Job ID = 2001165 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T19:32:38 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 ) 2019-07-04T19:33:30 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 ) 2019-07-04T19:36:11 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 ) 2019-07-04T19:40:10 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 109,001,389 reads read : 109,001,389 reads written : 109,001,389 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: 00:50:59 109001389 reads; of these: 109001389 (100.00%) were unpaired; of these: 2216651 (2.03%) aligned 0 times 95962563 (88.04%) aligned exactly 1 time 10822175 (9.93%) aligned >1 times 97.97% overall alignment rate Time searching: 00:51:02 Overall time: 00:51:02 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 44 files... [bam_rmdupse_core] 74180156 / 106784738 = 0.6947 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 06:01:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101854/ERX101854.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101854/ERX101854.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101854/ERX101854.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101854/ERX101854.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 06:01:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:01:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:01:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101854/ERX101854.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101854/ERX101854.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101854/ERX101854.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101854/ERX101854.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 06:01:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:01:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:01:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101854/ERX101854.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101854/ERX101854.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101854/ERX101854.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101854/ERX101854.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 06:01:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:01:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:01:31: 1000000 INFO @ Fri, 05 Jul 2019 06:01:32: 1000000 INFO @ Fri, 05 Jul 2019 06:01:33: 1000000 INFO @ Fri, 05 Jul 2019 06:01:39: 2000000 INFO @ Fri, 05 Jul 2019 06:01:40: 2000000 INFO @ Fri, 05 Jul 2019 06:01:41: 2000000 INFO @ Fri, 05 Jul 2019 06:01:47: 3000000 INFO @ Fri, 05 Jul 2019 06:01:48: 3000000 INFO @ Fri, 05 Jul 2019 06:01:49: 3000000 INFO @ Fri, 05 Jul 2019 06:01:54: 4000000 INFO @ Fri, 05 Jul 2019 06:01:56: 4000000 INFO @ Fri, 05 Jul 2019 06:01:58: 4000000 INFO @ Fri, 05 Jul 2019 06:02:02: 5000000 INFO @ Fri, 05 Jul 2019 06:02:04: 5000000 INFO @ Fri, 05 Jul 2019 06:02:06: 5000000 INFO @ Fri, 05 Jul 2019 06:02:10: 6000000 INFO @ Fri, 05 Jul 2019 06:02:12: 6000000 INFO @ Fri, 05 Jul 2019 06:02:14: 6000000 INFO @ Fri, 05 Jul 2019 06:02:17: 7000000 INFO @ Fri, 05 Jul 2019 06:02:20: 7000000 INFO @ Fri, 05 Jul 2019 06:02:22: 7000000 INFO @ Fri, 05 Jul 2019 06:02:25: 8000000 INFO @ Fri, 05 Jul 2019 06:02:29: 8000000 INFO @ Fri, 05 Jul 2019 06:02:31: 8000000 INFO @ Fri, 05 Jul 2019 06:02:32: 9000000 INFO @ Fri, 05 Jul 2019 06:02:37: 9000000 INFO @ Fri, 05 Jul 2019 06:02:39: 9000000 INFO @ Fri, 05 Jul 2019 06:02:40: 10000000 INFO @ Fri, 05 Jul 2019 06:02:45: 10000000 INFO @ Fri, 05 Jul 2019 06:02:47: 10000000 INFO @ Fri, 05 Jul 2019 06:02:48: 11000000 INFO @ Fri, 05 Jul 2019 06:02:53: 11000000 INFO @ Fri, 05 Jul 2019 06:02:55: 12000000 INFO @ Fri, 05 Jul 2019 06:02:56: 11000000 INFO @ Fri, 05 Jul 2019 06:03:01: 12000000 INFO @ Fri, 05 Jul 2019 06:03:03: 13000000 INFO @ Fri, 05 Jul 2019 06:03:04: 12000000 INFO @ Fri, 05 Jul 2019 06:03:09: 13000000 INFO @ Fri, 05 Jul 2019 06:03:11: 14000000 INFO @ Fri, 05 Jul 2019 06:03:12: 13000000 INFO @ Fri, 05 Jul 2019 06:03:17: 14000000 INFO @ Fri, 05 Jul 2019 06:03:18: 15000000 INFO @ Fri, 05 Jul 2019 06:03:20: 14000000 INFO @ Fri, 05 Jul 2019 06:03:25: 15000000 INFO @ Fri, 05 Jul 2019 06:03:26: 16000000 INFO @ Fri, 05 Jul 2019 06:03:29: 15000000 INFO @ Fri, 05 Jul 2019 06:03:33: 16000000 INFO @ Fri, 05 Jul 2019 06:03:34: 17000000 INFO @ Fri, 05 Jul 2019 06:03:37: 16000000 INFO @ Fri, 05 Jul 2019 06:03:41: 17000000 INFO @ Fri, 05 Jul 2019 06:03:41: 18000000 INFO @ Fri, 05 Jul 2019 06:03:45: 17000000 INFO @ Fri, 05 Jul 2019 06:03:49: 19000000 INFO @ Fri, 05 Jul 2019 06:03:49: 18000000 INFO @ Fri, 05 Jul 2019 06:03:53: 18000000 INFO @ Fri, 05 Jul 2019 06:03:56: 20000000 INFO @ Fri, 05 Jul 2019 06:03:57: 19000000 INFO @ Fri, 05 Jul 2019 06:04:02: 19000000 INFO @ Fri, 05 Jul 2019 06:04:04: 21000000 INFO @ Fri, 05 Jul 2019 06:04:05: 20000000 INFO @ Fri, 05 Jul 2019 06:04:10: 20000000 INFO @ Fri, 05 Jul 2019 06:04:11: 22000000 INFO @ Fri, 05 Jul 2019 06:04:13: 21000000 INFO @ Fri, 05 Jul 2019 06:04:18: 21000000 INFO @ Fri, 05 Jul 2019 06:04:19: 23000000 INFO @ Fri, 05 Jul 2019 06:04:21: 22000000 INFO @ Fri, 05 Jul 2019 06:04:26: 22000000 INFO @ Fri, 05 Jul 2019 06:04:27: 24000000 INFO @ Fri, 05 Jul 2019 06:04:29: 23000000 INFO @ Fri, 05 Jul 2019 06:04:34: 25000000 INFO @ Fri, 05 Jul 2019 06:04:34: 23000000 INFO @ Fri, 05 Jul 2019 06:04:37: 24000000 INFO @ Fri, 05 Jul 2019 06:04:42: 26000000 INFO @ Fri, 05 Jul 2019 06:04:43: 24000000 INFO @ Fri, 05 Jul 2019 06:04:45: 25000000 INFO @ Fri, 05 Jul 2019 06:04:49: 27000000 INFO @ Fri, 05 Jul 2019 06:04:51: 25000000 INFO @ Fri, 05 Jul 2019 06:04:53: 26000000 INFO @ Fri, 05 Jul 2019 06:04:57: 28000000 INFO @ Fri, 05 Jul 2019 06:04:59: 26000000 INFO @ Fri, 05 Jul 2019 06:05:01: 27000000 INFO @ Fri, 05 Jul 2019 06:05:05: 29000000 INFO @ Fri, 05 Jul 2019 06:05:07: 27000000 INFO @ Fri, 05 Jul 2019 06:05:09: 28000000 INFO @ Fri, 05 Jul 2019 06:05:12: 30000000 INFO @ Fri, 05 Jul 2019 06:05:16: 28000000 INFO @ Fri, 05 Jul 2019 06:05:17: 29000000 INFO @ Fri, 05 Jul 2019 06:05:20: 31000000 INFO @ Fri, 05 Jul 2019 06:05:24: 29000000 INFO @ Fri, 05 Jul 2019 06:05:25: 30000000 INFO @ Fri, 05 Jul 2019 06:05:28: 32000000 INFO @ Fri, 05 Jul 2019 06:05:32: 30000000 INFO @ Fri, 05 Jul 2019 06:05:33: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 06:05:33: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 06:05:33: #1 total tags in treatment: 32604582 INFO @ Fri, 05 Jul 2019 06:05:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:05:33: #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 06:05:33: #1 tags after filtering in treatment: 32604360 INFO @ Fri, 05 Jul 2019 06:05:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:05:33: #1 finished! INFO @ Fri, 05 Jul 2019 06:05:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:05:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:05:34: 31000000 INFO @ Fri, 05 Jul 2019 06:05:40: 31000000 INFO @ Fri, 05 Jul 2019 06:05:41: #2 number of paired peaks: 65250 INFO @ Fri, 05 Jul 2019 06:05:41: start model_add_line... INFO @ Fri, 05 Jul 2019 06:05:42: start X-correlation... INFO @ Fri, 05 Jul 2019 06:05:42: end of X-cor INFO @ Fri, 05 Jul 2019 06:05:42: #2 finished! INFO @ Fri, 05 Jul 2019 06:05:42: #2 predicted fragment length is 142 bps INFO @ Fri, 05 Jul 2019 06:05:42: #2 alternative fragment length(s) may be 4,142 bps INFO @ Fri, 05 Jul 2019 06:05:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101854/ERX101854.10_model.r INFO @ Fri, 05 Jul 2019 06:05:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:05:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:05:42: 32000000 INFO @ Fri, 05 Jul 2019 06:05:47: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 06:05:47: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 06:05:47: #1 total tags in treatment: 32604582 INFO @ Fri, 05 Jul 2019 06:05:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:05:47: #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 06:05:48: #1 tags after filtering in treatment: 32604360 INFO @ Fri, 05 Jul 2019 06:05:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:05:48: #1 finished! INFO @ Fri, 05 Jul 2019 06:05:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:05:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:05:48: 32000000 INFO @ Fri, 05 Jul 2019 06:05:54: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 06:05:54: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 06:05:54: #1 total tags in treatment: 32604582 INFO @ Fri, 05 Jul 2019 06:05:54: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:05:54: #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 06:05:54: #1 tags after filtering in treatment: 32604360 INFO @ Fri, 05 Jul 2019 06:05:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:05:54: #1 finished! INFO @ Fri, 05 Jul 2019 06:05:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:05:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:05:55: #2 number of paired peaks: 65250 INFO @ Fri, 05 Jul 2019 06:05:55: start model_add_line... INFO @ Fri, 05 Jul 2019 06:05:56: start X-correlation... INFO @ Fri, 05 Jul 2019 06:05:56: end of X-cor INFO @ Fri, 05 Jul 2019 06:05:56: #2 finished! INFO @ Fri, 05 Jul 2019 06:05:56: #2 predicted fragment length is 142 bps INFO @ Fri, 05 Jul 2019 06:05:56: #2 alternative fragment length(s) may be 4,142 bps INFO @ Fri, 05 Jul 2019 06:05:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101854/ERX101854.05_model.r INFO @ Fri, 05 Jul 2019 06:05:56: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:05:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:06:02: #2 number of paired peaks: 65250 INFO @ Fri, 05 Jul 2019 06:06:02: start model_add_line... INFO @ Fri, 05 Jul 2019 06:06:03: start X-correlation... INFO @ Fri, 05 Jul 2019 06:06:03: end of X-cor INFO @ Fri, 05 Jul 2019 06:06:03: #2 finished! INFO @ Fri, 05 Jul 2019 06:06:03: #2 predicted fragment length is 142 bps INFO @ Fri, 05 Jul 2019 06:06:03: #2 alternative fragment length(s) may be 4,142 bps INFO @ Fri, 05 Jul 2019 06:06:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101854/ERX101854.20_model.r INFO @ Fri, 05 Jul 2019 06:06:03: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:06:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:07:20: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:07:32: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:07:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:08:12: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101854/ERX101854.10_peaks.xls INFO @ Fri, 05 Jul 2019 06:08:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101854/ERX101854.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:08:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101854/ERX101854.10_summits.bed INFO @ Fri, 05 Jul 2019 06:08:13: Done! pass1 - making usageList (143 chroms): 17 millis pass2 - checking and writing primary data (47185 records, 4 fields): 72 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:08:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101854/ERX101854.05_peaks.xls INFO @ Fri, 05 Jul 2019 06:08:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101854/ERX101854.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:08:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101854/ERX101854.05_summits.bed INFO @ Fri, 05 Jul 2019 06:08:24: Done! pass1 - making usageList (162 chroms): 12 millis pass2 - checking and writing primary data (57863 records, 4 fields): 83 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:08:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101854/ERX101854.20_peaks.xls INFO @ Fri, 05 Jul 2019 06:08:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101854/ERX101854.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:08:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101854/ERX101854.20_summits.bed INFO @ Fri, 05 Jul 2019 06:08:32: Done! pass1 - making usageList (126 chroms): 12 millis pass2 - checking and writing primary data (35889 records, 4 fields): 52 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。