Job ID = 2001155 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T18:46:17 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 ) 2019-07-04T18:59:10 fasterq-dump.2.9.6 fatal: SIGNAL - Segmentation fault spots read : 55,257,844 reads read : 55,257,844 reads written : 55,257,844 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: 00:42:48 55257844 reads; of these: 55257844 (100.00%) were unpaired; of these: 1429440 (2.59%) aligned 0 times 48047959 (86.95%) aligned exactly 1 time 5780445 (10.46%) aligned >1 times 97.41% overall alignment rate Time searching: 00:42:51 Overall time: 00:42:51 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] 31296149 / 53828404 = 0.5814 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 05:08:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101845/ERX101845.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101845/ERX101845.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101845/ERX101845.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101845/ERX101845.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 05:08:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:08:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:08:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101845/ERX101845.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101845/ERX101845.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101845/ERX101845.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101845/ERX101845.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 05:08:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:08:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:08:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101845/ERX101845.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101845/ERX101845.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101845/ERX101845.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101845/ERX101845.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 05:08:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:08:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:09:07: 1000000 INFO @ Fri, 05 Jul 2019 05:09:07: 1000000 INFO @ Fri, 05 Jul 2019 05:09:08: 1000000 INFO @ Fri, 05 Jul 2019 05:09:18: 2000000 INFO @ Fri, 05 Jul 2019 05:09:18: 2000000 INFO @ Fri, 05 Jul 2019 05:09:19: 2000000 INFO @ Fri, 05 Jul 2019 05:09:29: 3000000 INFO @ Fri, 05 Jul 2019 05:09:30: 3000000 INFO @ Fri, 05 Jul 2019 05:09:30: 3000000 INFO @ Fri, 05 Jul 2019 05:09:39: 4000000 INFO @ Fri, 05 Jul 2019 05:09:41: 4000000 INFO @ Fri, 05 Jul 2019 05:09:41: 4000000 INFO @ Fri, 05 Jul 2019 05:09:50: 5000000 INFO @ Fri, 05 Jul 2019 05:09:53: 5000000 INFO @ Fri, 05 Jul 2019 05:09:53: 5000000 INFO @ Fri, 05 Jul 2019 05:10:01: 6000000 INFO @ Fri, 05 Jul 2019 05:10:04: 6000000 INFO @ Fri, 05 Jul 2019 05:10:04: 6000000 INFO @ Fri, 05 Jul 2019 05:10:12: 7000000 INFO @ Fri, 05 Jul 2019 05:10:15: 7000000 INFO @ Fri, 05 Jul 2019 05:10:15: 7000000 INFO @ Fri, 05 Jul 2019 05:10:23: 8000000 INFO @ Fri, 05 Jul 2019 05:10:26: 8000000 INFO @ Fri, 05 Jul 2019 05:10:26: 8000000 INFO @ Fri, 05 Jul 2019 05:10:33: 9000000 INFO @ Fri, 05 Jul 2019 05:10:36: 9000000 INFO @ Fri, 05 Jul 2019 05:10:37: 9000000 INFO @ Fri, 05 Jul 2019 05:10:44: 10000000 INFO @ Fri, 05 Jul 2019 05:10:47: 10000000 INFO @ Fri, 05 Jul 2019 05:10:48: 10000000 INFO @ Fri, 05 Jul 2019 05:10:54: 11000000 INFO @ Fri, 05 Jul 2019 05:10:58: 11000000 INFO @ Fri, 05 Jul 2019 05:10:59: 11000000 INFO @ Fri, 05 Jul 2019 05:11:05: 12000000 INFO @ Fri, 05 Jul 2019 05:11:07: 12000000 INFO @ Fri, 05 Jul 2019 05:11:09: 12000000 INFO @ Fri, 05 Jul 2019 05:11:16: 13000000 INFO @ Fri, 05 Jul 2019 05:11:16: 13000000 INFO @ Fri, 05 Jul 2019 05:11:19: 13000000 INFO @ Fri, 05 Jul 2019 05:11:24: 14000000 INFO @ Fri, 05 Jul 2019 05:11:26: 14000000 INFO @ Fri, 05 Jul 2019 05:11:29: 14000000 INFO @ Fri, 05 Jul 2019 05:11:32: 15000000 INFO @ Fri, 05 Jul 2019 05:11:37: 15000000 INFO @ Fri, 05 Jul 2019 05:11:39: 15000000 INFO @ Fri, 05 Jul 2019 05:11:40: 16000000 INFO @ Fri, 05 Jul 2019 05:11:47: 16000000 INFO @ Fri, 05 Jul 2019 05:11:49: 17000000 INFO @ Fri, 05 Jul 2019 05:11:49: 16000000 INFO @ Fri, 05 Jul 2019 05:11:57: 18000000 INFO @ Fri, 05 Jul 2019 05:11:57: 17000000 INFO @ Fri, 05 Jul 2019 05:11:59: 17000000 INFO @ Fri, 05 Jul 2019 05:12:05: 19000000 INFO @ Fri, 05 Jul 2019 05:12:08: 18000000 INFO @ Fri, 05 Jul 2019 05:12:10: 18000000 INFO @ Fri, 05 Jul 2019 05:12:14: 20000000 INFO @ Fri, 05 Jul 2019 05:12:18: 19000000 INFO @ Fri, 05 Jul 2019 05:12:20: 19000000 INFO @ Fri, 05 Jul 2019 05:12:23: 21000000 INFO @ Fri, 05 Jul 2019 05:12:28: 20000000 INFO @ Fri, 05 Jul 2019 05:12:30: 20000000 INFO @ Fri, 05 Jul 2019 05:12:33: 22000000 INFO @ Fri, 05 Jul 2019 05:12:38: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 05:12:38: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 05:12:38: #1 total tags in treatment: 22532255 INFO @ Fri, 05 Jul 2019 05:12:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:12:38: #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 05:12:39: #1 tags after filtering in treatment: 22532031 INFO @ Fri, 05 Jul 2019 05:12:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:12:39: #1 finished! INFO @ Fri, 05 Jul 2019 05:12:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:12:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:12:39: 21000000 INFO @ Fri, 05 Jul 2019 05:12:41: 21000000 INFO @ Fri, 05 Jul 2019 05:12:44: #2 number of paired peaks: 54610 INFO @ Fri, 05 Jul 2019 05:12:44: start model_add_line... INFO @ Fri, 05 Jul 2019 05:12:45: start X-correlation... INFO @ Fri, 05 Jul 2019 05:12:45: end of X-cor INFO @ Fri, 05 Jul 2019 05:12:45: #2 finished! INFO @ Fri, 05 Jul 2019 05:12:45: #2 predicted fragment length is 115 bps INFO @ Fri, 05 Jul 2019 05:12:45: #2 alternative fragment length(s) may be 115 bps INFO @ Fri, 05 Jul 2019 05:12:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101845/ERX101845.05_model.r INFO @ Fri, 05 Jul 2019 05:12:45: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:12:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:12:49: 22000000 INFO @ Fri, 05 Jul 2019 05:12:51: 22000000 INFO @ Fri, 05 Jul 2019 05:12:55: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 05:12:55: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 05:12:55: #1 total tags in treatment: 22532255 INFO @ Fri, 05 Jul 2019 05:12:55: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:12:55: #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 05:12:56: #1 tags after filtering in treatment: 22532031 INFO @ Fri, 05 Jul 2019 05:12:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:12:56: #1 finished! INFO @ Fri, 05 Jul 2019 05:12:56: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:12:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:12:57: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 05:12:57: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 05:12:57: #1 total tags in treatment: 22532255 INFO @ Fri, 05 Jul 2019 05:12:57: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:12:57: #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 05:12:58: #1 tags after filtering in treatment: 22532031 INFO @ Fri, 05 Jul 2019 05:12:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:12:58: #1 finished! INFO @ Fri, 05 Jul 2019 05:12:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:12:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:13:01: #2 number of paired peaks: 54610 INFO @ Fri, 05 Jul 2019 05:13:01: start model_add_line... INFO @ Fri, 05 Jul 2019 05:13:02: start X-correlation... INFO @ Fri, 05 Jul 2019 05:13:02: end of X-cor INFO @ Fri, 05 Jul 2019 05:13:02: #2 finished! INFO @ Fri, 05 Jul 2019 05:13:02: #2 predicted fragment length is 115 bps INFO @ Fri, 05 Jul 2019 05:13:02: #2 alternative fragment length(s) may be 115 bps INFO @ Fri, 05 Jul 2019 05:13:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101845/ERX101845.20_model.r INFO @ Fri, 05 Jul 2019 05:13:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:13:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:13:03: #2 number of paired peaks: 54610 INFO @ Fri, 05 Jul 2019 05:13:03: start model_add_line... INFO @ Fri, 05 Jul 2019 05:13:03: start X-correlation... INFO @ Fri, 05 Jul 2019 05:13:03: end of X-cor INFO @ Fri, 05 Jul 2019 05:13:03: #2 finished! INFO @ Fri, 05 Jul 2019 05:13:03: #2 predicted fragment length is 115 bps INFO @ Fri, 05 Jul 2019 05:13:03: #2 alternative fragment length(s) may be 115 bps INFO @ Fri, 05 Jul 2019 05:13:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101845/ERX101845.10_model.r INFO @ Fri, 05 Jul 2019 05:13:03: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:13:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:13:51: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 05:14:10: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:14:10: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:14:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101845/ERX101845.05_peaks.xls INFO @ Fri, 05 Jul 2019 05:14:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101845/ERX101845.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:14:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101845/ERX101845.05_summits.bed INFO @ Fri, 05 Jul 2019 05:14:32: Done! pass1 - making usageList (170 chroms): 11 millis pass2 - checking and writing primary data (54961 records, 4 fields): 77 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:14:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101845/ERX101845.20_peaks.xls INFO @ Fri, 05 Jul 2019 05:14:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101845/ERX101845.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:14:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101845/ERX101845.20_summits.bed INFO @ Fri, 05 Jul 2019 05:14:50: Done! INFO @ Fri, 05 Jul 2019 05:14:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101845/ERX101845.10_peaks.xls pass1 - making usageList (112 chroms): 9 millis pass2 - checking and writing primary data (32156 records, 4 fields): 52 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:14:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101845/ERX101845.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:14:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101845/ERX101845.10_summits.bed INFO @ Fri, 05 Jul 2019 05:14:51: Done! pass1 - making usageList (135 chroms): 9 millis pass2 - checking and writing primary data (43305 records, 4 fields): 61 millis CompletedMACS2peakCalling BigWig に変換しました。