Job ID = 1294766 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T01:00:55 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-03T01:00:55 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-03T01:03:54 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 ) 2019-06-03T01:03:56 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 ) spots read : 14,999,913 reads read : 14,999,913 reads written : 14,999,913 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:10 14999913 reads; of these: 14999913 (100.00%) were unpaired; of these: 1026393 (6.84%) aligned 0 times 12349824 (82.33%) aligned exactly 1 time 1623696 (10.82%) aligned >1 times 93.16% overall alignment rate Time searching: 00:04:10 Overall time: 00:04:10 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1799294 / 13973520 = 0.1288 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 @ Mon, 03 Jun 2019 10:15:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287867/SRX287867.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287867/SRX287867.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287867/SRX287867.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287867/SRX287867.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 10:15:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:15:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:15:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287867/SRX287867.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287867/SRX287867.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287867/SRX287867.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287867/SRX287867.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 10:15:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:15:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:15:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287867/SRX287867.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287867/SRX287867.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287867/SRX287867.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287867/SRX287867.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 10:15:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:15:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:15:24: 1000000 INFO @ Mon, 03 Jun 2019 10:15:24: 1000000 INFO @ Mon, 03 Jun 2019 10:15:25: 1000000 INFO @ Mon, 03 Jun 2019 10:15:32: 2000000 INFO @ Mon, 03 Jun 2019 10:15:33: 2000000 INFO @ Mon, 03 Jun 2019 10:15:34: 2000000 INFO @ Mon, 03 Jun 2019 10:15:41: 3000000 INFO @ Mon, 03 Jun 2019 10:15:41: 3000000 INFO @ Mon, 03 Jun 2019 10:15:43: 3000000 INFO @ Mon, 03 Jun 2019 10:15:49: 4000000 INFO @ Mon, 03 Jun 2019 10:15:50: 4000000 INFO @ Mon, 03 Jun 2019 10:15:52: 4000000 INFO @ Mon, 03 Jun 2019 10:15:58: 5000000 INFO @ Mon, 03 Jun 2019 10:15:58: 5000000 INFO @ Mon, 03 Jun 2019 10:16:02: 5000000 INFO @ Mon, 03 Jun 2019 10:16:06: 6000000 INFO @ Mon, 03 Jun 2019 10:16:07: 6000000 INFO @ Mon, 03 Jun 2019 10:16:11: 6000000 INFO @ Mon, 03 Jun 2019 10:16:15: 7000000 INFO @ Mon, 03 Jun 2019 10:16:15: 7000000 INFO @ Mon, 03 Jun 2019 10:16:20: 7000000 INFO @ Mon, 03 Jun 2019 10:16:23: 8000000 INFO @ Mon, 03 Jun 2019 10:16:24: 8000000 INFO @ Mon, 03 Jun 2019 10:16:30: 8000000 INFO @ Mon, 03 Jun 2019 10:16:32: 9000000 INFO @ Mon, 03 Jun 2019 10:16:32: 9000000 INFO @ Mon, 03 Jun 2019 10:16:39: 9000000 INFO @ Mon, 03 Jun 2019 10:16:40: 10000000 INFO @ Mon, 03 Jun 2019 10:16:41: 10000000 INFO @ Mon, 03 Jun 2019 10:16:49: 10000000 INFO @ Mon, 03 Jun 2019 10:16:49: 11000000 INFO @ Mon, 03 Jun 2019 10:16:50: 11000000 INFO @ Mon, 03 Jun 2019 10:16:58: 12000000 INFO @ Mon, 03 Jun 2019 10:16:58: 12000000 INFO @ Mon, 03 Jun 2019 10:16:59: 11000000 INFO @ Mon, 03 Jun 2019 10:16:59: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:16:59: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:16:59: #1 total tags in treatment: 12174226 INFO @ Mon, 03 Jun 2019 10:16:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:16:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 10:16:59: #1 tags after filtering in treatment: 12174226 INFO @ Mon, 03 Jun 2019 10:16:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:16:59: #1 finished! INFO @ Mon, 03 Jun 2019 10:16:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:16:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:17:00: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:17:00: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:17:00: #1 total tags in treatment: 12174226 INFO @ Mon, 03 Jun 2019 10:17:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:17:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 10:17:00: #1 tags after filtering in treatment: 12174226 INFO @ Mon, 03 Jun 2019 10:17:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:17:00: #1 finished! INFO @ Mon, 03 Jun 2019 10:17:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:17:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:17:01: #2 number of paired peaks: 1827 INFO @ Mon, 03 Jun 2019 10:17:01: start model_add_line... INFO @ Mon, 03 Jun 2019 10:17:01: start X-correlation... INFO @ Mon, 03 Jun 2019 10:17:01: end of X-cor INFO @ Mon, 03 Jun 2019 10:17:01: #2 finished! INFO @ Mon, 03 Jun 2019 10:17:01: #2 predicted fragment length is 268 bps INFO @ Mon, 03 Jun 2019 10:17:01: #2 alternative fragment length(s) may be 4,268 bps INFO @ Mon, 03 Jun 2019 10:17:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287867/SRX287867.05_model.r INFO @ Mon, 03 Jun 2019 10:17:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:17:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:17:01: #2 number of paired peaks: 1827 INFO @ Mon, 03 Jun 2019 10:17:01: start model_add_line... INFO @ Mon, 03 Jun 2019 10:17:01: start X-correlation... INFO @ Mon, 03 Jun 2019 10:17:02: end of X-cor INFO @ Mon, 03 Jun 2019 10:17:02: #2 finished! INFO @ Mon, 03 Jun 2019 10:17:02: #2 predicted fragment length is 268 bps INFO @ Mon, 03 Jun 2019 10:17:02: #2 alternative fragment length(s) may be 4,268 bps INFO @ Mon, 03 Jun 2019 10:17:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287867/SRX287867.20_model.r INFO @ Mon, 03 Jun 2019 10:17:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:17:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:17:08: 12000000 INFO @ Mon, 03 Jun 2019 10:17:10: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:17:10: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:17:10: #1 total tags in treatment: 12174226 INFO @ Mon, 03 Jun 2019 10:17:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:17:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 10:17:10: #1 tags after filtering in treatment: 12174226 INFO @ Mon, 03 Jun 2019 10:17:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:17:10: #1 finished! INFO @ Mon, 03 Jun 2019 10:17:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:17:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:17:11: #2 number of paired peaks: 1827 INFO @ Mon, 03 Jun 2019 10:17:11: start model_add_line... INFO @ Mon, 03 Jun 2019 10:17:12: start X-correlation... INFO @ Mon, 03 Jun 2019 10:17:12: end of X-cor INFO @ Mon, 03 Jun 2019 10:17:12: #2 finished! INFO @ Mon, 03 Jun 2019 10:17:12: #2 predicted fragment length is 268 bps INFO @ Mon, 03 Jun 2019 10:17:12: #2 alternative fragment length(s) may be 4,268 bps INFO @ Mon, 03 Jun 2019 10:17:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287867/SRX287867.10_model.r INFO @ Mon, 03 Jun 2019 10:17:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:17:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:17:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:17:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:17:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:18:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287867/SRX287867.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:18:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287867/SRX287867.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:18:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287867/SRX287867.05_summits.bed INFO @ Mon, 03 Jun 2019 10:18:00: Done! INFO @ Mon, 03 Jun 2019 10:18:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287867/SRX287867.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:18:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287867/SRX287867.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:18:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287867/SRX287867.20_summits.bed INFO @ Mon, 03 Jun 2019 10:18:00: Done! pass1 - making usageList (13 chroms): 1 millis pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (983 records, 4 fields): 4 millis pass2 - checking and writing primary data (6154 records, 4 fields): 35 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:18:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287867/SRX287867.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:18:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287867/SRX287867.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:18:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287867/SRX287867.10_summits.bed INFO @ Mon, 03 Jun 2019 10:18:13: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (2944 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。