Job ID = 1294257 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T20:49:33 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 ) 2019-06-02T20:49:34 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 ) 2019-06-02T20:49:34 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 : 14,666,843 reads read : 14,666,843 reads written : 14,666,843 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: 00:03:28 14666843 reads; of these: 14666843 (100.00%) were unpaired; of these: 2743969 (18.71%) aligned 0 times 10096387 (68.84%) aligned exactly 1 time 1826487 (12.45%) aligned >1 times 81.29% overall alignment rate Time searching: 00:03:28 Overall time: 00:03:28 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] 2656075 / 11922874 = 0.2228 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 05:59:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX215501/SRX215501.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX215501/SRX215501.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX215501/SRX215501.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX215501/SRX215501.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 05:59:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:59:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:59:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX215501/SRX215501.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX215501/SRX215501.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX215501/SRX215501.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX215501/SRX215501.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 05:59:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:59:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:59:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX215501/SRX215501.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX215501/SRX215501.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX215501/SRX215501.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX215501/SRX215501.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 05:59:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:59:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:59:51: 1000000 INFO @ Mon, 03 Jun 2019 05:59:52: 1000000 INFO @ Mon, 03 Jun 2019 05:59:53: 1000000 INFO @ Mon, 03 Jun 2019 05:59:58: 2000000 INFO @ Mon, 03 Jun 2019 06:00:00: 2000000 INFO @ Mon, 03 Jun 2019 06:00:01: 2000000 INFO @ Mon, 03 Jun 2019 06:00:05: 3000000 INFO @ Mon, 03 Jun 2019 06:00:09: 3000000 INFO @ Mon, 03 Jun 2019 06:00:09: 3000000 INFO @ Mon, 03 Jun 2019 06:00:12: 4000000 INFO @ Mon, 03 Jun 2019 06:00:16: 4000000 INFO @ Mon, 03 Jun 2019 06:00:17: 4000000 INFO @ Mon, 03 Jun 2019 06:00:19: 5000000 INFO @ Mon, 03 Jun 2019 06:00:24: 5000000 INFO @ Mon, 03 Jun 2019 06:00:25: 5000000 INFO @ Mon, 03 Jun 2019 06:00:26: 6000000 INFO @ Mon, 03 Jun 2019 06:00:31: 6000000 INFO @ Mon, 03 Jun 2019 06:00:32: 7000000 INFO @ Mon, 03 Jun 2019 06:00:32: 6000000 INFO @ Mon, 03 Jun 2019 06:00:39: 8000000 INFO @ Mon, 03 Jun 2019 06:00:39: 7000000 INFO @ Mon, 03 Jun 2019 06:00:40: 7000000 INFO @ Mon, 03 Jun 2019 06:00:46: 9000000 INFO @ Mon, 03 Jun 2019 06:00:47: 8000000 INFO @ Mon, 03 Jun 2019 06:00:48: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 06:00:48: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 06:00:48: #1 total tags in treatment: 9266799 INFO @ Mon, 03 Jun 2019 06:00:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:00:48: #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 06:00:48: #1 tags after filtering in treatment: 9266799 INFO @ Mon, 03 Jun 2019 06:00:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:00:48: #1 finished! INFO @ Mon, 03 Jun 2019 06:00:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:00:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:00:48: 8000000 INFO @ Mon, 03 Jun 2019 06:00:49: #2 number of paired peaks: 2545 INFO @ Mon, 03 Jun 2019 06:00:49: start model_add_line... INFO @ Mon, 03 Jun 2019 06:00:49: start X-correlation... INFO @ Mon, 03 Jun 2019 06:00:49: end of X-cor INFO @ Mon, 03 Jun 2019 06:00:49: #2 finished! INFO @ Mon, 03 Jun 2019 06:00:49: #2 predicted fragment length is 217 bps INFO @ Mon, 03 Jun 2019 06:00:49: #2 alternative fragment length(s) may be 217 bps INFO @ Mon, 03 Jun 2019 06:00:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX215501/SRX215501.10_model.r INFO @ Mon, 03 Jun 2019 06:00:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:00:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:00:55: 9000000 INFO @ Mon, 03 Jun 2019 06:00:56: 9000000 INFO @ Mon, 03 Jun 2019 06:00:57: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 06:00:57: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 06:00:57: #1 total tags in treatment: 9266799 INFO @ Mon, 03 Jun 2019 06:00:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:00:57: #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 06:00:57: #1 tags after filtering in treatment: 9266799 INFO @ Mon, 03 Jun 2019 06:00:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:00:57: #1 finished! INFO @ Mon, 03 Jun 2019 06:00:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:00:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:00:58: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 06:00:58: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 06:00:58: #1 total tags in treatment: 9266799 INFO @ Mon, 03 Jun 2019 06:00:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:00:58: #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 06:00:58: #1 tags after filtering in treatment: 9266799 INFO @ Mon, 03 Jun 2019 06:00:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:00:58: #1 finished! INFO @ Mon, 03 Jun 2019 06:00:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:00:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:00:59: #2 number of paired peaks: 2545 INFO @ Mon, 03 Jun 2019 06:00:59: start model_add_line... INFO @ Mon, 03 Jun 2019 06:00:59: start X-correlation... INFO @ Mon, 03 Jun 2019 06:00:59: end of X-cor INFO @ Mon, 03 Jun 2019 06:00:59: #2 finished! INFO @ Mon, 03 Jun 2019 06:00:59: #2 predicted fragment length is 217 bps INFO @ Mon, 03 Jun 2019 06:00:59: #2 alternative fragment length(s) may be 217 bps INFO @ Mon, 03 Jun 2019 06:00:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX215501/SRX215501.05_model.r INFO @ Mon, 03 Jun 2019 06:00:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:00:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:00:59: #2 number of paired peaks: 2545 INFO @ Mon, 03 Jun 2019 06:00:59: start model_add_line... INFO @ Mon, 03 Jun 2019 06:01:00: start X-correlation... INFO @ Mon, 03 Jun 2019 06:01:00: end of X-cor INFO @ Mon, 03 Jun 2019 06:01:00: #2 finished! INFO @ Mon, 03 Jun 2019 06:01:00: #2 predicted fragment length is 217 bps INFO @ Mon, 03 Jun 2019 06:01:00: #2 alternative fragment length(s) may be 217 bps INFO @ Mon, 03 Jun 2019 06:01:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX215501/SRX215501.20_model.r INFO @ Mon, 03 Jun 2019 06:01:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:01:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:01:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:01:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:01:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:01:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX215501/SRX215501.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:01:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX215501/SRX215501.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:01:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX215501/SRX215501.10_summits.bed INFO @ Mon, 03 Jun 2019 06:01:33: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3680 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:01:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX215501/SRX215501.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:01:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX215501/SRX215501.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:01:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX215501/SRX215501.05_summits.bed INFO @ Mon, 03 Jun 2019 06:01:43: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (7017 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:01:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX215501/SRX215501.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:01:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX215501/SRX215501.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:01:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX215501/SRX215501.20_summits.bed INFO @ Mon, 03 Jun 2019 06:01:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1192 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。