Job ID = 2001600 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T20:59:17 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 : 63,435,726 reads read : 63,435,726 reads written : 63,435,726 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: 00:00:00 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:07:19 63435726 reads; of these: 63435726 (100.00%) were unpaired; of these: 1799250 (2.84%) aligned 0 times 47224718 (74.44%) aligned exactly 1 time 14411758 (22.72%) aligned >1 times 97.16% overall alignment rate Time searching: 01:07:21 Overall time: 01:07:21 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 28 files... [bam_rmdupse_core] 6661037 / 61636476 = 0.1081 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 07:51:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101928/ERX101928.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101928/ERX101928.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101928/ERX101928.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101928/ERX101928.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 07:51:39: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:51:39: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:51:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101928/ERX101928.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101928/ERX101928.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101928/ERX101928.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101928/ERX101928.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 07:51:40: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:51:40: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:51:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101928/ERX101928.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101928/ERX101928.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101928/ERX101928.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101928/ERX101928.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 07:51:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:51:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:51:49: 1000000 INFO @ Fri, 05 Jul 2019 07:51:50: 1000000 INFO @ Fri, 05 Jul 2019 07:51:51: 1000000 INFO @ Fri, 05 Jul 2019 07:51:56: 2000000 INFO @ Fri, 05 Jul 2019 07:51:59: 2000000 INFO @ Fri, 05 Jul 2019 07:52:02: 2000000 INFO @ Fri, 05 Jul 2019 07:52:04: 3000000 INFO @ Fri, 05 Jul 2019 07:52:09: 3000000 INFO @ Fri, 05 Jul 2019 07:52:11: 4000000 INFO @ Fri, 05 Jul 2019 07:52:12: 3000000 INFO @ Fri, 05 Jul 2019 07:52:19: 4000000 INFO @ Fri, 05 Jul 2019 07:52:19: 5000000 INFO @ Fri, 05 Jul 2019 07:52:22: 4000000 INFO @ Fri, 05 Jul 2019 07:52:26: 6000000 INFO @ Fri, 05 Jul 2019 07:52:28: 5000000 INFO @ Fri, 05 Jul 2019 07:52:32: 5000000 INFO @ Fri, 05 Jul 2019 07:52:34: 7000000 INFO @ Fri, 05 Jul 2019 07:52:38: 6000000 INFO @ Fri, 05 Jul 2019 07:52:41: 8000000 INFO @ Fri, 05 Jul 2019 07:52:43: 6000000 INFO @ Fri, 05 Jul 2019 07:52:47: 7000000 INFO @ Fri, 05 Jul 2019 07:52:49: 9000000 INFO @ Fri, 05 Jul 2019 07:52:53: 7000000 INFO @ Fri, 05 Jul 2019 07:52:56: 10000000 INFO @ Fri, 05 Jul 2019 07:52:57: 8000000 INFO @ Fri, 05 Jul 2019 07:53:03: 8000000 INFO @ Fri, 05 Jul 2019 07:53:03: 11000000 INFO @ Fri, 05 Jul 2019 07:53:06: 9000000 INFO @ Fri, 05 Jul 2019 07:53:11: 12000000 INFO @ Fri, 05 Jul 2019 07:53:12: 9000000 INFO @ Fri, 05 Jul 2019 07:53:16: 10000000 INFO @ Fri, 05 Jul 2019 07:53:19: 13000000 INFO @ Fri, 05 Jul 2019 07:53:22: 10000000 INFO @ Fri, 05 Jul 2019 07:53:26: 11000000 INFO @ Fri, 05 Jul 2019 07:53:26: 14000000 INFO @ Fri, 05 Jul 2019 07:53:32: 11000000 INFO @ Fri, 05 Jul 2019 07:53:33: 15000000 INFO @ Fri, 05 Jul 2019 07:53:36: 12000000 INFO @ Fri, 05 Jul 2019 07:53:41: 16000000 INFO @ Fri, 05 Jul 2019 07:53:42: 12000000 INFO @ Fri, 05 Jul 2019 07:53:46: 13000000 INFO @ Fri, 05 Jul 2019 07:53:48: 17000000 INFO @ Fri, 05 Jul 2019 07:53:52: 13000000 INFO @ Fri, 05 Jul 2019 07:53:56: 14000000 INFO @ Fri, 05 Jul 2019 07:53:56: 18000000 INFO @ Fri, 05 Jul 2019 07:54:02: 14000000 INFO @ Fri, 05 Jul 2019 07:54:03: 19000000 INFO @ Fri, 05 Jul 2019 07:54:05: 15000000 INFO @ Fri, 05 Jul 2019 07:54:11: 20000000 INFO @ Fri, 05 Jul 2019 07:54:12: 15000000 INFO @ Fri, 05 Jul 2019 07:54:15: 16000000 INFO @ Fri, 05 Jul 2019 07:54:18: 21000000 INFO @ Fri, 05 Jul 2019 07:54:22: 16000000 INFO @ Fri, 05 Jul 2019 07:54:25: 17000000 INFO @ Fri, 05 Jul 2019 07:54:25: 22000000 INFO @ Fri, 05 Jul 2019 07:54:31: 17000000 INFO @ Fri, 05 Jul 2019 07:54:33: 23000000 INFO @ Fri, 05 Jul 2019 07:54:35: 18000000 INFO @ Fri, 05 Jul 2019 07:54:41: 18000000 INFO @ Fri, 05 Jul 2019 07:54:41: 24000000 INFO @ Fri, 05 Jul 2019 07:54:45: 19000000 INFO @ Fri, 05 Jul 2019 07:54:49: 25000000 INFO @ Fri, 05 Jul 2019 07:54:51: 19000000 INFO @ Fri, 05 Jul 2019 07:54:55: 20000000 INFO @ Fri, 05 Jul 2019 07:54:56: 26000000 INFO @ Fri, 05 Jul 2019 07:55:00: 20000000 INFO @ Fri, 05 Jul 2019 07:55:03: 27000000 INFO @ Fri, 05 Jul 2019 07:55:04: 21000000 INFO @ Fri, 05 Jul 2019 07:55:10: 21000000 INFO @ Fri, 05 Jul 2019 07:55:11: 28000000 INFO @ Fri, 05 Jul 2019 07:55:14: 22000000 INFO @ Fri, 05 Jul 2019 07:55:18: 29000000 INFO @ Fri, 05 Jul 2019 07:55:20: 22000000 INFO @ Fri, 05 Jul 2019 07:55:24: 23000000 INFO @ Fri, 05 Jul 2019 07:55:26: 30000000 INFO @ Fri, 05 Jul 2019 07:55:29: 23000000 INFO @ Fri, 05 Jul 2019 07:55:33: 31000000 INFO @ Fri, 05 Jul 2019 07:55:34: 24000000 INFO @ Fri, 05 Jul 2019 07:55:39: 24000000 INFO @ Fri, 05 Jul 2019 07:55:41: 32000000 INFO @ Fri, 05 Jul 2019 07:55:43: 25000000 INFO @ Fri, 05 Jul 2019 07:55:48: 33000000 INFO @ Fri, 05 Jul 2019 07:55:49: 25000000 INFO @ Fri, 05 Jul 2019 07:55:53: 26000000 INFO @ Fri, 05 Jul 2019 07:55:56: 34000000 INFO @ Fri, 05 Jul 2019 07:55:58: 26000000 INFO @ Fri, 05 Jul 2019 07:56:03: 27000000 INFO @ Fri, 05 Jul 2019 07:56:03: 35000000 INFO @ Fri, 05 Jul 2019 07:56:08: 27000000 INFO @ Fri, 05 Jul 2019 07:56:11: 36000000 INFO @ Fri, 05 Jul 2019 07:56:12: 28000000 INFO @ Fri, 05 Jul 2019 07:56:17: 28000000 INFO @ Fri, 05 Jul 2019 07:56:18: 37000000 INFO @ Fri, 05 Jul 2019 07:56:22: 29000000 INFO @ Fri, 05 Jul 2019 07:56:25: 38000000 INFO @ Fri, 05 Jul 2019 07:56:27: 29000000 INFO @ Fri, 05 Jul 2019 07:56:31: 30000000 INFO @ Fri, 05 Jul 2019 07:56:33: 39000000 INFO @ Fri, 05 Jul 2019 07:56:37: 30000000 INFO @ Fri, 05 Jul 2019 07:56:40: 40000000 INFO @ Fri, 05 Jul 2019 07:56:41: 31000000 INFO @ Fri, 05 Jul 2019 07:56:46: 31000000 INFO @ Fri, 05 Jul 2019 07:56:48: 41000000 INFO @ Fri, 05 Jul 2019 07:56:51: 32000000 INFO @ Fri, 05 Jul 2019 07:56:55: 42000000 INFO @ Fri, 05 Jul 2019 07:56:56: 32000000 INFO @ Fri, 05 Jul 2019 07:57:01: 33000000 INFO @ Fri, 05 Jul 2019 07:57:03: 43000000 INFO @ Fri, 05 Jul 2019 07:57:06: 33000000 INFO @ Fri, 05 Jul 2019 07:57:10: 44000000 INFO @ Fri, 05 Jul 2019 07:57:10: 34000000 INFO @ Fri, 05 Jul 2019 07:57:15: 34000000 INFO @ Fri, 05 Jul 2019 07:57:17: 45000000 INFO @ Fri, 05 Jul 2019 07:57:20: 35000000 INFO @ Fri, 05 Jul 2019 07:57:25: 46000000 INFO @ Fri, 05 Jul 2019 07:57:25: 35000000 INFO @ Fri, 05 Jul 2019 07:57:29: 36000000 INFO @ Fri, 05 Jul 2019 07:57:32: 47000000 INFO @ Fri, 05 Jul 2019 07:57:34: 36000000 INFO @ Fri, 05 Jul 2019 07:57:39: 37000000 INFO @ Fri, 05 Jul 2019 07:57:40: 48000000 INFO @ Fri, 05 Jul 2019 07:57:44: 37000000 INFO @ Fri, 05 Jul 2019 07:57:47: 49000000 INFO @ Fri, 05 Jul 2019 07:57:48: 38000000 INFO @ Fri, 05 Jul 2019 07:57:54: 38000000 INFO @ Fri, 05 Jul 2019 07:57:54: 50000000 INFO @ Fri, 05 Jul 2019 07:57:58: 39000000 INFO @ Fri, 05 Jul 2019 07:58:02: 51000000 INFO @ Fri, 05 Jul 2019 07:58:03: 39000000 INFO @ Fri, 05 Jul 2019 07:58:07: 40000000 INFO @ Fri, 05 Jul 2019 07:58:09: 52000000 INFO @ Fri, 05 Jul 2019 07:58:13: 40000000 INFO @ Fri, 05 Jul 2019 07:58:17: 53000000 INFO @ Fri, 05 Jul 2019 07:58:17: 41000000 INFO @ Fri, 05 Jul 2019 07:58:23: 41000000 INFO @ Fri, 05 Jul 2019 07:58:24: 54000000 INFO @ Fri, 05 Jul 2019 07:58:26: 42000000 INFO @ Fri, 05 Jul 2019 07:58:32: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 07:58:32: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 07:58:32: #1 total tags in treatment: 54975439 INFO @ Fri, 05 Jul 2019 07:58:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:58:32: #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 07:58:32: 42000000 INFO @ Fri, 05 Jul 2019 07:58:33: #1 tags after filtering in treatment: 54975345 INFO @ Fri, 05 Jul 2019 07:58:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:58:33: #1 finished! INFO @ Fri, 05 Jul 2019 07:58:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:58:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:58:36: 43000000 INFO @ Fri, 05 Jul 2019 07:58:41: #2 number of paired peaks: 38659 INFO @ Fri, 05 Jul 2019 07:58:41: start model_add_line... INFO @ Fri, 05 Jul 2019 07:58:42: start X-correlation... INFO @ Fri, 05 Jul 2019 07:58:42: end of X-cor INFO @ Fri, 05 Jul 2019 07:58:42: #2 finished! INFO @ Fri, 05 Jul 2019 07:58:42: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 07:58:42: #2 alternative fragment length(s) may be 134,296,506 bps INFO @ Fri, 05 Jul 2019 07:58:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101928/ERX101928.20_model.r INFO @ Fri, 05 Jul 2019 07:58:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:58:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:58:42: 43000000 INFO @ Fri, 05 Jul 2019 07:58:46: 44000000 INFO @ Fri, 05 Jul 2019 07:58:52: 44000000 INFO @ Fri, 05 Jul 2019 07:58:55: 45000000 INFO @ Fri, 05 Jul 2019 07:59:01: 45000000 INFO @ Fri, 05 Jul 2019 07:59:05: 46000000 INFO @ Fri, 05 Jul 2019 07:59:11: 46000000 INFO @ Fri, 05 Jul 2019 07:59:15: 47000000 INFO @ Fri, 05 Jul 2019 07:59:22: 47000000 INFO @ Fri, 05 Jul 2019 07:59:26: 48000000 INFO @ Fri, 05 Jul 2019 07:59:32: 48000000 INFO @ Fri, 05 Jul 2019 07:59:37: 49000000 INFO @ Fri, 05 Jul 2019 07:59:42: 49000000 INFO @ Fri, 05 Jul 2019 07:59:48: 50000000 INFO @ Fri, 05 Jul 2019 07:59:53: 50000000 INFO @ Fri, 05 Jul 2019 07:59:59: 51000000 INFO @ Fri, 05 Jul 2019 08:00:03: 51000000 INFO @ Fri, 05 Jul 2019 08:00:10: 52000000 INFO @ Fri, 05 Jul 2019 08:00:13: 52000000 INFO @ Fri, 05 Jul 2019 08:00:20: 53000000 INFO @ Fri, 05 Jul 2019 08:00:23: 53000000 INFO @ Fri, 05 Jul 2019 08:00:32: 54000000 INFO @ Fri, 05 Jul 2019 08:00:34: 54000000 INFO @ Fri, 05 Jul 2019 08:00:42: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 08:00:42: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 08:00:42: #1 total tags in treatment: 54975439 INFO @ Fri, 05 Jul 2019 08:00:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:00:42: #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 08:00:43: #1 tags after filtering in treatment: 54975345 INFO @ Fri, 05 Jul 2019 08:00:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:00:43: #1 finished! INFO @ Fri, 05 Jul 2019 08:00:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:00:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:00:45: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 08:00:45: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 08:00:45: #1 total tags in treatment: 54975439 INFO @ Fri, 05 Jul 2019 08:00:45: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:00:45: #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 08:00:46: #1 tags after filtering in treatment: 54975345 INFO @ Fri, 05 Jul 2019 08:00:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:00:46: #1 finished! INFO @ Fri, 05 Jul 2019 08:00:46: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:00:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:00:51: #2 number of paired peaks: 38659 INFO @ Fri, 05 Jul 2019 08:00:51: start model_add_line... INFO @ Fri, 05 Jul 2019 08:00:52: start X-correlation... INFO @ Fri, 05 Jul 2019 08:00:52: end of X-cor INFO @ Fri, 05 Jul 2019 08:00:52: #2 finished! INFO @ Fri, 05 Jul 2019 08:00:52: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 08:00:52: #2 alternative fragment length(s) may be 134,296,506 bps INFO @ Fri, 05 Jul 2019 08:00:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101928/ERX101928.10_model.r INFO @ Fri, 05 Jul 2019 08:00:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:00:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:00:53: #2 number of paired peaks: 38659 INFO @ Fri, 05 Jul 2019 08:00:53: start model_add_line... INFO @ Fri, 05 Jul 2019 08:00:54: start X-correlation... INFO @ Fri, 05 Jul 2019 08:00:54: end of X-cor INFO @ Fri, 05 Jul 2019 08:00:54: #2 finished! INFO @ Fri, 05 Jul 2019 08:00:54: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 08:00:54: #2 alternative fragment length(s) may be 134,296,506 bps INFO @ Fri, 05 Jul 2019 08:00:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101928/ERX101928.05_model.r INFO @ Fri, 05 Jul 2019 08:00:54: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:00:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:01:35: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:03:02: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101928/ERX101928.20_peaks.xls INFO @ Fri, 05 Jul 2019 08:03:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101928/ERX101928.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:03:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101928/ERX101928.20_summits.bed INFO @ Fri, 05 Jul 2019 08:03:02: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (321 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 08:03:46: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:03:49: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:05:16: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101928/ERX101928.10_peaks.xls INFO @ Fri, 05 Jul 2019 08:05:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101928/ERX101928.05_peaks.xls INFO @ Fri, 05 Jul 2019 08:05:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101928/ERX101928.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:05:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101928/ERX101928.10_summits.bed INFO @ Fri, 05 Jul 2019 08:05:26: Done! INFO @ Fri, 05 Jul 2019 08:05:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101928/ERX101928.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:05:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101928/ERX101928.05_summits.bed INFO @ Fri, 05 Jul 2019 08:05:26: Done! pass1 - making usageList (55 chroms): 2 millis pass2 - checking and writing primary data (1535 records, 4 fields): 12 millis pass1 - making usageList (93 chroms): 4 millis pass2 - checking and writing primary data (6142 records, 4 fields): 14 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。