Job ID = 2003220 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T03:07:44 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 ) 2019-07-05T03:07:51 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 ) 2019-07-05T03:13:39 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 ) 2019-07-05T03:15:50 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 : 43,546,697 reads read : 43,546,697 reads written : 43,546,697 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: 00:00:01 Multiseed full-index search: 00:15:36 43546697 reads; of these: 43546697 (100.00%) were unpaired; of these: 5114019 (11.74%) aligned 0 times 28113755 (64.56%) aligned exactly 1 time 10318923 (23.70%) aligned >1 times 88.26% overall alignment rate Time searching: 00:15:40 Overall time: 00:15:40 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] 1419331 / 38432678 = 0.0369 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 12:58:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX181519/SRX181519.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX181519/SRX181519.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX181519/SRX181519.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX181519/SRX181519.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 @ Fri, 05 Jul 2019 12:58:40: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:58:40: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:58:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX181519/SRX181519.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX181519/SRX181519.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX181519/SRX181519.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX181519/SRX181519.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 @ Fri, 05 Jul 2019 12:58:40: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:58:40: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:58:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX181519/SRX181519.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX181519/SRX181519.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX181519/SRX181519.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX181519/SRX181519.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 @ Fri, 05 Jul 2019 12:58:40: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:58:40: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:58:46: 1000000 INFO @ Fri, 05 Jul 2019 12:58:46: 1000000 INFO @ Fri, 05 Jul 2019 12:58:47: 1000000 INFO @ Fri, 05 Jul 2019 12:58:52: 2000000 INFO @ Fri, 05 Jul 2019 12:58:52: 2000000 INFO @ Fri, 05 Jul 2019 12:58:54: 2000000 INFO @ Fri, 05 Jul 2019 12:58:58: 3000000 INFO @ Fri, 05 Jul 2019 12:58:58: 3000000 INFO @ Fri, 05 Jul 2019 12:59:00: 3000000 INFO @ Fri, 05 Jul 2019 12:59:05: 4000000 INFO @ Fri, 05 Jul 2019 12:59:05: 4000000 INFO @ Fri, 05 Jul 2019 12:59:07: 4000000 INFO @ Fri, 05 Jul 2019 12:59:11: 5000000 INFO @ Fri, 05 Jul 2019 12:59:11: 5000000 INFO @ Fri, 05 Jul 2019 12:59:13: 5000000 INFO @ Fri, 05 Jul 2019 12:59:17: 6000000 INFO @ Fri, 05 Jul 2019 12:59:17: 6000000 INFO @ Fri, 05 Jul 2019 12:59:20: 6000000 INFO @ Fri, 05 Jul 2019 12:59:23: 7000000 INFO @ Fri, 05 Jul 2019 12:59:23: 7000000 INFO @ Fri, 05 Jul 2019 12:59:26: 7000000 INFO @ Fri, 05 Jul 2019 12:59:29: 8000000 INFO @ Fri, 05 Jul 2019 12:59:29: 8000000 INFO @ Fri, 05 Jul 2019 12:59:33: 8000000 INFO @ Fri, 05 Jul 2019 12:59:36: 9000000 INFO @ Fri, 05 Jul 2019 12:59:36: 9000000 INFO @ Fri, 05 Jul 2019 12:59:39: 9000000 INFO @ Fri, 05 Jul 2019 12:59:42: 10000000 INFO @ Fri, 05 Jul 2019 12:59:42: 10000000 INFO @ Fri, 05 Jul 2019 12:59:46: 10000000 INFO @ Fri, 05 Jul 2019 12:59:49: 11000000 INFO @ Fri, 05 Jul 2019 12:59:49: 11000000 INFO @ Fri, 05 Jul 2019 12:59:52: 11000000 INFO @ Fri, 05 Jul 2019 12:59:55: 12000000 INFO @ Fri, 05 Jul 2019 12:59:55: 12000000 INFO @ Fri, 05 Jul 2019 12:59:59: 12000000 INFO @ Fri, 05 Jul 2019 13:00:01: 13000000 INFO @ Fri, 05 Jul 2019 13:00:01: 13000000 INFO @ Fri, 05 Jul 2019 13:00:05: 13000000 INFO @ Fri, 05 Jul 2019 13:00:08: 14000000 INFO @ Fri, 05 Jul 2019 13:00:08: 14000000 INFO @ Fri, 05 Jul 2019 13:00:12: 14000000 INFO @ Fri, 05 Jul 2019 13:00:14: 15000000 INFO @ Fri, 05 Jul 2019 13:00:14: 15000000 INFO @ Fri, 05 Jul 2019 13:00:18: 15000000 INFO @ Fri, 05 Jul 2019 13:00:20: 16000000 INFO @ Fri, 05 Jul 2019 13:00:20: 16000000 INFO @ Fri, 05 Jul 2019 13:00:25: 16000000 INFO @ Fri, 05 Jul 2019 13:00:26: 17000000 INFO @ Fri, 05 Jul 2019 13:00:26: 17000000 INFO @ Fri, 05 Jul 2019 13:00:31: 17000000 INFO @ Fri, 05 Jul 2019 13:00:32: 18000000 INFO @ Fri, 05 Jul 2019 13:00:32: 18000000 INFO @ Fri, 05 Jul 2019 13:00:37: 18000000 INFO @ Fri, 05 Jul 2019 13:00:38: 19000000 INFO @ Fri, 05 Jul 2019 13:00:38: 19000000 INFO @ Fri, 05 Jul 2019 13:00:44: 19000000 INFO @ Fri, 05 Jul 2019 13:00:44: 20000000 INFO @ Fri, 05 Jul 2019 13:00:44: 20000000 INFO @ Fri, 05 Jul 2019 13:00:50: 21000000 INFO @ Fri, 05 Jul 2019 13:00:50: 21000000 INFO @ Fri, 05 Jul 2019 13:00:51: 20000000 INFO @ Fri, 05 Jul 2019 13:00:56: 22000000 INFO @ Fri, 05 Jul 2019 13:00:56: 22000000 INFO @ Fri, 05 Jul 2019 13:00:58: 21000000 INFO @ Fri, 05 Jul 2019 13:01:02: 23000000 INFO @ Fri, 05 Jul 2019 13:01:02: 23000000 INFO @ Fri, 05 Jul 2019 13:01:04: 22000000 INFO @ Fri, 05 Jul 2019 13:01:08: 24000000 INFO @ Fri, 05 Jul 2019 13:01:08: 24000000 INFO @ Fri, 05 Jul 2019 13:01:11: 23000000 INFO @ Fri, 05 Jul 2019 13:01:14: 25000000 INFO @ Fri, 05 Jul 2019 13:01:14: 25000000 INFO @ Fri, 05 Jul 2019 13:01:18: 24000000 INFO @ Fri, 05 Jul 2019 13:01:20: 26000000 INFO @ Fri, 05 Jul 2019 13:01:20: 26000000 INFO @ Fri, 05 Jul 2019 13:01:24: 25000000 INFO @ Fri, 05 Jul 2019 13:01:27: 27000000 INFO @ Fri, 05 Jul 2019 13:01:27: 27000000 INFO @ Fri, 05 Jul 2019 13:01:30: 26000000 INFO @ Fri, 05 Jul 2019 13:01:33: 28000000 INFO @ Fri, 05 Jul 2019 13:01:33: 28000000 INFO @ Fri, 05 Jul 2019 13:01:37: 27000000 INFO @ Fri, 05 Jul 2019 13:01:39: 29000000 INFO @ Fri, 05 Jul 2019 13:01:39: 29000000 INFO @ Fri, 05 Jul 2019 13:01:43: 28000000 INFO @ Fri, 05 Jul 2019 13:01:45: 30000000 INFO @ Fri, 05 Jul 2019 13:01:45: 30000000 INFO @ Fri, 05 Jul 2019 13:01:50: 29000000 INFO @ Fri, 05 Jul 2019 13:01:52: 31000000 INFO @ Fri, 05 Jul 2019 13:01:52: 31000000 INFO @ Fri, 05 Jul 2019 13:01:56: 30000000 INFO @ Fri, 05 Jul 2019 13:01:58: 32000000 INFO @ Fri, 05 Jul 2019 13:01:58: 32000000 INFO @ Fri, 05 Jul 2019 13:02:03: 31000000 INFO @ Fri, 05 Jul 2019 13:02:04: 33000000 INFO @ Fri, 05 Jul 2019 13:02:04: 33000000 INFO @ Fri, 05 Jul 2019 13:02:09: 32000000 INFO @ Fri, 05 Jul 2019 13:02:10: 34000000 INFO @ Fri, 05 Jul 2019 13:02:10: 34000000 INFO @ Fri, 05 Jul 2019 13:02:16: 33000000 INFO @ Fri, 05 Jul 2019 13:02:16: 35000000 INFO @ Fri, 05 Jul 2019 13:02:16: 35000000 INFO @ Fri, 05 Jul 2019 13:02:22: 36000000 INFO @ Fri, 05 Jul 2019 13:02:22: 34000000 INFO @ Fri, 05 Jul 2019 13:02:22: 36000000 INFO @ Fri, 05 Jul 2019 13:02:28: 37000000 INFO @ Fri, 05 Jul 2019 13:02:28: 37000000 INFO @ Fri, 05 Jul 2019 13:02:29: 35000000 INFO @ Fri, 05 Jul 2019 13:02:29: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 13:02:29: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 13:02:29: #1 total tags in treatment: 37013347 INFO @ Fri, 05 Jul 2019 13:02:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:02:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 13:02:29: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 13:02:29: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 13:02:29: #1 total tags in treatment: 37013347 INFO @ Fri, 05 Jul 2019 13:02:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:02:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 13:02:30: #1 tags after filtering in treatment: 37013263 INFO @ Fri, 05 Jul 2019 13:02:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:02:30: #1 finished! INFO @ Fri, 05 Jul 2019 13:02:30: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:02:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:02:30: #1 tags after filtering in treatment: 37013263 INFO @ Fri, 05 Jul 2019 13:02:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:02:30: #1 finished! INFO @ Fri, 05 Jul 2019 13:02:30: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:02:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:02:33: #2 number of paired peaks: 8495 INFO @ Fri, 05 Jul 2019 13:02:33: start model_add_line... INFO @ Fri, 05 Jul 2019 13:02:33: #2 number of paired peaks: 8495 INFO @ Fri, 05 Jul 2019 13:02:33: start model_add_line... INFO @ Fri, 05 Jul 2019 13:02:33: start X-correlation... INFO @ Fri, 05 Jul 2019 13:02:33: start X-correlation... INFO @ Fri, 05 Jul 2019 13:02:33: end of X-cor INFO @ Fri, 05 Jul 2019 13:02:33: end of X-cor INFO @ Fri, 05 Jul 2019 13:02:33: #2 finished! INFO @ Fri, 05 Jul 2019 13:02:33: #2 finished! INFO @ Fri, 05 Jul 2019 13:02:33: #2 predicted fragment length is 109 bps INFO @ Fri, 05 Jul 2019 13:02:33: #2 predicted fragment length is 109 bps INFO @ Fri, 05 Jul 2019 13:02:33: #2 alternative fragment length(s) may be 109 bps INFO @ Fri, 05 Jul 2019 13:02:33: #2 alternative fragment length(s) may be 109 bps INFO @ Fri, 05 Jul 2019 13:02:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX181519/SRX181519.05_model.r INFO @ Fri, 05 Jul 2019 13:02:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX181519/SRX181519.10_model.r INFO @ Fri, 05 Jul 2019 13:02:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:02:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:02:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:02:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:02:35: 36000000 INFO @ Fri, 05 Jul 2019 13:02:40: 37000000 INFO @ Fri, 05 Jul 2019 13:02:41: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 13:02:41: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 13:02:41: #1 total tags in treatment: 37013347 INFO @ Fri, 05 Jul 2019 13:02:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:02:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 13:02:41: #1 tags after filtering in treatment: 37013263 INFO @ Fri, 05 Jul 2019 13:02:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:02:41: #1 finished! INFO @ Fri, 05 Jul 2019 13:02:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:02:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:02:45: #2 number of paired peaks: 8495 INFO @ Fri, 05 Jul 2019 13:02:45: start model_add_line... INFO @ Fri, 05 Jul 2019 13:02:45: start X-correlation... INFO @ Fri, 05 Jul 2019 13:02:45: end of X-cor INFO @ Fri, 05 Jul 2019 13:02:45: #2 finished! INFO @ Fri, 05 Jul 2019 13:02:45: #2 predicted fragment length is 109 bps INFO @ Fri, 05 Jul 2019 13:02:45: #2 alternative fragment length(s) may be 109 bps INFO @ Fri, 05 Jul 2019 13:02:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX181519/SRX181519.20_model.r INFO @ Fri, 05 Jul 2019 13:02:45: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:02:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:03:45: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:03:45: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:03:56: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:04:26: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX181519/SRX181519.10_peaks.xls INFO @ Fri, 05 Jul 2019 13:04:26: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX181519/SRX181519.05_peaks.xls INFO @ Fri, 05 Jul 2019 13:04:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX181519/SRX181519.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:04:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX181519/SRX181519.10_summits.bed INFO @ Fri, 05 Jul 2019 13:04:26: Done! INFO @ Fri, 05 Jul 2019 13:04:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX181519/SRX181519.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:04:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX181519/SRX181519.05_summits.bed INFO @ Fri, 05 Jul 2019 13:04:26: Done! pass1 - making usageList (54 chroms): 1 millis pass2 - checking and writing primary data (5394 records, 4 fields): 11 millis pass1 - making usageList (72 chroms): 2 millis pass2 - checking and writing primary data (10183 records, 4 fields): 16 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 13:04:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX181519/SRX181519.20_peaks.xls INFO @ Fri, 05 Jul 2019 13:04:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX181519/SRX181519.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:04:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX181519/SRX181519.20_summits.bed INFO @ Fri, 05 Jul 2019 13:04:37: Done! pass1 - making usageList (38 chroms): 1 millis pass2 - checking and writing primary data (2412 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。