Job ID = 2001559 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T19:46:10 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 : 22,600,184 reads read : 22,600,184 reads written : 22,600,184 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: 00:00:01 Multiseed full-index search: 00:05:43 22600184 reads; of these: 22600184 (100.00%) were unpaired; of these: 445588 (1.97%) aligned 0 times 19986050 (88.43%) aligned exactly 1 time 2168546 (9.60%) aligned >1 times 98.03% overall alignment rate Time searching: 00:05:45 Overall time: 00:05:45 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] 12242539 / 22154596 = 0.5526 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 05:04:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101902/ERX101902.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101902/ERX101902.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101902/ERX101902.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101902/ERX101902.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 05:04:52: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:04:52: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:04:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101902/ERX101902.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101902/ERX101902.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101902/ERX101902.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101902/ERX101902.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 05:04:53: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:04:53: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:04:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101902/ERX101902.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101902/ERX101902.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101902/ERX101902.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101902/ERX101902.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 05:04:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:04:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:05:01: 1000000 INFO @ Fri, 05 Jul 2019 05:05:01: 1000000 INFO @ Fri, 05 Jul 2019 05:05:02: 1000000 INFO @ Fri, 05 Jul 2019 05:05:08: 2000000 INFO @ Fri, 05 Jul 2019 05:05:09: 2000000 INFO @ Fri, 05 Jul 2019 05:05:09: 2000000 INFO @ Fri, 05 Jul 2019 05:05:15: 3000000 INFO @ Fri, 05 Jul 2019 05:05:16: 3000000 INFO @ Fri, 05 Jul 2019 05:05:18: 3000000 INFO @ Fri, 05 Jul 2019 05:05:21: 4000000 INFO @ Fri, 05 Jul 2019 05:05:23: 4000000 INFO @ Fri, 05 Jul 2019 05:05:26: 4000000 INFO @ Fri, 05 Jul 2019 05:05:28: 5000000 INFO @ Fri, 05 Jul 2019 05:05:30: 5000000 INFO @ Fri, 05 Jul 2019 05:05:35: 5000000 INFO @ Fri, 05 Jul 2019 05:05:35: 6000000 INFO @ Fri, 05 Jul 2019 05:05:37: 6000000 INFO @ Fri, 05 Jul 2019 05:05:42: 7000000 INFO @ Fri, 05 Jul 2019 05:05:43: 6000000 INFO @ Fri, 05 Jul 2019 05:05:44: 7000000 INFO @ Fri, 05 Jul 2019 05:05:49: 8000000 INFO @ Fri, 05 Jul 2019 05:05:51: 8000000 INFO @ Fri, 05 Jul 2019 05:05:51: 7000000 INFO @ Fri, 05 Jul 2019 05:05:56: 9000000 INFO @ Fri, 05 Jul 2019 05:05:57: 9000000 INFO @ Fri, 05 Jul 2019 05:05:59: 8000000 INFO @ Fri, 05 Jul 2019 05:06:03: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:06:03: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:06:03: #1 total tags in treatment: 9912057 INFO @ Fri, 05 Jul 2019 05:06:03: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:06:03: #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 05:06:03: #1 tags after filtering in treatment: 9911765 INFO @ Fri, 05 Jul 2019 05:06:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:06:03: #1 finished! INFO @ Fri, 05 Jul 2019 05:06:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:06:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:06:04: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:06:04: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:06:04: #1 total tags in treatment: 9912057 INFO @ Fri, 05 Jul 2019 05:06:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:06:04: #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 05:06:05: #1 tags after filtering in treatment: 9911765 INFO @ Fri, 05 Jul 2019 05:06:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:06:05: #1 finished! INFO @ Fri, 05 Jul 2019 05:06:05: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:06:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:06:06: #2 number of paired peaks: 47599 INFO @ Fri, 05 Jul 2019 05:06:06: start model_add_line... INFO @ Fri, 05 Jul 2019 05:06:06: start X-correlation... INFO @ Fri, 05 Jul 2019 05:06:06: end of X-cor INFO @ Fri, 05 Jul 2019 05:06:06: #2 finished! INFO @ Fri, 05 Jul 2019 05:06:06: #2 predicted fragment length is 141 bps INFO @ Fri, 05 Jul 2019 05:06:06: #2 alternative fragment length(s) may be 4,141 bps INFO @ Fri, 05 Jul 2019 05:06:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101902/ERX101902.10_model.r INFO @ Fri, 05 Jul 2019 05:06:06: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:06:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:06:08: 9000000 INFO @ Fri, 05 Jul 2019 05:06:08: #2 number of paired peaks: 47599 INFO @ Fri, 05 Jul 2019 05:06:08: start model_add_line... INFO @ Fri, 05 Jul 2019 05:06:08: start X-correlation... INFO @ Fri, 05 Jul 2019 05:06:08: end of X-cor INFO @ Fri, 05 Jul 2019 05:06:08: #2 finished! INFO @ Fri, 05 Jul 2019 05:06:08: #2 predicted fragment length is 141 bps INFO @ Fri, 05 Jul 2019 05:06:08: #2 alternative fragment length(s) may be 4,141 bps INFO @ Fri, 05 Jul 2019 05:06:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101902/ERX101902.20_model.r INFO @ Fri, 05 Jul 2019 05:06:08: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:06:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:06:15: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:06:15: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:06:15: #1 total tags in treatment: 9912057 INFO @ Fri, 05 Jul 2019 05:06:15: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:06:15: #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 05:06:16: #1 tags after filtering in treatment: 9911765 INFO @ Fri, 05 Jul 2019 05:06:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:06:16: #1 finished! INFO @ Fri, 05 Jul 2019 05:06:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:06:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:06:19: #2 number of paired peaks: 47599 INFO @ Fri, 05 Jul 2019 05:06:19: start model_add_line... INFO @ Fri, 05 Jul 2019 05:06:19: start X-correlation... INFO @ Fri, 05 Jul 2019 05:06:19: end of X-cor INFO @ Fri, 05 Jul 2019 05:06:19: #2 finished! INFO @ Fri, 05 Jul 2019 05:06:19: #2 predicted fragment length is 141 bps INFO @ Fri, 05 Jul 2019 05:06:19: #2 alternative fragment length(s) may be 4,141 bps INFO @ Fri, 05 Jul 2019 05:06:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101902/ERX101902.05_model.r INFO @ Fri, 05 Jul 2019 05:06:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:06:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:06:39: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:06:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:06:52: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:06:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101902/ERX101902.10_peaks.xls INFO @ Fri, 05 Jul 2019 05:06:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101902/ERX101902.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:06:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101902/ERX101902.10_summits.bed INFO @ Fri, 05 Jul 2019 05:06:57: Done! pass1 - making usageList (105 chroms): 10 millis pass2 - checking and writing primary data (32344 records, 4 fields): 46 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:06:58: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101902/ERX101902.20_peaks.xls INFO @ Fri, 05 Jul 2019 05:06:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101902/ERX101902.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:06:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101902/ERX101902.20_summits.bed INFO @ Fri, 05 Jul 2019 05:06:59: Done! pass1 - making usageList (80 chroms): 5 millis pass2 - checking and writing primary data (19487 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:07:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101902/ERX101902.05_peaks.xls INFO @ Fri, 05 Jul 2019 05:07:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101902/ERX101902.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:07:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101902/ERX101902.05_summits.bed INFO @ Fri, 05 Jul 2019 05:07:11: Done! pass1 - making usageList (134 chroms): 9 millis pass2 - checking and writing primary data (42866 records, 4 fields): 63 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。