Job ID = 2001564 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T19:57:56 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 ) 2019-07-04T19:59:37 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 : 22,485,372 reads read : 22,485,372 reads written : 22,485,372 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:05:18 22485372 reads; of these: 22485372 (100.00%) were unpaired; of these: 460022 (2.05%) aligned 0 times 19842544 (88.25%) aligned exactly 1 time 2182806 (9.71%) aligned >1 times 97.95% overall alignment rate Time searching: 00:05:22 Overall time: 00:05:22 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] 11180105 / 22025350 = 0.5076 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 05:14:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101907/ERX101907.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101907/ERX101907.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101907/ERX101907.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101907/ERX101907.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 05:14:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:14:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:14:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101907/ERX101907.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101907/ERX101907.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101907/ERX101907.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101907/ERX101907.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 05:14:21: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:14:21: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:14:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101907/ERX101907.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101907/ERX101907.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101907/ERX101907.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101907/ERX101907.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 05:14:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:14:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:14:30: 1000000 INFO @ Fri, 05 Jul 2019 05:14:30: 1000000 INFO @ Fri, 05 Jul 2019 05:14:31: 1000000 INFO @ Fri, 05 Jul 2019 05:14:38: 2000000 INFO @ Fri, 05 Jul 2019 05:14:40: 2000000 INFO @ Fri, 05 Jul 2019 05:14:41: 2000000 INFO @ Fri, 05 Jul 2019 05:14:46: 3000000 INFO @ Fri, 05 Jul 2019 05:14:49: 3000000 INFO @ Fri, 05 Jul 2019 05:14:51: 3000000 INFO @ Fri, 05 Jul 2019 05:14:55: 4000000 INFO @ Fri, 05 Jul 2019 05:14:59: 4000000 INFO @ Fri, 05 Jul 2019 05:15:01: 4000000 INFO @ Fri, 05 Jul 2019 05:15:03: 5000000 INFO @ Fri, 05 Jul 2019 05:15:08: 5000000 INFO @ Fri, 05 Jul 2019 05:15:10: 5000000 INFO @ Fri, 05 Jul 2019 05:15:11: 6000000 INFO @ Fri, 05 Jul 2019 05:15:17: 6000000 INFO @ Fri, 05 Jul 2019 05:15:19: 7000000 INFO @ Fri, 05 Jul 2019 05:15:20: 6000000 INFO @ Fri, 05 Jul 2019 05:15:27: 8000000 INFO @ Fri, 05 Jul 2019 05:15:27: 7000000 INFO @ Fri, 05 Jul 2019 05:15:30: 7000000 INFO @ Fri, 05 Jul 2019 05:15:35: 9000000 INFO @ Fri, 05 Jul 2019 05:15:37: 8000000 INFO @ Fri, 05 Jul 2019 05:15:40: 8000000 INFO @ Fri, 05 Jul 2019 05:15:43: 10000000 INFO @ Fri, 05 Jul 2019 05:15:47: 9000000 INFO @ Fri, 05 Jul 2019 05:15:49: 9000000 INFO @ Fri, 05 Jul 2019 05:15:50: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:15:50: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:15:50: #1 total tags in treatment: 10845245 INFO @ Fri, 05 Jul 2019 05:15:50: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:15:50: #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 05:15:50: #1 tags after filtering in treatment: 10844955 INFO @ Fri, 05 Jul 2019 05:15:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:15:50: #1 finished! INFO @ Fri, 05 Jul 2019 05:15:50: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:15:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:15:54: #2 number of paired peaks: 50758 INFO @ Fri, 05 Jul 2019 05:15:54: start model_add_line... INFO @ Fri, 05 Jul 2019 05:15:54: start X-correlation... INFO @ Fri, 05 Jul 2019 05:15:54: end of X-cor INFO @ Fri, 05 Jul 2019 05:15:54: #2 finished! INFO @ Fri, 05 Jul 2019 05:15:54: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 05:15:54: #2 alternative fragment length(s) may be 4,136 bps INFO @ Fri, 05 Jul 2019 05:15:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101907/ERX101907.10_model.r INFO @ Fri, 05 Jul 2019 05:15:54: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:15:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:15:57: 10000000 INFO @ Fri, 05 Jul 2019 05:15:59: 10000000 INFO @ Fri, 05 Jul 2019 05:16:04: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:16:04: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:16:04: #1 total tags in treatment: 10845245 INFO @ Fri, 05 Jul 2019 05:16:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:16:04: #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 05:16:05: #1 tags after filtering in treatment: 10844955 INFO @ Fri, 05 Jul 2019 05:16:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:16:05: #1 finished! INFO @ Fri, 05 Jul 2019 05:16:05: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:16:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:16:07: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:16:07: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:16:07: #1 total tags in treatment: 10845245 INFO @ Fri, 05 Jul 2019 05:16:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:16:07: #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 05:16:07: #1 tags after filtering in treatment: 10844955 INFO @ Fri, 05 Jul 2019 05:16:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:16:07: #1 finished! INFO @ Fri, 05 Jul 2019 05:16:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:16:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:16:09: #2 number of paired peaks: 50758 INFO @ Fri, 05 Jul 2019 05:16:09: start model_add_line... INFO @ Fri, 05 Jul 2019 05:16:09: start X-correlation... INFO @ Fri, 05 Jul 2019 05:16:09: end of X-cor INFO @ Fri, 05 Jul 2019 05:16:09: #2 finished! INFO @ Fri, 05 Jul 2019 05:16:09: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 05:16:09: #2 alternative fragment length(s) may be 4,136 bps INFO @ Fri, 05 Jul 2019 05:16:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101907/ERX101907.05_model.r INFO @ Fri, 05 Jul 2019 05:16:09: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:16:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:16:11: #2 number of paired peaks: 50758 INFO @ Fri, 05 Jul 2019 05:16:11: start model_add_line... INFO @ Fri, 05 Jul 2019 05:16:11: start X-correlation... INFO @ Fri, 05 Jul 2019 05:16:11: end of X-cor INFO @ Fri, 05 Jul 2019 05:16:11: #2 finished! INFO @ Fri, 05 Jul 2019 05:16:11: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 05:16:11: #2 alternative fragment length(s) may be 4,136 bps INFO @ Fri, 05 Jul 2019 05:16:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101907/ERX101907.20_model.r INFO @ Fri, 05 Jul 2019 05:16:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:16:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:16:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:16:47: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:16:49: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:16:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101907/ERX101907.10_peaks.xls INFO @ Fri, 05 Jul 2019 05:16:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101907/ERX101907.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:16:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101907/ERX101907.10_summits.bed INFO @ Fri, 05 Jul 2019 05:16:55: Done! pass1 - making usageList (107 chroms): 8 millis pass2 - checking and writing primary data (33591 records, 4 fields): 52 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:17:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101907/ERX101907.05_peaks.xls INFO @ Fri, 05 Jul 2019 05:17:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101907/ERX101907.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:17:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101907/ERX101907.05_summits.bed INFO @ Fri, 05 Jul 2019 05:17:09: Done! INFO @ Fri, 05 Jul 2019 05:17:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101907/ERX101907.20_peaks.xls INFO @ Fri, 05 Jul 2019 05:17:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101907/ERX101907.20_peaks.narrowPeak pass1 - making usageList (137 chroms): 11 millis INFO @ Fri, 05 Jul 2019 05:17:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101907/ERX101907.20_summits.bed pass2 - checking and writing primary data (45368 records, 4 fields): 85 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:17:10: Done! pass1 - making usageList (78 chroms): 5 millis pass2 - checking and writing primary data (20038 records, 4 fields): 30 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。