Job ID = 1294237 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T20:41:15 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 ) 2019-06-02T20:41:15 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 ) 2019-06-02T20:41:15 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 : 14,480,165 reads read : 14,480,165 reads written : 14,480,165 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: 00:02:31 14480165 reads; of these: 14480165 (100.00%) were unpaired; of these: 7868490 (54.34%) aligned 0 times 5072089 (35.03%) aligned exactly 1 time 1539586 (10.63%) aligned >1 times 45.66% overall alignment rate Time searching: 00:02:31 Overall time: 00:02:31 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 2020100 / 6611675 = 0.3055 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 05:49:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX202125/SRX202125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX202125/SRX202125.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX202125/SRX202125.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX202125/SRX202125.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 05:49:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:49:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:49:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX202125/SRX202125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX202125/SRX202125.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX202125/SRX202125.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX202125/SRX202125.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 05:49:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:49:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:49:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX202125/SRX202125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX202125/SRX202125.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX202125/SRX202125.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX202125/SRX202125.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 05:49:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:49:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:49:54: 1000000 INFO @ Mon, 03 Jun 2019 05:49:55: 1000000 INFO @ Mon, 03 Jun 2019 05:49:55: 1000000 INFO @ Mon, 03 Jun 2019 05:50:00: 2000000 INFO @ Mon, 03 Jun 2019 05:50:03: 2000000 INFO @ Mon, 03 Jun 2019 05:50:03: 2000000 INFO @ Mon, 03 Jun 2019 05:50:06: 3000000 INFO @ Mon, 03 Jun 2019 05:50:11: 3000000 INFO @ Mon, 03 Jun 2019 05:50:11: 3000000 INFO @ Mon, 03 Jun 2019 05:50:13: 4000000 INFO @ Mon, 03 Jun 2019 05:50:17: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:50:17: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:50:17: #1 total tags in treatment: 4591575 INFO @ Mon, 03 Jun 2019 05:50:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:50:17: #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 05:50:17: #1 tags after filtering in treatment: 4591575 INFO @ Mon, 03 Jun 2019 05:50:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:50:17: #1 finished! INFO @ Mon, 03 Jun 2019 05:50:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:50:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:50:17: #2 number of paired peaks: 1504 INFO @ Mon, 03 Jun 2019 05:50:17: start model_add_line... INFO @ Mon, 03 Jun 2019 05:50:17: start X-correlation... INFO @ Mon, 03 Jun 2019 05:50:17: end of X-cor INFO @ Mon, 03 Jun 2019 05:50:17: #2 finished! INFO @ Mon, 03 Jun 2019 05:50:17: #2 predicted fragment length is 87 bps INFO @ Mon, 03 Jun 2019 05:50:17: #2 alternative fragment length(s) may be 87 bps INFO @ Mon, 03 Jun 2019 05:50:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX202125/SRX202125.20_model.r INFO @ Mon, 03 Jun 2019 05:50:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:50:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:50:19: 4000000 INFO @ Mon, 03 Jun 2019 05:50:20: 4000000 INFO @ Mon, 03 Jun 2019 05:50:24: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:50:24: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:50:24: #1 total tags in treatment: 4591575 INFO @ Mon, 03 Jun 2019 05:50:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:50:24: #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 05:50:24: #1 tags after filtering in treatment: 4591575 INFO @ Mon, 03 Jun 2019 05:50:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:50:24: #1 finished! INFO @ Mon, 03 Jun 2019 05:50:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:50:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:50:24: #2 number of paired peaks: 1504 INFO @ Mon, 03 Jun 2019 05:50:24: start model_add_line... INFO @ Mon, 03 Jun 2019 05:50:24: start X-correlation... INFO @ Mon, 03 Jun 2019 05:50:24: end of X-cor INFO @ Mon, 03 Jun 2019 05:50:24: #2 finished! INFO @ Mon, 03 Jun 2019 05:50:24: #2 predicted fragment length is 87 bps INFO @ Mon, 03 Jun 2019 05:50:24: #2 alternative fragment length(s) may be 87 bps INFO @ Mon, 03 Jun 2019 05:50:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX202125/SRX202125.05_model.r INFO @ Mon, 03 Jun 2019 05:50:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:50:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:50:25: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:50:25: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:50:25: #1 total tags in treatment: 4591575 INFO @ Mon, 03 Jun 2019 05:50:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:50:25: #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 05:50:25: #1 tags after filtering in treatment: 4591575 INFO @ Mon, 03 Jun 2019 05:50:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:50:25: #1 finished! INFO @ Mon, 03 Jun 2019 05:50:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:50:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:50:25: #2 number of paired peaks: 1504 INFO @ Mon, 03 Jun 2019 05:50:25: start model_add_line... INFO @ Mon, 03 Jun 2019 05:50:25: start X-correlation... INFO @ Mon, 03 Jun 2019 05:50:25: end of X-cor INFO @ Mon, 03 Jun 2019 05:50:25: #2 finished! INFO @ Mon, 03 Jun 2019 05:50:25: #2 predicted fragment length is 87 bps INFO @ Mon, 03 Jun 2019 05:50:25: #2 alternative fragment length(s) may be 87 bps INFO @ Mon, 03 Jun 2019 05:50:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX202125/SRX202125.10_model.r INFO @ Mon, 03 Jun 2019 05:50:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:50:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:50:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:50:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:50:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX202125/SRX202125.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:50:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX202125/SRX202125.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:50:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX202125/SRX202125.20_summits.bed INFO @ Mon, 03 Jun 2019 05:50:39: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1238 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:50:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:50:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX202125/SRX202125.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:50:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX202125/SRX202125.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:50:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX202125/SRX202125.05_summits.bed INFO @ Mon, 03 Jun 2019 05:50:46: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5052 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:50:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX202125/SRX202125.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:50:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX202125/SRX202125.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:50:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX202125/SRX202125.10_summits.bed INFO @ Mon, 03 Jun 2019 05:50:47: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2855 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。