Job ID = 2001695 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T23:45:44 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 ) spots read : 27,690,878 reads read : 27,690,878 reads written : 27,690,878 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: 00:05:38 27690878 reads; of these: 27690878 (100.00%) were unpaired; of these: 611667 (2.21%) aligned 0 times 24250416 (87.58%) aligned exactly 1 time 2828795 (10.22%) aligned >1 times 97.79% overall alignment rate Time searching: 00:05:41 Overall time: 00:05:41 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] 14111871 / 27079211 = 0.5211 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 09:04:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102005/ERX102005.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102005/ERX102005.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102005/ERX102005.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102005/ERX102005.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 09:04:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:04:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:04:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102005/ERX102005.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102005/ERX102005.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102005/ERX102005.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102005/ERX102005.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 09:04:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:04:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:04:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102005/ERX102005.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102005/ERX102005.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102005/ERX102005.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102005/ERX102005.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 09:04:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:04:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:04:41: 1000000 INFO @ Fri, 05 Jul 2019 09:04:42: 1000000 INFO @ Fri, 05 Jul 2019 09:04:42: 1000000 INFO @ Fri, 05 Jul 2019 09:04:47: 2000000 INFO @ Fri, 05 Jul 2019 09:04:48: 2000000 INFO @ Fri, 05 Jul 2019 09:04:49: 2000000 INFO @ Fri, 05 Jul 2019 09:04:53: 3000000 INFO @ Fri, 05 Jul 2019 09:04:54: 3000000 INFO @ Fri, 05 Jul 2019 09:04:55: 3000000 INFO @ Fri, 05 Jul 2019 09:04:59: 4000000 INFO @ Fri, 05 Jul 2019 09:05:00: 4000000 INFO @ Fri, 05 Jul 2019 09:05:01: 4000000 INFO @ Fri, 05 Jul 2019 09:05:05: 5000000 INFO @ Fri, 05 Jul 2019 09:05:06: 5000000 INFO @ Fri, 05 Jul 2019 09:05:08: 5000000 INFO @ Fri, 05 Jul 2019 09:05:11: 6000000 INFO @ Fri, 05 Jul 2019 09:05:12: 6000000 INFO @ Fri, 05 Jul 2019 09:05:14: 6000000 INFO @ Fri, 05 Jul 2019 09:05:17: 7000000 INFO @ Fri, 05 Jul 2019 09:05:18: 7000000 INFO @ Fri, 05 Jul 2019 09:05:21: 7000000 INFO @ Fri, 05 Jul 2019 09:05:23: 8000000 INFO @ Fri, 05 Jul 2019 09:05:24: 8000000 INFO @ Fri, 05 Jul 2019 09:05:27: 8000000 INFO @ Fri, 05 Jul 2019 09:05:29: 9000000 INFO @ Fri, 05 Jul 2019 09:05:30: 9000000 INFO @ Fri, 05 Jul 2019 09:05:34: 9000000 INFO @ Fri, 05 Jul 2019 09:05:34: 10000000 INFO @ Fri, 05 Jul 2019 09:05:36: 10000000 INFO @ Fri, 05 Jul 2019 09:05:40: 10000000 INFO @ Fri, 05 Jul 2019 09:05:40: 11000000 INFO @ Fri, 05 Jul 2019 09:05:42: 11000000 INFO @ Fri, 05 Jul 2019 09:05:46: 12000000 INFO @ Fri, 05 Jul 2019 09:05:46: 11000000 INFO @ Fri, 05 Jul 2019 09:05:48: 12000000 INFO @ Fri, 05 Jul 2019 09:05:52: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:05:52: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:05:52: #1 total tags in treatment: 12967340 INFO @ Fri, 05 Jul 2019 09:05:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:05:52: #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 09:05:53: #1 tags after filtering in treatment: 12967078 INFO @ Fri, 05 Jul 2019 09:05:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:05:53: #1 finished! INFO @ Fri, 05 Jul 2019 09:05:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:05:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:05:53: 12000000 INFO @ Fri, 05 Jul 2019 09:05:54: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:05:54: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:05:54: #1 total tags in treatment: 12967340 INFO @ Fri, 05 Jul 2019 09:05:54: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:05:54: #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 09:05:54: #1 tags after filtering in treatment: 12967078 INFO @ Fri, 05 Jul 2019 09:05:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:05:54: #1 finished! INFO @ Fri, 05 Jul 2019 09:05:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:05:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:05:56: #2 number of paired peaks: 57550 INFO @ Fri, 05 Jul 2019 09:05:56: start model_add_line... INFO @ Fri, 05 Jul 2019 09:05:57: start X-correlation... INFO @ Fri, 05 Jul 2019 09:05:57: end of X-cor INFO @ Fri, 05 Jul 2019 09:05:57: #2 finished! INFO @ Fri, 05 Jul 2019 09:05:57: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 09:05:57: #2 alternative fragment length(s) may be 4,136 bps INFO @ Fri, 05 Jul 2019 09:05:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102005/ERX102005.05_model.r INFO @ Fri, 05 Jul 2019 09:05:57: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:05:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:05:58: #2 number of paired peaks: 57550 INFO @ Fri, 05 Jul 2019 09:05:58: start model_add_line... INFO @ Fri, 05 Jul 2019 09:05:58: start X-correlation... INFO @ Fri, 05 Jul 2019 09:05:58: end of X-cor INFO @ Fri, 05 Jul 2019 09:05:58: #2 finished! INFO @ Fri, 05 Jul 2019 09:05:58: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 09:05:58: #2 alternative fragment length(s) may be 4,136 bps INFO @ Fri, 05 Jul 2019 09:05:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102005/ERX102005.20_model.r INFO @ Fri, 05 Jul 2019 09:05:58: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:05:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:05:59: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:05:59: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:05:59: #1 total tags in treatment: 12967340 INFO @ Fri, 05 Jul 2019 09:05:59: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:05:59: #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 09:05:59: #1 tags after filtering in treatment: 12967078 INFO @ Fri, 05 Jul 2019 09:05:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:05:59: #1 finished! INFO @ Fri, 05 Jul 2019 09:05:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:05:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:06:03: #2 number of paired peaks: 57550 INFO @ Fri, 05 Jul 2019 09:06:03: start model_add_line... INFO @ Fri, 05 Jul 2019 09:06:03: start X-correlation... INFO @ Fri, 05 Jul 2019 09:06:03: end of X-cor INFO @ Fri, 05 Jul 2019 09:06:03: #2 finished! INFO @ Fri, 05 Jul 2019 09:06:03: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 09:06:03: #2 alternative fragment length(s) may be 4,136 bps INFO @ Fri, 05 Jul 2019 09:06:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102005/ERX102005.10_model.r INFO @ Fri, 05 Jul 2019 09:06:03: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:06:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:06:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:06:37: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:06:43: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:06:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102005/ERX102005.05_peaks.xls INFO @ Fri, 05 Jul 2019 09:06:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102005/ERX102005.20_peaks.xls INFO @ Fri, 05 Jul 2019 09:06:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102005/ERX102005.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:06:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102005/ERX102005.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:06:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102005/ERX102005.20_summits.bed INFO @ Fri, 05 Jul 2019 09:06:58: Done! INFO @ Fri, 05 Jul 2019 09:06:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102005/ERX102005.05_summits.bed INFO @ Fri, 05 Jul 2019 09:06:58: Done! pass1 - making usageList (82 chroms): 8 millis pass2 - checking and writing primary data (22091 records, 4 fields): 34 millis pass1 - making usageList (140 chroms): 9 millis pass2 - checking and writing primary data (48298 records, 4 fields): 64 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:07:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102005/ERX102005.10_peaks.xls INFO @ Fri, 05 Jul 2019 09:07:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102005/ERX102005.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:07:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102005/ERX102005.10_summits.bed INFO @ Fri, 05 Jul 2019 09:07:05: Done! pass1 - making usageList (110 chroms): 7 millis pass2 - checking and writing primary data (36438 records, 4 fields): 50 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。