Job ID = 2001640 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T21:49:56 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 ) 2019-07-04T21:49:56 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 ) 2019-07-04T21:50:59 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 : 27,291,438 reads read : 27,291,438 reads written : 27,291,438 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: 00:05:12 27291438 reads; of these: 27291438 (100.00%) were unpaired; of these: 526014 (1.93%) aligned 0 times 24082915 (88.24%) aligned exactly 1 time 2682509 (9.83%) aligned >1 times 98.07% overall alignment rate Time searching: 00:05:15 Overall time: 00:05:15 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 8 files... [bam_rmdupse_core] 12399172 / 26765424 = 0.4633 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 07:04:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101955/ERX101955.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101955/ERX101955.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101955/ERX101955.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101955/ERX101955.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 07:04:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:04:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:04:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101955/ERX101955.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101955/ERX101955.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101955/ERX101955.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101955/ERX101955.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 07:04:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:04:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:04:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101955/ERX101955.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101955/ERX101955.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101955/ERX101955.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101955/ERX101955.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 07:04:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:04:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:04:16: 1000000 INFO @ Fri, 05 Jul 2019 07:04:18: 1000000 INFO @ Fri, 05 Jul 2019 07:04:19: 1000000 INFO @ Fri, 05 Jul 2019 07:04:23: 2000000 INFO @ Fri, 05 Jul 2019 07:04:26: 2000000 INFO @ Fri, 05 Jul 2019 07:04:27: 2000000 INFO @ Fri, 05 Jul 2019 07:04:30: 3000000 INFO @ Fri, 05 Jul 2019 07:04:35: 3000000 INFO @ Fri, 05 Jul 2019 07:04:36: 3000000 INFO @ Fri, 05 Jul 2019 07:04:37: 4000000 INFO @ Fri, 05 Jul 2019 07:04:43: 4000000 INFO @ Fri, 05 Jul 2019 07:04:43: 4000000 INFO @ Fri, 05 Jul 2019 07:04:44: 5000000 INFO @ Fri, 05 Jul 2019 07:04:50: 6000000 INFO @ Fri, 05 Jul 2019 07:04:51: 5000000 INFO @ Fri, 05 Jul 2019 07:04:51: 5000000 INFO @ Fri, 05 Jul 2019 07:04:57: 7000000 INFO @ Fri, 05 Jul 2019 07:04:59: 6000000 INFO @ Fri, 05 Jul 2019 07:05:00: 6000000 INFO @ Fri, 05 Jul 2019 07:05:04: 8000000 INFO @ Fri, 05 Jul 2019 07:05:07: 7000000 INFO @ Fri, 05 Jul 2019 07:05:08: 7000000 INFO @ Fri, 05 Jul 2019 07:05:11: 9000000 INFO @ Fri, 05 Jul 2019 07:05:15: 8000000 INFO @ Fri, 05 Jul 2019 07:05:16: 8000000 INFO @ Fri, 05 Jul 2019 07:05:18: 10000000 INFO @ Fri, 05 Jul 2019 07:05:24: 9000000 INFO @ Fri, 05 Jul 2019 07:05:25: 9000000 INFO @ Fri, 05 Jul 2019 07:05:25: 11000000 INFO @ Fri, 05 Jul 2019 07:05:32: 10000000 INFO @ Fri, 05 Jul 2019 07:05:32: 12000000 INFO @ Fri, 05 Jul 2019 07:05:33: 10000000 INFO @ Fri, 05 Jul 2019 07:05:39: 13000000 INFO @ Fri, 05 Jul 2019 07:05:40: 11000000 INFO @ Fri, 05 Jul 2019 07:05:42: 11000000 INFO @ Fri, 05 Jul 2019 07:05:46: 14000000 INFO @ Fri, 05 Jul 2019 07:05:48: 12000000 INFO @ Fri, 05 Jul 2019 07:05:48: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 07:05:48: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 07:05:48: #1 total tags in treatment: 14366252 INFO @ Fri, 05 Jul 2019 07:05:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:05:48: #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 07:05:49: #1 tags after filtering in treatment: 14365948 INFO @ Fri, 05 Jul 2019 07:05:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:05:49: #1 finished! INFO @ Fri, 05 Jul 2019 07:05:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:05:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:05:50: 12000000 INFO @ Fri, 05 Jul 2019 07:05:52: #2 number of paired peaks: 49823 INFO @ Fri, 05 Jul 2019 07:05:52: start model_add_line... INFO @ Fri, 05 Jul 2019 07:05:53: start X-correlation... INFO @ Fri, 05 Jul 2019 07:05:53: end of X-cor INFO @ Fri, 05 Jul 2019 07:05:53: #2 finished! INFO @ Fri, 05 Jul 2019 07:05:53: #2 predicted fragment length is 117 bps INFO @ Fri, 05 Jul 2019 07:05:53: #2 alternative fragment length(s) may be 4,117 bps INFO @ Fri, 05 Jul 2019 07:05:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101955/ERX101955.05_model.r INFO @ Fri, 05 Jul 2019 07:05:53: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:05:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:05:56: 13000000 INFO @ Fri, 05 Jul 2019 07:05:58: 13000000 INFO @ Fri, 05 Jul 2019 07:06:04: 14000000 INFO @ Fri, 05 Jul 2019 07:06:06: 14000000 INFO @ Fri, 05 Jul 2019 07:06:07: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 07:06:07: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 07:06:07: #1 total tags in treatment: 14366252 INFO @ Fri, 05 Jul 2019 07:06:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:06:07: #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 07:06:08: #1 tags after filtering in treatment: 14365948 INFO @ Fri, 05 Jul 2019 07:06:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:06:08: #1 finished! INFO @ Fri, 05 Jul 2019 07:06:08: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:06:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:06:09: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 07:06:09: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 07:06:09: #1 total tags in treatment: 14366252 INFO @ Fri, 05 Jul 2019 07:06:09: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:06:09: #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 07:06:09: #1 tags after filtering in treatment: 14365948 INFO @ Fri, 05 Jul 2019 07:06:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:06:09: #1 finished! INFO @ Fri, 05 Jul 2019 07:06:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:06:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:06:11: #2 number of paired peaks: 49823 INFO @ Fri, 05 Jul 2019 07:06:11: start model_add_line... INFO @ Fri, 05 Jul 2019 07:06:12: start X-correlation... INFO @ Fri, 05 Jul 2019 07:06:12: end of X-cor INFO @ Fri, 05 Jul 2019 07:06:12: #2 finished! INFO @ Fri, 05 Jul 2019 07:06:12: #2 predicted fragment length is 117 bps INFO @ Fri, 05 Jul 2019 07:06:12: #2 alternative fragment length(s) may be 4,117 bps INFO @ Fri, 05 Jul 2019 07:06:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101955/ERX101955.10_model.r INFO @ Fri, 05 Jul 2019 07:06:12: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:06:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:06:13: #2 number of paired peaks: 49823 INFO @ Fri, 05 Jul 2019 07:06:13: start model_add_line... INFO @ Fri, 05 Jul 2019 07:06:13: start X-correlation... INFO @ Fri, 05 Jul 2019 07:06:13: end of X-cor INFO @ Fri, 05 Jul 2019 07:06:13: #2 finished! INFO @ Fri, 05 Jul 2019 07:06:13: #2 predicted fragment length is 117 bps INFO @ Fri, 05 Jul 2019 07:06:13: #2 alternative fragment length(s) may be 4,117 bps INFO @ Fri, 05 Jul 2019 07:06:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101955/ERX101955.20_model.r INFO @ Fri, 05 Jul 2019 07:06:13: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:06:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:06:35: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:06:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:06:56: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:06:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101955/ERX101955.05_peaks.xls INFO @ Fri, 05 Jul 2019 07:07:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101955/ERX101955.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:07:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101955/ERX101955.05_summits.bed INFO @ Fri, 05 Jul 2019 07:07:01: Done! pass1 - making usageList (136 chroms): 15 millis pass2 - checking and writing primary data (49959 records, 4 fields): 68 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:07:17: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101955/ERX101955.10_peaks.xls INFO @ Fri, 05 Jul 2019 07:07:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101955/ERX101955.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:07:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101955/ERX101955.10_summits.bed INFO @ Fri, 05 Jul 2019 07:07:18: Done! pass1 - making usageList (113 chroms): 13 millis pass2 - checking and writing primary data (39706 records, 4 fields): 54 millis INFO @ Fri, 05 Jul 2019 07:07:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101955/ERX101955.20_peaks.xls CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:07:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101955/ERX101955.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:07:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101955/ERX101955.20_summits.bed INFO @ Fri, 05 Jul 2019 07:07:20: Done! pass1 - making usageList (80 chroms): 10 millis pass2 - checking and writing primary data (26824 records, 4 fields): 38 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。