 2019 18:01:07: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:01:12: 7000000 INFO @ Sat, 24 Aug 2019 18:01:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4320108/SRX4320108.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4320108/SRX4320108.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4320108/SRX4320108.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4320108/SRX4320108.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 18:01:12: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:01:12: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:01:16: 4000000 INFO @ Sat, 24 Aug 2019 18:01:21: 8000000 INFO @ Sat, 24 Aug 2019 18:01:21: 1000000 INFO @ Sat, 24 Aug 2019 18:01:24: 5000000 INFO @ Sat, 24 Aug 2019 18:01:29: 2000000 INFO @ Sat, 24 Aug 2019 18:01:29: 9000000 INFO @ Sat, 24 Aug 2019 18:01:32: 6000000 INFO @ Sat, 24 Aug 2019 18:01:37: 3000000 INFO @ Sat, 24 Aug 2019 18:01:38: 10000000 INFO @ Sat, 24 Aug 2019 18:01:41: 7000000 INFO @ Sat, 24 Aug 2019 18:01:45: 4000000 INFO @ Sat, 24 Aug 2019 18:01:47: 11000000 INFO @ Sat, 24 Aug 2019 18:01:49: 8000000 INFO @ Sat, 24 Aug 2019 18:01:53: 5000000 INFO @ Sat, 24 Aug 2019 18:01:56: 12000000 INFO @ Sat, 24 Aug 2019 18:01:59: 9000000 INFO @ Sat, 24 Aug 2019 18:02:05: 6000000 INFO @ Sat, 24 Aug 2019 18:02:09: 13000000 INFO @ Sat, 24 Aug 2019 18:02:11: 10000000 INFO @ Sat, 24 Aug 2019 18:02:16: 7000000 INFO @ Sat, 24 Aug 2019 18:02:18: 14000000 INFO @ Sat, 24 Aug 2019 18:02:20: 11000000 INFO @ Sat, 24 Aug 2019 18:02:24: 8000000 INFO @ Sat, 24 Aug 2019 18:02:26: 15000000 INFO @ Sat, 24 Aug 2019 18:02:28: 12000000 INFO @ Sat, 24 Aug 2019 18:02:32: 9000000 INFO @ Sat, 24 Aug 2019 18:02:34: 16000000 INFO @ Sat, 24 Aug 2019 18:02:37: 13000000 INFO @ Sat, 24 Aug 2019 18:02:40: 10000000 INFO @ Sat, 24 Aug 2019 18:02:42: 17000000 INFO @ Sat, 24 Aug 2019 18:02:45: 14000000 INFO @ Sat, 24 Aug 2019 18:02:48: 11000000 INFO @ Sat, 24 Aug 2019 18:02:50: 18000000 INFO @ Sat, 24 Aug 2019 18:02:54: 15000000 INFO @ Sat, 24 Aug 2019 18:02:56: 12000000 INFO @ Sat, 24 Aug 2019 18:02:58: 19000000 INFO @ Sat, 24 Aug 2019 18:03:02: 16000000 INFO @ Sat, 24 Aug 2019 18:03:05: 13000000 INFO @ Sat, 24 Aug 2019 18:03:06: 20000000 INFO @ Sat, 24 Aug 2019 18:03:10: 17000000 INFO @ Sat, 24 Aug 2019 18:03:13: 14000000 INFO @ Sat, 24 Aug 2019 18:03:15: 21000000 INFO @ Sat, 24 Aug 2019 18:03:18: 18000000 INFO @ Sat, 24 Aug 2019 18:03:22: 15000000 INFO @ Sat, 24 Aug 2019 18:03:23: 22000000 INFO @ Sat, 24 Aug 2019 18:03:27: 19000000 INFO @ Sat, 24 Aug 2019 18:03:30: 16000000 INFO @ Sat, 24 Aug 2019 18:03:31: 23000000 INFO @ Sat, 24 Aug 2019 18:03:35: 20000000 INFO @ Sat, 24 Aug 2019 18:03:38: 17000000 INFO @ Sat, 24 Aug 2019 18:03:40: 24000000 INFO @ Sat, 24 Aug 2019 18:03:43: 21000000 INFO @ Sat, 24 Aug 2019 18:03:47: 18000000 INFO @ Sat, 24 Aug 2019 18:03:48: 25000000 INFO @ Sat, 24 Aug 2019 18:03:52: 22000000 INFO @ Sat, 24 Aug 2019 18:03:55: 19000000 INFO @ Sat, 24 Aug 2019 18:03:56: 26000000 INFO @ Sat, 24 Aug 2019 18:04:00: 23000000 INFO @ Sat, 24 Aug 2019 18:04:03: 20000000 INFO @ Sat, 24 Aug 2019 18:04:05: 27000000 INFO @ Sat, 24 Aug 2019 18:04:05: #1 tag size is determined as 75 bps INFO @ Sat, 24 Aug 2019 18:04:05: #1 tag size = 75 INFO @ Sat, 24 Aug 2019 18:04:05: #1 total tags in treatment: 27040584 INFO @ Sat, 24 Aug 2019 18:04:05: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:04:05: #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 18:04:06: #1 tags after filtering in treatment: 27040454 INFO @ Sat, 24 Aug 2019 18:04:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:04:06: #1 finished! INFO @ Sat, 24 Aug 2019 18:04:06: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:04:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:04:08: 24000000 INFO @ Sat, 24 Aug 2019 18:04:10: #2 number of paired peaks: 16629 INFO @ Sat, 24 Aug 2019 18:04:10: start model_add_line... INFO @ Sat, 24 Aug 2019 18:04:10: start X-correlation... INFO @ Sat, 24 Aug 2019 18:04:10: end of X-cor INFO @ Sat, 24 Aug 2019 18:04:10: #2 finished! INFO @ Sat, 24 Aug 2019 18:04:10: #2 predicted fragment length is 155 bps INFO @ Sat, 24 Aug 2019 18:04:10: #2 alternative fragment length(s) may be 155 bps INFO @ Sat, 24 Aug 2019 18:04:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4320108/SRX4320108.05_model.r INFO @ Sat, 24 Aug 2019 18:04:10: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:04:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:04:11: 21000000 INFO @ Sat, 24 Aug 2019 18:04:16: 25000000 INFO @ Sat, 24 Aug 2019 18:04:20: 22000000 INFO @ Sat, 24 Aug 2019 18:04:25: 26000000 INFO @ Sat, 24 Aug 2019 18:04:28: 23000000 INFO @ Sat, 24 Aug 2019 18:04:33: 27000000 INFO @ Sat, 24 Aug 2019 18:04:34: #1 tag size is determined as 75 bps INFO @ Sat, 24 Aug 2019 18:04:34: #1 tag size = 75 INFO @ Sat, 24 Aug 2019 18:04:34: #1 total tags in treatment: 27040584 INFO @ Sat, 24 Aug 2019 18:04:34: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:04:34: #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 18:04:34: #1 tags after filtering in treatment: 27040454 INFO @ Sat, 24 Aug 2019 18:04:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:04:34: #1 finished! INFO @ Sat, 24 Aug 2019 18:04:34: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:04:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:04:36: 24000000 INFO @ Sat, 24 Aug 2019 18:04:38: #2 number of paired peaks: 16629 INFO @ Sat, 24 Aug 2019 18:04:38: start model_add_line... INFO @ Sat, 24 Aug 2019 18:04:38: start X-correlation... INFO @ Sat, 24 Aug 2019 18:04:38: end of X-cor INFO @ Sat, 24 Aug 2019 18:04:38: #2 finished! INFO @ Sat, 24 Aug 2019 18:04:38: #2 predicted fragment length is 155 bps INFO @ Sat, 24 Aug 2019 18:04:38: #2 alternative fragment length(s) may be 155 bps INFO @ Sat, 24 Aug 2019 18:04:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4320108/SRX4320108.10_model.r INFO @ Sat, 24 Aug 2019 18:04:38: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:04:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:04:44: 25000000 INFO @ Sat, 24 Aug 2019 18:04:52: 26000000 INFO @ Sat, 24 Aug 2019 18:05:00: 27000000 INFO @ Sat, 24 Aug 2019 18:05:01: #1 tag size is determined as 75 bps INFO @ Sat, 24 Aug 2019 18:05:01: #1 tag size = 75 INFO @ Sat, 24 Aug 2019 18:05:01: #1 total tags in treatment: 27040584 INFO @ Sat, 24 Aug 2019 18:05:01: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:05:01: #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 18:05:02: #1 tags after filtering in treatment: 27040454 INFO @ Sat, 24 Aug 2019 18:05:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:05:02: #1 finished! INFO @ Sat, 24 Aug 2019 18:05:02: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:05:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:05:05: #2 number of paired peaks: 16629 INFO @ Sat, 24 Aug 2019 18:05:05: start model_add_line... INFO @ Sat, 24 Aug 2019 18:05:06: start X-correlation... INFO @ Sat, 24 Aug 2019 18:05:06: end of X-cor INFO @ Sat, 24 Aug 2019 18:05:06: #2 finished! INFO @ Sat, 24 Aug 2019 18:05:06: #2 predicted fragment length is 155 bps INFO @ Sat, 24 Aug 2019 18:05:06: #2 alternative fragment length(s) may be 155 bps INFO @ Sat, 24 Aug 2019 18:05:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4320108/SRX4320108.20_model.r INFO @ Sat, 24 Aug 2019 18:05:06: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:05:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:05:36: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:06:03: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:06:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4320108/SRX4320108.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:06:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4320108/SRX4320108.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:06:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4320108/SRX4320108.05_summits.bed INFO @ Sat, 24 Aug 2019 18:06:22: Done! pass1 - making usageList (89 chroms): 4 millis pass2 - checking and writing primary data (8789 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:06:31: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:06:47: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4320108/SRX4320108.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:06:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4320108/SRX4320108.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:06:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4320108/SRX4320108.10_summits.bed INFO @ Sat, 24 Aug 2019 18:06:47: Done! pass1 - making usageList (58 chroms): 2 millis pass2 - checking and writing primary data (2238 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:07:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4320108/SRX4320108.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:07:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4320108/SRX4320108.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:07:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4320108/SRX4320108.20_summits.bed INFO @ Sat, 24 Aug 2019 18:07:15: Done! pass1 - making usageList (36 chroms): 2 millis pass2 - checking and writing primary data (429 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。