Job ID = 2001151 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T18:40:06 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 : 22,660,068 reads read : 22,660,068 reads written : 22,660,068 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: 00:09:28 22660068 reads; of these: 22660068 (100.00%) were unpaired; of these: 495398 (2.19%) aligned 0 times 16925870 (74.69%) aligned exactly 1 time 5238800 (23.12%) aligned >1 times 97.81% overall alignment rate Time searching: 00:09:31 Overall time: 00:09:31 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] 1371229 / 22164670 = 0.0619 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 04:04:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101841/ERX101841.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101841/ERX101841.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101841/ERX101841.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101841/ERX101841.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 04:04:52: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:04:52: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:04:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101841/ERX101841.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101841/ERX101841.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101841/ERX101841.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101841/ERX101841.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 04:04:52: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:04:52: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:04:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101841/ERX101841.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101841/ERX101841.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101841/ERX101841.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101841/ERX101841.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 04:04:52: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:04:52: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:05:04: 1000000 INFO @ Fri, 05 Jul 2019 04:05:05: 1000000 INFO @ Fri, 05 Jul 2019 04:05:06: 1000000 INFO @ Fri, 05 Jul 2019 04:05:16: 2000000 INFO @ Fri, 05 Jul 2019 04:05:18: 2000000 INFO @ Fri, 05 Jul 2019 04:05:18: 2000000 INFO @ Fri, 05 Jul 2019 04:05:28: 3000000 INFO @ Fri, 05 Jul 2019 04:05:30: 3000000 INFO @ Fri, 05 Jul 2019 04:05:31: 3000000 INFO @ Fri, 05 Jul 2019 04:05:41: 4000000 INFO @ Fri, 05 Jul 2019 04:05:43: 4000000 INFO @ Fri, 05 Jul 2019 04:05:44: 4000000 INFO @ Fri, 05 Jul 2019 04:05:54: 5000000 INFO @ Fri, 05 Jul 2019 04:05:56: 5000000 INFO @ Fri, 05 Jul 2019 04:05:56: 5000000 INFO @ Fri, 05 Jul 2019 04:06:06: 6000000 INFO @ Fri, 05 Jul 2019 04:06:08: 6000000 INFO @ Fri, 05 Jul 2019 04:06:09: 6000000 INFO @ Fri, 05 Jul 2019 04:06:15: 7000000 INFO @ Fri, 05 Jul 2019 04:06:19: 7000000 INFO @ Fri, 05 Jul 2019 04:06:20: 7000000 INFO @ Fri, 05 Jul 2019 04:06:25: 8000000 INFO @ Fri, 05 Jul 2019 04:06:29: 8000000 INFO @ Fri, 05 Jul 2019 04:06:30: 8000000 INFO @ Fri, 05 Jul 2019 04:06:35: 9000000 INFO @ Fri, 05 Jul 2019 04:06:41: 9000000 INFO @ Fri, 05 Jul 2019 04:06:41: 9000000 INFO @ Fri, 05 Jul 2019 04:06:48: 10000000 INFO @ Fri, 05 Jul 2019 04:06:53: 10000000 INFO @ Fri, 05 Jul 2019 04:06:54: 10000000 INFO @ Fri, 05 Jul 2019 04:07:00: 11000000 INFO @ Fri, 05 Jul 2019 04:07:07: 11000000 INFO @ Fri, 05 Jul 2019 04:07:07: 11000000 INFO @ Fri, 05 Jul 2019 04:07:12: 12000000 INFO @ Fri, 05 Jul 2019 04:07:19: 12000000 INFO @ Fri, 05 Jul 2019 04:07:21: 12000000 INFO @ Fri, 05 Jul 2019 04:07:25: 13000000 INFO @ Fri, 05 Jul 2019 04:07:32: 13000000 INFO @ Fri, 05 Jul 2019 04:07:33: 13000000 INFO @ Fri, 05 Jul 2019 04:07:37: 14000000 INFO @ Fri, 05 Jul 2019 04:07:45: 14000000 INFO @ Fri, 05 Jul 2019 04:07:46: 14000000 INFO @ Fri, 05 Jul 2019 04:07:49: 15000000 INFO @ Fri, 05 Jul 2019 04:07:58: 15000000 INFO @ Fri, 05 Jul 2019 04:07:58: 15000000 INFO @ Fri, 05 Jul 2019 04:08:02: 16000000 INFO @ Fri, 05 Jul 2019 04:08:09: 16000000 INFO @ Fri, 05 Jul 2019 04:08:11: 16000000 INFO @ Fri, 05 Jul 2019 04:08:13: 17000000 INFO @ Fri, 05 Jul 2019 04:08:23: 17000000 INFO @ Fri, 05 Jul 2019 04:08:24: 17000000 INFO @ Fri, 05 Jul 2019 04:08:27: 18000000 INFO @ Fri, 05 Jul 2019 04:08:36: 18000000 INFO @ Fri, 05 Jul 2019 04:08:36: 18000000 INFO @ Fri, 05 Jul 2019 04:08:38: 19000000 INFO @ Fri, 05 Jul 2019 04:08:49: 19000000 INFO @ Fri, 05 Jul 2019 04:08:50: 19000000 INFO @ Fri, 05 Jul 2019 04:08:50: 20000000 INFO @ Fri, 05 Jul 2019 04:09:00: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:09:00: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:09:00: #1 total tags in treatment: 20793441 INFO @ Fri, 05 Jul 2019 04:09:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:09:00: #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 04:09:01: #1 tags after filtering in treatment: 20793263 INFO @ Fri, 05 Jul 2019 04:09:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:09:01: #1 finished! INFO @ Fri, 05 Jul 2019 04:09:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:09:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:09:01: 20000000 INFO @ Fri, 05 Jul 2019 04:09:03: 20000000 INFO @ Fri, 05 Jul 2019 04:09:07: #2 number of paired peaks: 59645 INFO @ Fri, 05 Jul 2019 04:09:07: start model_add_line... INFO @ Fri, 05 Jul 2019 04:09:08: start X-correlation... INFO @ Fri, 05 Jul 2019 04:09:08: end of X-cor INFO @ Fri, 05 Jul 2019 04:09:08: #2 finished! INFO @ Fri, 05 Jul 2019 04:09:08: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 04:09:08: #2 alternative fragment length(s) may be 3,130,491 bps INFO @ Fri, 05 Jul 2019 04:09:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101841/ERX101841.10_model.r INFO @ Fri, 05 Jul 2019 04:09:08: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:09:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:09:11: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:09:11: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:09:11: #1 total tags in treatment: 20793441 INFO @ Fri, 05 Jul 2019 04:09:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:09:11: #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 04:09:12: #1 tags after filtering in treatment: 20793263 INFO @ Fri, 05 Jul 2019 04:09:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:09:12: #1 finished! INFO @ Fri, 05 Jul 2019 04:09:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:09:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:09:14: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:09:14: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:09:14: #1 total tags in treatment: 20793441 INFO @ Fri, 05 Jul 2019 04:09:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:09:14: #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 04:09:15: #1 tags after filtering in treatment: 20793263 INFO @ Fri, 05 Jul 2019 04:09:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:09:15: #1 finished! INFO @ Fri, 05 Jul 2019 04:09:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:09:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:09:18: #2 number of paired peaks: 59645 INFO @ Fri, 05 Jul 2019 04:09:18: start model_add_line... INFO @ Fri, 05 Jul 2019 04:09:19: start X-correlation... INFO @ Fri, 05 Jul 2019 04:09:19: end of X-cor INFO @ Fri, 05 Jul 2019 04:09:19: #2 finished! INFO @ Fri, 05 Jul 2019 04:09:19: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 04:09:19: #2 alternative fragment length(s) may be 3,130,491 bps INFO @ Fri, 05 Jul 2019 04:09:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101841/ERX101841.05_model.r INFO @ Fri, 05 Jul 2019 04:09:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:09:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:09:20: #2 number of paired peaks: 59645 INFO @ Fri, 05 Jul 2019 04:09:20: start model_add_line... INFO @ Fri, 05 Jul 2019 04:09:21: start X-correlation... INFO @ Fri, 05 Jul 2019 04:09:21: end of X-cor INFO @ Fri, 05 Jul 2019 04:09:21: #2 finished! INFO @ Fri, 05 Jul 2019 04:09:21: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 04:09:21: #2 alternative fragment length(s) may be 3,130,491 bps INFO @ Fri, 05 Jul 2019 04:09:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101841/ERX101841.20_model.r INFO @ Fri, 05 Jul 2019 04:09:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:09:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:10:34: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:10:47: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:10:49: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:11:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101841/ERX101841.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:11:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101841/ERX101841.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:11:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101841/ERX101841.10_summits.bed INFO @ Fri, 05 Jul 2019 04:11:22: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (950 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:11:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101841/ERX101841.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:11:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101841/ERX101841.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:11:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101841/ERX101841.05_summits.bed INFO @ Fri, 05 Jul 2019 04:11:31: Done! pass1 - making usageList (57 chroms): 2 millis pass2 - checking and writing primary data (4366 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:11:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101841/ERX101841.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:11:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101841/ERX101841.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:11:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101841/ERX101841.20_summits.bed INFO @ Fri, 05 Jul 2019 04:11:34: Done! pass1 - making usageList (23 chroms): 0 millis pass2 - checking and writing primary data (116 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。