Job ID = 1294120 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T19:54:12 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 : 12,220,759 reads read : 12,220,759 reads written : 12,220,759 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: 00:02:43 12220759 reads; of these: 12220759 (100.00%) were unpaired; of these: 2868012 (23.47%) aligned 0 times 7905925 (64.69%) aligned exactly 1 time 1446822 (11.84%) aligned >1 times 76.53% overall alignment rate Time searching: 00:02:43 Overall time: 00:02:43 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_rmdupse_core] 3707809 / 9352747 = 0.3964 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 05:09:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX191912/SRX191912.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX191912/SRX191912.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX191912/SRX191912.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX191912/SRX191912.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 05:09:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:09:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:09:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX191912/SRX191912.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX191912/SRX191912.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX191912/SRX191912.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX191912/SRX191912.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 05:09:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:09:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:09:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX191912/SRX191912.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX191912/SRX191912.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX191912/SRX191912.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX191912/SRX191912.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 05:09:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:09:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:09:43: 1000000 INFO @ Mon, 03 Jun 2019 05:09:43: 1000000 INFO @ Mon, 03 Jun 2019 05:09:43: 1000000 INFO @ Mon, 03 Jun 2019 05:09:49: 2000000 INFO @ Mon, 03 Jun 2019 05:09:51: 2000000 INFO @ Mon, 03 Jun 2019 05:09:51: 2000000 INFO @ Mon, 03 Jun 2019 05:09:56: 3000000 INFO @ Mon, 03 Jun 2019 05:09:58: 3000000 INFO @ Mon, 03 Jun 2019 05:09:59: 3000000 INFO @ Mon, 03 Jun 2019 05:10:03: 4000000 INFO @ Mon, 03 Jun 2019 05:10:06: 4000000 INFO @ Mon, 03 Jun 2019 05:10:07: 4000000 INFO @ Mon, 03 Jun 2019 05:10:10: 5000000 INFO @ Mon, 03 Jun 2019 05:10:14: 5000000 INFO @ Mon, 03 Jun 2019 05:10:15: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:10:15: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:10:15: #1 total tags in treatment: 5644938 INFO @ Mon, 03 Jun 2019 05:10:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:10:15: #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 05:10:15: #1 tags after filtering in treatment: 5644938 INFO @ Mon, 03 Jun 2019 05:10:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:10:15: #1 finished! INFO @ Mon, 03 Jun 2019 05:10:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:10:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:10:15: 5000000 INFO @ Mon, 03 Jun 2019 05:10:16: #2 number of paired peaks: 4198 INFO @ Mon, 03 Jun 2019 05:10:16: start model_add_line... INFO @ Mon, 03 Jun 2019 05:10:16: start X-correlation... INFO @ Mon, 03 Jun 2019 05:10:16: end of X-cor INFO @ Mon, 03 Jun 2019 05:10:16: #2 finished! INFO @ Mon, 03 Jun 2019 05:10:16: #2 predicted fragment length is 114 bps INFO @ Mon, 03 Jun 2019 05:10:16: #2 alternative fragment length(s) may be 114 bps INFO @ Mon, 03 Jun 2019 05:10:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX191912/SRX191912.10_model.r INFO @ Mon, 03 Jun 2019 05:10:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:10:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:10:19: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:10:19: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:10:19: #1 total tags in treatment: 5644938 INFO @ Mon, 03 Jun 2019 05:10:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:10:19: #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 05:10:19: #1 tags after filtering in treatment: 5644938 INFO @ Mon, 03 Jun 2019 05:10:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:10:19: #1 finished! INFO @ Mon, 03 Jun 2019 05:10:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:10:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:10:20: #2 number of paired peaks: 4198 INFO @ Mon, 03 Jun 2019 05:10:20: start model_add_line... INFO @ Mon, 03 Jun 2019 05:10:20: start X-correlation... INFO @ Mon, 03 Jun 2019 05:10:20: end of X-cor INFO @ Mon, 03 Jun 2019 05:10:20: #2 finished! INFO @ Mon, 03 Jun 2019 05:10:20: #2 predicted fragment length is 114 bps INFO @ Mon, 03 Jun 2019 05:10:20: #2 alternative fragment length(s) may be 114 bps INFO @ Mon, 03 Jun 2019 05:10:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX191912/SRX191912.20_model.r INFO @ Mon, 03 Jun 2019 05:10:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:10:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:10:20: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:10:20: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:10:20: #1 total tags in treatment: 5644938 INFO @ Mon, 03 Jun 2019 05:10:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:10:20: #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 05:10:20: #1 tags after filtering in treatment: 5644938 INFO @ Mon, 03 Jun 2019 05:10:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:10:20: #1 finished! INFO @ Mon, 03 Jun 2019 05:10:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:10:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:10:21: #2 number of paired peaks: 4198 INFO @ Mon, 03 Jun 2019 05:10:21: start model_add_line... INFO @ Mon, 03 Jun 2019 05:10:21: start X-correlation... INFO @ Mon, 03 Jun 2019 05:10:21: end of X-cor INFO @ Mon, 03 Jun 2019 05:10:21: #2 finished! INFO @ Mon, 03 Jun 2019 05:10:21: #2 predicted fragment length is 114 bps INFO @ Mon, 03 Jun 2019 05:10:21: #2 alternative fragment length(s) may be 114 bps INFO @ Mon, 03 Jun 2019 05:10:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX191912/SRX191912.05_model.r INFO @ Mon, 03 Jun 2019 05:10:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:10:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:10:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:10:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:10:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:10:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX191912/SRX191912.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:10:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX191912/SRX191912.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:10:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX191912/SRX191912.10_summits.bed INFO @ Mon, 03 Jun 2019 05:10:44: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6785 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:10:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX191912/SRX191912.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:10:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX191912/SRX191912.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:10:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX191912/SRX191912.20_summits.bed INFO @ Mon, 03 Jun 2019 05:10:48: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4617 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:10:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX191912/SRX191912.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:10:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX191912/SRX191912.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:10:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX191912/SRX191912.05_summits.bed INFO @ Mon, 03 Jun 2019 05:10:50: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (9048 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。