Job ID = 1293808 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T17:29:45 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 ) 2019-06-02T17:32:18 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 ) 2019-06-02T17:33:26 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 ) 2019-06-02T17:33:26 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 : 21,857,555 reads read : 21,857,555 reads written : 21,857,555 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: 00:05:17 21857555 reads; of these: 21857555 (100.00%) were unpaired; of these: 2638271 (12.07%) aligned 0 times 16875309 (77.21%) aligned exactly 1 time 2343975 (10.72%) aligned >1 times 87.93% overall alignment rate Time searching: 00:05:17 Overall time: 00:05:17 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] 12375287 / 19219284 = 0.6439 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 02:50:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1134708/SRX1134708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1134708/SRX1134708.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1134708/SRX1134708.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1134708/SRX1134708.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 02:50:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:50:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:50:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1134708/SRX1134708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1134708/SRX1134708.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1134708/SRX1134708.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1134708/SRX1134708.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 02:50:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:50:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:50:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1134708/SRX1134708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1134708/SRX1134708.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1134708/SRX1134708.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1134708/SRX1134708.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 02:50:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:50:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:50:15: 1000000 INFO @ Mon, 03 Jun 2019 02:50:18: 1000000 INFO @ Mon, 03 Jun 2019 02:50:18: 1000000 INFO @ Mon, 03 Jun 2019 02:50:23: 2000000 INFO @ Mon, 03 Jun 2019 02:50:29: 2000000 INFO @ Mon, 03 Jun 2019 02:50:29: 2000000 INFO @ Mon, 03 Jun 2019 02:50:31: 3000000 INFO @ Mon, 03 Jun 2019 02:50:39: 4000000 INFO @ Mon, 03 Jun 2019 02:50:39: 3000000 INFO @ Mon, 03 Jun 2019 02:50:39: 3000000 INFO @ Mon, 03 Jun 2019 02:50:46: 5000000 INFO @ Mon, 03 Jun 2019 02:50:49: 4000000 INFO @ Mon, 03 Jun 2019 02:50:50: 4000000 INFO @ Mon, 03 Jun 2019 02:50:54: 6000000 INFO @ Mon, 03 Jun 2019 02:50:59: 5000000 INFO @ Mon, 03 Jun 2019 02:51:00: 5000000 INFO @ Mon, 03 Jun 2019 02:51:01: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:51:01: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:51:01: #1 total tags in treatment: 6843997 INFO @ Mon, 03 Jun 2019 02:51:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:51:01: #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 02:51:01: #1 tags after filtering in treatment: 6843997 INFO @ Mon, 03 Jun 2019 02:51:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:51:01: #1 finished! INFO @ Mon, 03 Jun 2019 02:51:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:51:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:51:02: #2 number of paired peaks: 3223 INFO @ Mon, 03 Jun 2019 02:51:02: start model_add_line... INFO @ Mon, 03 Jun 2019 02:51:02: start X-correlation... INFO @ Mon, 03 Jun 2019 02:51:02: end of X-cor INFO @ Mon, 03 Jun 2019 02:51:02: #2 finished! INFO @ Mon, 03 Jun 2019 02:51:02: #2 predicted fragment length is 202 bps INFO @ Mon, 03 Jun 2019 02:51:02: #2 alternative fragment length(s) may be 202 bps INFO @ Mon, 03 Jun 2019 02:51:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1134708/SRX1134708.20_model.r INFO @ Mon, 03 Jun 2019 02:51:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:51:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:51:09: 6000000 INFO @ Mon, 03 Jun 2019 02:51:11: 6000000 INFO @ Mon, 03 Jun 2019 02:51:17: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:51:17: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:51:17: #1 total tags in treatment: 6843997 INFO @ Mon, 03 Jun 2019 02:51:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:51:17: #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 02:51:17: #1 tags after filtering in treatment: 6843997 INFO @ Mon, 03 Jun 2019 02:51:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:51:17: #1 finished! INFO @ Mon, 03 Jun 2019 02:51:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:51:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:51:18: #2 number of paired peaks: 3223 INFO @ Mon, 03 Jun 2019 02:51:18: start model_add_line... INFO @ Mon, 03 Jun 2019 02:51:18: start X-correlation... INFO @ Mon, 03 Jun 2019 02:51:18: end of X-cor INFO @ Mon, 03 Jun 2019 02:51:18: #2 finished! INFO @ Mon, 03 Jun 2019 02:51:18: #2 predicted fragment length is 202 bps INFO @ Mon, 03 Jun 2019 02:51:18: #2 alternative fragment length(s) may be 202 bps INFO @ Mon, 03 Jun 2019 02:51:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1134708/SRX1134708.05_model.r INFO @ Mon, 03 Jun 2019 02:51:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:51:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:51:19: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:51:19: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:51:19: #1 total tags in treatment: 6843997 INFO @ Mon, 03 Jun 2019 02:51:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:51:19: #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 02:51:19: #1 tags after filtering in treatment: 6843997 INFO @ Mon, 03 Jun 2019 02:51:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:51:19: #1 finished! INFO @ Mon, 03 Jun 2019 02:51:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:51:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:51:20: #2 number of paired peaks: 3223 INFO @ Mon, 03 Jun 2019 02:51:20: start model_add_line... INFO @ Mon, 03 Jun 2019 02:51:20: start X-correlation... INFO @ Mon, 03 Jun 2019 02:51:20: end of X-cor INFO @ Mon, 03 Jun 2019 02:51:20: #2 finished! INFO @ Mon, 03 Jun 2019 02:51:20: #2 predicted fragment length is 202 bps INFO @ Mon, 03 Jun 2019 02:51:20: #2 alternative fragment length(s) may be 202 bps INFO @ Mon, 03 Jun 2019 02:51:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1134708/SRX1134708.10_model.r INFO @ Mon, 03 Jun 2019 02:51:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:51:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:51:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:51:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1134708/SRX1134708.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:51:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1134708/SRX1134708.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:51:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1134708/SRX1134708.20_summits.bed INFO @ Mon, 03 Jun 2019 02:51:37: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (2955 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:51:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:51:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:51:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1134708/SRX1134708.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:51:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1134708/SRX1134708.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:51:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1134708/SRX1134708.05_summits.bed INFO @ Mon, 03 Jun 2019 02:51:53: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5880 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:51:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1134708/SRX1134708.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:51:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1134708/SRX1134708.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:51:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1134708/SRX1134708.10_summits.bed INFO @ Mon, 03 Jun 2019 02:51:55: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4327 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。