Job ID = 2001599 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T21:19:23 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 ) 2019-07-04T21:19:23 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 ) 2019-07-04T21:34:09 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 : 109,948,276 reads read : 109,948,276 reads written : 109,948,276 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: 00:57:55 109948276 reads; of these: 109948276 (100.00%) were unpaired; of these: 1970346 (1.79%) aligned 0 times 96019656 (87.33%) aligned exactly 1 time 11958274 (10.88%) aligned >1 times 98.21% overall alignment rate Time searching: 00:57:58 Overall time: 00:57:58 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] 63105442 / 107977930 = 0.5844 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 08:02:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101927/ERX101927.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101927/ERX101927.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101927/ERX101927.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101927/ERX101927.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 08:02:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:02:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:02:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101927/ERX101927.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101927/ERX101927.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101927/ERX101927.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101927/ERX101927.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 08:02:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:02:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:02:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101927/ERX101927.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101927/ERX101927.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101927/ERX101927.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101927/ERX101927.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 08:02:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:02:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:03:07: 1000000 INFO @ Fri, 05 Jul 2019 08:03:08: 1000000 INFO @ Fri, 05 Jul 2019 08:03:08: 1000000 INFO @ Fri, 05 Jul 2019 08:03:15: 2000000 INFO @ Fri, 05 Jul 2019 08:03:17: 2000000 INFO @ Fri, 05 Jul 2019 08:03:18: 2000000 INFO @ Fri, 05 Jul 2019 08:03:23: 3000000 INFO @ Fri, 05 Jul 2019 08:03:25: 3000000 INFO @ Fri, 05 Jul 2019 08:03:27: 3000000 INFO @ Fri, 05 Jul 2019 08:03:31: 4000000 INFO @ Fri, 05 Jul 2019 08:03:34: 4000000 INFO @ Fri, 05 Jul 2019 08:03:37: 4000000 INFO @ Fri, 05 Jul 2019 08:03:39: 5000000 INFO @ Fri, 05 Jul 2019 08:03:43: 5000000 INFO @ Fri, 05 Jul 2019 08:03:47: 5000000 INFO @ Fri, 05 Jul 2019 08:03:48: 6000000 INFO @ Fri, 05 Jul 2019 08:03:51: 6000000 INFO @ Fri, 05 Jul 2019 08:03:56: 7000000 INFO @ Fri, 05 Jul 2019 08:03:57: 6000000 INFO @ Fri, 05 Jul 2019 08:04:00: 7000000 INFO @ Fri, 05 Jul 2019 08:04:04: 8000000 INFO @ Fri, 05 Jul 2019 08:04:07: 7000000 INFO @ Fri, 05 Jul 2019 08:04:08: 8000000 INFO @ Fri, 05 Jul 2019 08:04:12: 9000000 INFO @ Fri, 05 Jul 2019 08:04:16: 8000000 INFO @ Fri, 05 Jul 2019 08:04:16: 9000000 INFO @ Fri, 05 Jul 2019 08:04:20: 10000000 INFO @ Fri, 05 Jul 2019 08:04:25: 10000000 INFO @ Fri, 05 Jul 2019 08:04:26: 9000000 INFO @ Fri, 05 Jul 2019 08:04:28: 11000000 INFO @ Fri, 05 Jul 2019 08:04:33: 11000000 INFO @ Fri, 05 Jul 2019 08:04:36: 10000000 INFO @ Fri, 05 Jul 2019 08:04:36: 12000000 INFO @ Fri, 05 Jul 2019 08:04:42: 12000000 INFO @ Fri, 05 Jul 2019 08:04:44: 13000000 INFO @ Fri, 05 Jul 2019 08:04:46: 11000000 INFO @ Fri, 05 Jul 2019 08:04:50: 13000000 INFO @ Fri, 05 Jul 2019 08:04:52: 14000000 INFO @ Fri, 05 Jul 2019 08:04:55: 12000000 INFO @ Fri, 05 Jul 2019 08:04:58: 14000000 INFO @ Fri, 05 Jul 2019 08:05:00: 15000000 INFO @ Fri, 05 Jul 2019 08:05:05: 13000000 INFO @ Fri, 05 Jul 2019 08:05:07: 15000000 INFO @ Fri, 05 Jul 2019 08:05:08: 16000000 INFO @ Fri, 05 Jul 2019 08:05:15: 14000000 INFO @ Fri, 05 Jul 2019 08:05:15: 16000000 INFO @ Fri, 05 Jul 2019 08:05:16: 17000000 INFO @ Fri, 05 Jul 2019 08:05:23: 17000000 INFO @ Fri, 05 Jul 2019 08:05:24: 18000000 INFO @ Fri, 05 Jul 2019 08:05:24: 15000000 INFO @ Fri, 05 Jul 2019 08:05:32: 18000000 INFO @ Fri, 05 Jul 2019 08:05:32: 19000000 INFO @ Fri, 05 Jul 2019 08:05:34: 16000000 INFO @ Fri, 05 Jul 2019 08:05:40: 19000000 INFO @ Fri, 05 Jul 2019 08:05:41: 20000000 INFO @ Fri, 05 Jul 2019 08:05:44: 17000000 INFO @ Fri, 05 Jul 2019 08:05:48: 21000000 INFO @ Fri, 05 Jul 2019 08:05:48: 20000000 INFO @ Fri, 05 Jul 2019 08:05:53: 18000000 INFO @ Fri, 05 Jul 2019 08:05:56: 22000000 INFO @ Fri, 05 Jul 2019 08:05:57: 21000000 INFO @ Fri, 05 Jul 2019 08:06:03: 19000000 INFO @ Fri, 05 Jul 2019 08:06:04: 23000000 INFO @ Fri, 05 Jul 2019 08:06:05: 22000000 INFO @ Fri, 05 Jul 2019 08:06:12: 24000000 INFO @ Fri, 05 Jul 2019 08:06:13: 20000000 INFO @ Fri, 05 Jul 2019 08:06:14: 23000000 INFO @ Fri, 05 Jul 2019 08:06:20: 25000000 INFO @ Fri, 05 Jul 2019 08:06:22: 24000000 INFO @ Fri, 05 Jul 2019 08:06:23: 21000000 INFO @ Fri, 05 Jul 2019 08:06:27: 26000000 INFO @ Fri, 05 Jul 2019 08:06:31: 25000000 INFO @ Fri, 05 Jul 2019 08:06:32: 22000000 INFO @ Fri, 05 Jul 2019 08:06:35: 27000000 INFO @ Fri, 05 Jul 2019 08:06:39: 26000000 INFO @ Fri, 05 Jul 2019 08:06:42: 23000000 INFO @ Fri, 05 Jul 2019 08:06:42: 28000000 INFO @ Fri, 05 Jul 2019 08:06:48: 27000000 INFO @ Fri, 05 Jul 2019 08:06:51: 29000000 INFO @ Fri, 05 Jul 2019 08:06:52: 24000000 INFO @ Fri, 05 Jul 2019 08:06:56: 28000000 INFO @ Fri, 05 Jul 2019 08:06:59: 30000000 INFO @ Fri, 05 Jul 2019 08:07:02: 25000000 INFO @ Fri, 05 Jul 2019 08:07:05: 29000000 INFO @ Fri, 05 Jul 2019 08:07:07: 31000000 INFO @ Fri, 05 Jul 2019 08:07:11: 26000000 INFO @ Fri, 05 Jul 2019 08:07:14: 30000000 INFO @ Fri, 05 Jul 2019 08:07:15: 32000000 INFO @ Fri, 05 Jul 2019 08:07:21: 27000000 INFO @ Fri, 05 Jul 2019 08:07:23: 31000000 INFO @ Fri, 05 Jul 2019 08:07:24: 33000000 INFO @ Fri, 05 Jul 2019 08:07:31: 28000000 INFO @ Fri, 05 Jul 2019 08:07:32: 34000000 INFO @ Fri, 05 Jul 2019 08:07:32: 32000000 INFO @ Fri, 05 Jul 2019 08:07:40: 35000000 INFO @ Fri, 05 Jul 2019 08:07:41: 29000000 INFO @ Fri, 05 Jul 2019 08:07:41: 33000000 INFO @ Fri, 05 Jul 2019 08:07:48: 36000000 INFO @ Fri, 05 Jul 2019 08:07:50: 34000000 INFO @ Fri, 05 Jul 2019 08:07:51: 30000000 INFO @ Fri, 05 Jul 2019 08:07:56: 37000000 INFO @ Fri, 05 Jul 2019 08:07:59: 35000000 INFO @ Fri, 05 Jul 2019 08:08:02: 31000000 INFO @ Fri, 05 Jul 2019 08:08:03: 38000000 INFO @ Fri, 05 Jul 2019 08:08:07: 36000000 INFO @ Fri, 05 Jul 2019 08:08:11: 39000000 INFO @ Fri, 05 Jul 2019 08:08:12: 32000000 INFO @ Fri, 05 Jul 2019 08:08:16: 37000000 INFO @ Fri, 05 Jul 2019 08:08:19: 40000000 INFO @ Fri, 05 Jul 2019 08:08:22: 33000000 INFO @ Fri, 05 Jul 2019 08:08:24: 38000000 INFO @ Fri, 05 Jul 2019 08:08:27: 41000000 INFO @ Fri, 05 Jul 2019 08:08:32: 34000000 INFO @ Fri, 05 Jul 2019 08:08:33: 39000000 INFO @ Fri, 05 Jul 2019 08:08:35: 42000000 INFO @ Fri, 05 Jul 2019 08:08:42: 40000000 INFO @ Fri, 05 Jul 2019 08:08:42: 43000000 INFO @ Fri, 05 Jul 2019 08:08:43: 35000000 INFO @ Fri, 05 Jul 2019 08:08:50: 41000000 INFO @ Fri, 05 Jul 2019 08:08:50: 44000000 INFO @ Fri, 05 Jul 2019 08:08:53: 36000000 INFO @ Fri, 05 Jul 2019 08:08:58: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 08:08:58: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 08:08:58: #1 total tags in treatment: 44872488 INFO @ Fri, 05 Jul 2019 08:08:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:08:58: #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 08:08:58: 42000000 INFO @ Fri, 05 Jul 2019 08:08:59: #1 tags after filtering in treatment: 44872298 INFO @ Fri, 05 Jul 2019 08:08:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:08:59: #1 finished! INFO @ Fri, 05 Jul 2019 08:08:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:08:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:09:03: 37000000 INFO @ Fri, 05 Jul 2019 08:09:06: 43000000 INFO @ Fri, 05 Jul 2019 08:09:11: #2 number of paired peaks: 108060 INFO @ Fri, 05 Jul 2019 08:09:11: start model_add_line... INFO @ Fri, 05 Jul 2019 08:09:12: start X-correlation... INFO @ Fri, 05 Jul 2019 08:09:12: end of X-cor INFO @ Fri, 05 Jul 2019 08:09:12: #2 finished! INFO @ Fri, 05 Jul 2019 08:09:12: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 08:09:12: #2 alternative fragment length(s) may be 3,133 bps INFO @ Fri, 05 Jul 2019 08:09:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101927/ERX101927.10_model.r INFO @ Fri, 05 Jul 2019 08:09:12: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:09:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:09:13: 38000000 INFO @ Fri, 05 Jul 2019 08:09:15: 44000000 INFO @ Fri, 05 Jul 2019 08:09:22: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 08:09:22: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 08:09:22: #1 total tags in treatment: 44872488 INFO @ Fri, 05 Jul 2019 08:09:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:09:22: #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 08:09:23: #1 tags after filtering in treatment: 44872298 INFO @ Fri, 05 Jul 2019 08:09:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:09:23: #1 finished! INFO @ Fri, 05 Jul 2019 08:09:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:09:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:09:23: 39000000 INFO @ Fri, 05 Jul 2019 08:09:34: 40000000 INFO @ Fri, 05 Jul 2019 08:09:35: #2 number of paired peaks: 108060 INFO @ Fri, 05 Jul 2019 08:09:35: start model_add_line... INFO @ Fri, 05 Jul 2019 08:09:36: start X-correlation... INFO @ Fri, 05 Jul 2019 08:09:36: end of X-cor INFO @ Fri, 05 Jul 2019 08:09:36: #2 finished! INFO @ Fri, 05 Jul 2019 08:09:36: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 08:09:36: #2 alternative fragment length(s) may be 3,133 bps INFO @ Fri, 05 Jul 2019 08:09:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101927/ERX101927.20_model.r INFO @ Fri, 05 Jul 2019 08:09:36: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:09:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:09:44: 41000000 INFO @ Fri, 05 Jul 2019 08:09:53: 42000000 INFO @ Fri, 05 Jul 2019 08:10:03: 43000000 INFO @ Fri, 05 Jul 2019 08:10:12: 44000000 INFO @ Fri, 05 Jul 2019 08:10:21: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 08:10:21: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 08:10:21: #1 total tags in treatment: 44872488 INFO @ Fri, 05 Jul 2019 08:10:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:10:21: #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 08:10:22: #1 tags after filtering in treatment: 44872298 INFO @ Fri, 05 Jul 2019 08:10:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:10:22: #1 finished! INFO @ Fri, 05 Jul 2019 08:10:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:10:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:10:34: #2 number of paired peaks: 108060 INFO @ Fri, 05 Jul 2019 08:10:34: start model_add_line... INFO @ Fri, 05 Jul 2019 08:10:35: start X-correlation... INFO @ Fri, 05 Jul 2019 08:10:35: end of X-cor INFO @ Fri, 05 Jul 2019 08:10:35: #2 finished! INFO @ Fri, 05 Jul 2019 08:10:35: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 08:10:35: #2 alternative fragment length(s) may be 3,133 bps INFO @ Fri, 05 Jul 2019 08:10:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101927/ERX101927.05_model.r INFO @ Fri, 05 Jul 2019 08:10:35: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:10:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:11:27: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:11:48: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:12:39: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101927/ERX101927.10_peaks.xls INFO @ Fri, 05 Jul 2019 08:12:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101927/ERX101927.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:12:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101927/ERX101927.10_summits.bed INFO @ Fri, 05 Jul 2019 08:12:41: Done! pass1 - making usageList (165 chroms): 16 millis pass2 - checking and writing primary data (65507 records, 4 fields): 90 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 08:12:47: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:12:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101927/ERX101927.20_peaks.xls INFO @ Fri, 05 Jul 2019 08:12:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101927/ERX101927.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:12:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101927/ERX101927.20_summits.bed INFO @ Fri, 05 Jul 2019 08:12:57: Done! pass1 - making usageList (133 chroms): 9 millis pass2 - checking and writing primary data (43722 records, 4 fields): 60 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 08:13:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101927/ERX101927.05_peaks.xls INFO @ Fri, 05 Jul 2019 08:13:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101927/ERX101927.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:13:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101927/ERX101927.05_summits.bed INFO @ Fri, 05 Jul 2019 08:13:59: Done! pass1 - making usageList (191 chroms): 21 millis pass2 - checking and writing primary data (86927 records, 4 fields): 113 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。