Job ID = 2001563 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T20:03:47 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 : 25,983,667 reads read : 25,983,667 reads written : 25,983,667 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: 00:05:38 25983667 reads; of these: 25983667 (100.00%) were unpaired; of these: 562754 (2.17%) aligned 0 times 22836967 (87.89%) aligned exactly 1 time 2583946 (9.94%) aligned >1 times 97.83% overall alignment rate Time searching: 00:05:39 Overall time: 00:05:39 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] 12249796 / 25420913 = 0.4819 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 05:15:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101906/ERX101906.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101906/ERX101906.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101906/ERX101906.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101906/ERX101906.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 05:15:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:15:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:15:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101906/ERX101906.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101906/ERX101906.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101906/ERX101906.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101906/ERX101906.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 05:15:13: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:15:13: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:15:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101906/ERX101906.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101906/ERX101906.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101906/ERX101906.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101906/ERX101906.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 05:15:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:15:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:15:22: 1000000 INFO @ Fri, 05 Jul 2019 05:15:22: 1000000 INFO @ Fri, 05 Jul 2019 05:15:24: 1000000 INFO @ Fri, 05 Jul 2019 05:15:30: 2000000 INFO @ Fri, 05 Jul 2019 05:15:32: 2000000 INFO @ Fri, 05 Jul 2019 05:15:34: 2000000 INFO @ Fri, 05 Jul 2019 05:15:39: 3000000 INFO @ Fri, 05 Jul 2019 05:15:42: 3000000 INFO @ Fri, 05 Jul 2019 05:15:43: 3000000 INFO @ Fri, 05 Jul 2019 05:15:46: 4000000 INFO @ Fri, 05 Jul 2019 05:15:52: 4000000 INFO @ Fri, 05 Jul 2019 05:15:54: 4000000 INFO @ Fri, 05 Jul 2019 05:15:54: 5000000 INFO @ Fri, 05 Jul 2019 05:16:02: 5000000 INFO @ Fri, 05 Jul 2019 05:16:02: 6000000 INFO @ Fri, 05 Jul 2019 05:16:03: 5000000 INFO @ Fri, 05 Jul 2019 05:16:10: 7000000 INFO @ Fri, 05 Jul 2019 05:16:12: 6000000 INFO @ Fri, 05 Jul 2019 05:16:13: 6000000 INFO @ Fri, 05 Jul 2019 05:16:19: 8000000 INFO @ Fri, 05 Jul 2019 05:16:21: 7000000 INFO @ Fri, 05 Jul 2019 05:16:23: 7000000 INFO @ Fri, 05 Jul 2019 05:16:27: 9000000 INFO @ Fri, 05 Jul 2019 05:16:31: 8000000 INFO @ Fri, 05 Jul 2019 05:16:33: 8000000 INFO @ Fri, 05 Jul 2019 05:16:35: 10000000 INFO @ Fri, 05 Jul 2019 05:16:41: 9000000 INFO @ Fri, 05 Jul 2019 05:16:43: 9000000 INFO @ Fri, 05 Jul 2019 05:16:43: 11000000 INFO @ Fri, 05 Jul 2019 05:16:51: 12000000 INFO @ Fri, 05 Jul 2019 05:16:51: 10000000 INFO @ Fri, 05 Jul 2019 05:16:53: 10000000 INFO @ Fri, 05 Jul 2019 05:16:59: 13000000 INFO @ Fri, 05 Jul 2019 05:17:00: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:17:00: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:17:00: #1 total tags in treatment: 13171117 INFO @ Fri, 05 Jul 2019 05:17:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:17:00: #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 05:17:00: #1 tags after filtering in treatment: 13170815 INFO @ Fri, 05 Jul 2019 05:17:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:17:00: #1 finished! INFO @ Fri, 05 Jul 2019 05:17:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:17:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:17:01: 11000000 INFO @ Fri, 05 Jul 2019 05:17:03: 11000000 INFO @ Fri, 05 Jul 2019 05:17:04: #2 number of paired peaks: 46406 INFO @ Fri, 05 Jul 2019 05:17:04: start model_add_line... INFO @ Fri, 05 Jul 2019 05:17:04: start X-correlation... INFO @ Fri, 05 Jul 2019 05:17:04: end of X-cor INFO @ Fri, 05 Jul 2019 05:17:04: #2 finished! INFO @ Fri, 05 Jul 2019 05:17:04: #2 predicted fragment length is 140 bps INFO @ Fri, 05 Jul 2019 05:17:04: #2 alternative fragment length(s) may be 4,140 bps INFO @ Fri, 05 Jul 2019 05:17:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101906/ERX101906.10_model.r INFO @ Fri, 05 Jul 2019 05:17:04: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:17:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:17:10: 12000000 INFO @ Fri, 05 Jul 2019 05:17:12: 12000000 INFO @ Fri, 05 Jul 2019 05:17:20: 13000000 INFO @ Fri, 05 Jul 2019 05:17:21: 13000000 INFO @ Fri, 05 Jul 2019 05:17:21: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:17:21: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:17:21: #1 total tags in treatment: 13171117 INFO @ Fri, 05 Jul 2019 05:17:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:17:21: #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 05:17:22: #1 tags after filtering in treatment: 13170815 INFO @ Fri, 05 Jul 2019 05:17:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:17:22: #1 finished! INFO @ Fri, 05 Jul 2019 05:17:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:17:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:17:23: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:17:23: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:17:23: #1 total tags in treatment: 13171117 INFO @ Fri, 05 Jul 2019 05:17:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:17:23: #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 05:17:23: #1 tags after filtering in treatment: 13170815 INFO @ Fri, 05 Jul 2019 05:17:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:17:23: #1 finished! INFO @ Fri, 05 Jul 2019 05:17:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:17:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:17:25: #2 number of paired peaks: 46406 INFO @ Fri, 05 Jul 2019 05:17:25: start model_add_line... INFO @ Fri, 05 Jul 2019 05:17:26: start X-correlation... INFO @ Fri, 05 Jul 2019 05:17:26: end of X-cor INFO @ Fri, 05 Jul 2019 05:17:26: #2 finished! INFO @ Fri, 05 Jul 2019 05:17:26: #2 predicted fragment length is 140 bps INFO @ Fri, 05 Jul 2019 05:17:26: #2 alternative fragment length(s) may be 4,140 bps INFO @ Fri, 05 Jul 2019 05:17:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101906/ERX101906.05_model.r INFO @ Fri, 05 Jul 2019 05:17:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:17:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:17:26: #2 number of paired peaks: 46406 INFO @ Fri, 05 Jul 2019 05:17:26: start model_add_line... INFO @ Fri, 05 Jul 2019 05:17:27: start X-correlation... INFO @ Fri, 05 Jul 2019 05:17:27: end of X-cor INFO @ Fri, 05 Jul 2019 05:17:27: #2 finished! INFO @ Fri, 05 Jul 2019 05:17:27: #2 predicted fragment length is 140 bps INFO @ Fri, 05 Jul 2019 05:17:27: #2 alternative fragment length(s) may be 4,140 bps INFO @ Fri, 05 Jul 2019 05:17:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101906/ERX101906.20_model.r INFO @ Fri, 05 Jul 2019 05:17:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:17:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:17:45: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:18:07: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:18:08: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:18:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101906/ERX101906.10_peaks.xls INFO @ Fri, 05 Jul 2019 05:18:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101906/ERX101906.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:18:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101906/ERX101906.10_summits.bed INFO @ Fri, 05 Jul 2019 05:18:10: Done! pass1 - making usageList (114 chroms): 8 millis pass2 - checking and writing primary data (35068 records, 4 fields): 57 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:18:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101906/ERX101906.05_peaks.xls INFO @ Fri, 05 Jul 2019 05:18:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101906/ERX101906.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:18:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101906/ERX101906.05_summits.bed INFO @ Fri, 05 Jul 2019 05:18:32: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (133 chroms): 10 millis pass2 - checking and writing primary data (44137 records, 4 fields): 60 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:18:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101906/ERX101906.20_peaks.xls INFO @ Fri, 05 Jul 2019 05:18:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101906/ERX101906.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:18:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101906/ERX101906.20_summits.bed INFO @ Fri, 05 Jul 2019 05:18:35: Done! pass1 - making usageList (90 chroms): 8 millis pass2 - checking and writing primary data (25167 records, 4 fields): 36 millis CompletedMACS2peakCalling BigWig に変換しました。