Job ID = 2001159 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T19:10:34 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 : 57,283,020 reads read : 57,283,020 reads written : 57,283,020 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:43:10 57283020 reads; of these: 57283020 (100.00%) were unpaired; of these: 1389849 (2.43%) aligned 0 times 49758668 (86.86%) aligned exactly 1 time 6134503 (10.71%) aligned >1 times 97.57% overall alignment rate Time searching: 00:43:11 Overall time: 00:43:11 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 24 files... [bam_rmdupse_core] 31533653 / 55893171 = 0.5642 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 05:14:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101849/ERX101849.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101849/ERX101849.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101849/ERX101849.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101849/ERX101849.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 05:14:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:14:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:14:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101849/ERX101849.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101849/ERX101849.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101849/ERX101849.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101849/ERX101849.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 05:14:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:14:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:14:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101849/ERX101849.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101849/ERX101849.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101849/ERX101849.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101849/ERX101849.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 05:14:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:14:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:14:27: 1000000 INFO @ Fri, 05 Jul 2019 05:14:28: 1000000 INFO @ Fri, 05 Jul 2019 05:14:28: 1000000 INFO @ Fri, 05 Jul 2019 05:14:37: 2000000 INFO @ Fri, 05 Jul 2019 05:14:38: 2000000 INFO @ Fri, 05 Jul 2019 05:14:39: 2000000 INFO @ Fri, 05 Jul 2019 05:14:47: 3000000 INFO @ Fri, 05 Jul 2019 05:14:49: 3000000 INFO @ Fri, 05 Jul 2019 05:14:49: 3000000 INFO @ Fri, 05 Jul 2019 05:14:56: 4000000 INFO @ Fri, 05 Jul 2019 05:14:58: 4000000 INFO @ Fri, 05 Jul 2019 05:14:59: 4000000 INFO @ Fri, 05 Jul 2019 05:15:05: 5000000 INFO @ Fri, 05 Jul 2019 05:15:08: 5000000 INFO @ Fri, 05 Jul 2019 05:15:08: 5000000 INFO @ Fri, 05 Jul 2019 05:15:14: 6000000 INFO @ Fri, 05 Jul 2019 05:15:18: 6000000 INFO @ Fri, 05 Jul 2019 05:15:18: 6000000 INFO @ Fri, 05 Jul 2019 05:15:23: 7000000 INFO @ Fri, 05 Jul 2019 05:15:28: 7000000 INFO @ Fri, 05 Jul 2019 05:15:28: 7000000 INFO @ Fri, 05 Jul 2019 05:15:31: 8000000 INFO @ Fri, 05 Jul 2019 05:15:37: 8000000 INFO @ Fri, 05 Jul 2019 05:15:38: 8000000 INFO @ Fri, 05 Jul 2019 05:15:40: 9000000 INFO @ Fri, 05 Jul 2019 05:15:47: 9000000 INFO @ Fri, 05 Jul 2019 05:15:48: 9000000 INFO @ Fri, 05 Jul 2019 05:15:50: 10000000 INFO @ Fri, 05 Jul 2019 05:15:57: 10000000 INFO @ Fri, 05 Jul 2019 05:15:58: 11000000 INFO @ Fri, 05 Jul 2019 05:15:58: 10000000 INFO @ Fri, 05 Jul 2019 05:16:06: 11000000 INFO @ Fri, 05 Jul 2019 05:16:07: 12000000 INFO @ Fri, 05 Jul 2019 05:16:08: 11000000 INFO @ Fri, 05 Jul 2019 05:16:16: 13000000 INFO @ Fri, 05 Jul 2019 05:16:16: 12000000 INFO @ Fri, 05 Jul 2019 05:16:18: 12000000 INFO @ Fri, 05 Jul 2019 05:16:24: 14000000 INFO @ Fri, 05 Jul 2019 05:16:26: 13000000 INFO @ Fri, 05 Jul 2019 05:16:28: 13000000 INFO @ Fri, 05 Jul 2019 05:16:33: 15000000 INFO @ Fri, 05 Jul 2019 05:16:36: 14000000 INFO @ Fri, 05 Jul 2019 05:16:37: 14000000 INFO @ Fri, 05 Jul 2019 05:16:42: 16000000 INFO @ Fri, 05 Jul 2019 05:16:45: 15000000 INFO @ Fri, 05 Jul 2019 05:16:47: 15000000 INFO @ Fri, 05 Jul 2019 05:16:51: 17000000 INFO @ Fri, 05 Jul 2019 05:16:54: 16000000 INFO @ Fri, 05 Jul 2019 05:16:57: 16000000 INFO @ Fri, 05 Jul 2019 05:17:00: 18000000 INFO @ Fri, 05 Jul 2019 05:17:03: 17000000 INFO @ Fri, 05 Jul 2019 05:17:07: 17000000 INFO @ Fri, 05 Jul 2019 05:17:09: 19000000 INFO @ Fri, 05 Jul 2019 05:17:13: 18000000 INFO @ Fri, 05 Jul 2019 05:17:16: 18000000 INFO @ Fri, 05 Jul 2019 05:17:18: 20000000 INFO @ Fri, 05 Jul 2019 05:17:22: 19000000 INFO @ Fri, 05 Jul 2019 05:17:26: 19000000 INFO @ Fri, 05 Jul 2019 05:17:27: 21000000 INFO @ Fri, 05 Jul 2019 05:17:31: 20000000 INFO @ Fri, 05 Jul 2019 05:17:36: 20000000 INFO @ Fri, 05 Jul 2019 05:17:36: 22000000 INFO @ Fri, 05 Jul 2019 05:17:41: 21000000 INFO @ Fri, 05 Jul 2019 05:17:45: 23000000 INFO @ Fri, 05 Jul 2019 05:17:45: 21000000 INFO @ Fri, 05 Jul 2019 05:17:51: 22000000 INFO @ Fri, 05 Jul 2019 05:17:55: 24000000 INFO @ Fri, 05 Jul 2019 05:17:55: 22000000 INFO @ Fri, 05 Jul 2019 05:17:58: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 05:17:58: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 05:17:58: #1 total tags in treatment: 24359518 INFO @ Fri, 05 Jul 2019 05:17:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:17:58: #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 05:17:59: #1 tags after filtering in treatment: 24359290 INFO @ Fri, 05 Jul 2019 05:17:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:17:59: #1 finished! INFO @ Fri, 05 Jul 2019 05:17:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:17:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:18:00: 23000000 INFO @ Fri, 05 Jul 2019 05:18:04: 23000000 INFO @ Fri, 05 Jul 2019 05:18:05: #2 number of paired peaks: 60039 INFO @ Fri, 05 Jul 2019 05:18:05: start model_add_line... INFO @ Fri, 05 Jul 2019 05:18:05: start X-correlation... INFO @ Fri, 05 Jul 2019 05:18:06: end of X-cor INFO @ Fri, 05 Jul 2019 05:18:06: #2 finished! INFO @ Fri, 05 Jul 2019 05:18:06: #2 predicted fragment length is 108 bps INFO @ Fri, 05 Jul 2019 05:18:06: #2 alternative fragment length(s) may be 108 bps INFO @ Fri, 05 Jul 2019 05:18:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101849/ERX101849.05_model.r INFO @ Fri, 05 Jul 2019 05:18:06: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:18:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:18:10: 24000000 INFO @ Fri, 05 Jul 2019 05:18:13: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 05:18:13: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 05:18:13: #1 total tags in treatment: 24359518 INFO @ Fri, 05 Jul 2019 05:18:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:18:13: #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 05:18:14: 24000000 INFO @ Fri, 05 Jul 2019 05:18:14: #1 tags after filtering in treatment: 24359290 INFO @ Fri, 05 Jul 2019 05:18:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:18:14: #1 finished! INFO @ Fri, 05 Jul 2019 05:18:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:18:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:18:17: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 05:18:17: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 05:18:17: #1 total tags in treatment: 24359518 INFO @ Fri, 05 Jul 2019 05:18:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:18:17: #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 05:18:18: #1 tags after filtering in treatment: 24359290 INFO @ Fri, 05 Jul 2019 05:18:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:18:18: #1 finished! INFO @ Fri, 05 Jul 2019 05:18:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:18:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:18:20: #2 number of paired peaks: 60039 INFO @ Fri, 05 Jul 2019 05:18:20: start model_add_line... INFO @ Fri, 05 Jul 2019 05:18:21: start X-correlation... INFO @ Fri, 05 Jul 2019 05:18:21: end of X-cor INFO @ Fri, 05 Jul 2019 05:18:21: #2 finished! INFO @ Fri, 05 Jul 2019 05:18:21: #2 predicted fragment length is 108 bps INFO @ Fri, 05 Jul 2019 05:18:21: #2 alternative fragment length(s) may be 108 bps INFO @ Fri, 05 Jul 2019 05:18:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101849/ERX101849.20_model.r INFO @ Fri, 05 Jul 2019 05:18:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:18:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:18:24: #2 number of paired peaks: 60039 INFO @ Fri, 05 Jul 2019 05:18:24: start model_add_line... INFO @ Fri, 05 Jul 2019 05:18:24: start X-correlation... INFO @ Fri, 05 Jul 2019 05:18:24: end of X-cor INFO @ Fri, 05 Jul 2019 05:18:24: #2 finished! INFO @ Fri, 05 Jul 2019 05:18:24: #2 predicted fragment length is 108 bps INFO @ Fri, 05 Jul 2019 05:18:24: #2 alternative fragment length(s) may be 108 bps INFO @ Fri, 05 Jul 2019 05:18:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101849/ERX101849.10_model.r INFO @ Fri, 05 Jul 2019 05:18:24: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:18:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:19:26: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:19:37: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:19:43: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:20:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101849/ERX101849.05_peaks.xls INFO @ Fri, 05 Jul 2019 05:20:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101849/ERX101849.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:20:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101849/ERX101849.05_summits.bed INFO @ Fri, 05 Jul 2019 05:20:17: Done! pass1 - making usageList (175 chroms): 17 millis pass2 - checking and writing primary data (61095 records, 4 fields): 95 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:20:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101849/ERX101849.20_peaks.xls INFO @ Fri, 05 Jul 2019 05:20:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101849/ERX101849.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:20:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101849/ERX101849.20_summits.bed INFO @ Fri, 05 Jul 2019 05:20:21: Done! pass1 - making usageList (114 chroms): 13 millis pass2 - checking and writing primary data (34424 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:20:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101849/ERX101849.10_peaks.xls INFO @ Fri, 05 Jul 2019 05:20:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101849/ERX101849.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:20:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101849/ERX101849.10_summits.bed INFO @ Fri, 05 Jul 2019 05:20:30: Done! pass1 - making usageList (141 chroms): 16 millis pass2 - checking and writing primary data (47655 records, 4 fields): 78 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。