Job ID = 1301491 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T10:54:02 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 ) 2019-06-03T10:58:55 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 ) 2019-06-03T10:58:55 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 ) 2019-06-03T11:00:53 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 ) 2019-06-03T11:03:45 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 ) 2019-06-03T11:03:45 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 ) spots read : 28,181,672 reads read : 28,181,672 reads written : 28,181,672 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: 00:07:06 28181672 reads; of these: 28181672 (100.00%) were unpaired; of these: 2039282 (7.24%) aligned 0 times 23647869 (83.91%) aligned exactly 1 time 2494521 (8.85%) aligned >1 times 92.76% overall alignment rate Time searching: 00:07:06 Overall time: 00:07:06 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 12 files... [bam_rmdupse_core] 11677288 / 26142390 = 0.4467 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 20:23:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485219/SRX485219.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485219/SRX485219.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485219/SRX485219.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485219/SRX485219.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 20:23:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:23:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:23:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485219/SRX485219.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485219/SRX485219.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485219/SRX485219.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485219/SRX485219.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 20:23:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:23:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:23:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485219/SRX485219.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485219/SRX485219.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485219/SRX485219.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485219/SRX485219.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 20:23:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:23:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:23:08: 1000000 INFO @ Mon, 03 Jun 2019 20:23:08: 1000000 INFO @ Mon, 03 Jun 2019 20:23:08: 1000000 INFO @ Mon, 03 Jun 2019 20:23:15: 2000000 INFO @ Mon, 03 Jun 2019 20:23:15: 2000000 INFO @ Mon, 03 Jun 2019 20:23:17: 2000000 INFO @ Mon, 03 Jun 2019 20:23:22: 3000000 INFO @ Mon, 03 Jun 2019 20:23:22: 3000000 INFO @ Mon, 03 Jun 2019 20:23:26: 3000000 INFO @ Mon, 03 Jun 2019 20:23:29: 4000000 INFO @ Mon, 03 Jun 2019 20:23:29: 4000000 INFO @ Mon, 03 Jun 2019 20:23:36: 4000000 INFO @ Mon, 03 Jun 2019 20:23:36: 5000000 INFO @ Mon, 03 Jun 2019 20:23:37: 5000000 INFO @ Mon, 03 Jun 2019 20:23:44: 6000000 INFO @ Mon, 03 Jun 2019 20:23:44: 6000000 INFO @ Mon, 03 Jun 2019 20:23:45: 5000000 INFO @ Mon, 03 Jun 2019 20:23:51: 7000000 INFO @ Mon, 03 Jun 2019 20:23:51: 7000000 INFO @ Mon, 03 Jun 2019 20:23:54: 6000000 INFO @ Mon, 03 Jun 2019 20:23:58: 8000000 INFO @ Mon, 03 Jun 2019 20:23:58: 8000000 INFO @ Mon, 03 Jun 2019 20:24:03: 7000000 INFO @ Mon, 03 Jun 2019 20:24:05: 9000000 INFO @ Mon, 03 Jun 2019 20:24:05: 9000000 INFO @ Mon, 03 Jun 2019 20:24:12: 8000000 INFO @ Mon, 03 Jun 2019 20:24:12: 10000000 INFO @ Mon, 03 Jun 2019 20:24:12: 10000000 INFO @ Mon, 03 Jun 2019 20:24:19: 11000000 INFO @ Mon, 03 Jun 2019 20:24:19: 11000000 INFO @ Mon, 03 Jun 2019 20:24:21: 9000000 INFO @ Mon, 03 Jun 2019 20:24:26: 12000000 INFO @ Mon, 03 Jun 2019 20:24:26: 12000000 INFO @ Mon, 03 Jun 2019 20:24:30: 10000000 INFO @ Mon, 03 Jun 2019 20:24:33: 13000000 INFO @ Mon, 03 Jun 2019 20:24:33: 13000000 INFO @ Mon, 03 Jun 2019 20:24:39: 11000000 INFO @ Mon, 03 Jun 2019 20:24:40: 14000000 INFO @ Mon, 03 Jun 2019 20:24:40: 14000000 INFO @ Mon, 03 Jun 2019 20:24:44: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:24:44: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:24:44: #1 total tags in treatment: 14465102 INFO @ Mon, 03 Jun 2019 20:24:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:24:44: #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 20:24:44: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:24:44: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:24:44: #1 total tags in treatment: 14465102 INFO @ Mon, 03 Jun 2019 20:24:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:24:44: #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 20:24:44: #1 tags after filtering in treatment: 14465102 INFO @ Mon, 03 Jun 2019 20:24:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:24:44: #1 finished! INFO @ Mon, 03 Jun 2019 20:24:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:24:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:24:44: #1 tags after filtering in treatment: 14465102 INFO @ Mon, 03 Jun 2019 20:24:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:24:44: #1 finished! INFO @ Mon, 03 Jun 2019 20:24:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:24:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:24:46: #2 number of paired peaks: 8061 INFO @ Mon, 03 Jun 2019 20:24:46: start model_add_line... INFO @ Mon, 03 Jun 2019 20:24:46: #2 number of paired peaks: 8061 INFO @ Mon, 03 Jun 2019 20:24:46: start model_add_line... INFO @ Mon, 03 Jun 2019 20:24:46: start X-correlation... INFO @ Mon, 03 Jun 2019 20:24:47: end of X-cor INFO @ Mon, 03 Jun 2019 20:24:47: #2 finished! INFO @ Mon, 03 Jun 2019 20:24:47: #2 predicted fragment length is 190 bps INFO @ Mon, 03 Jun 2019 20:24:47: #2 alternative fragment length(s) may be 190 bps INFO @ Mon, 03 Jun 2019 20:24:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485219/SRX485219.05_model.r INFO @ Mon, 03 Jun 2019 20:24:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:24:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:24:47: start X-correlation... INFO @ Mon, 03 Jun 2019 20:24:47: end of X-cor INFO @ Mon, 03 Jun 2019 20:24:47: #2 finished! INFO @ Mon, 03 Jun 2019 20:24:47: #2 predicted fragment length is 190 bps INFO @ Mon, 03 Jun 2019 20:24:47: #2 alternative fragment length(s) may be 190 bps INFO @ Mon, 03 Jun 2019 20:24:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485219/SRX485219.10_model.r INFO @ Mon, 03 Jun 2019 20:24:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:24:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:24:48: 12000000 INFO @ Mon, 03 Jun 2019 20:24:57: 13000000 INFO @ Mon, 03 Jun 2019 20:25:05: 14000000 INFO @ Mon, 03 Jun 2019 20:25:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:25:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:25:09: #1 total tags in treatment: 14465102 INFO @ Mon, 03 Jun 2019 20:25:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:25:09: #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 20:25:10: #1 tags after filtering in treatment: 14465102 INFO @ Mon, 03 Jun 2019 20:25:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:25:10: #1 finished! INFO @ Mon, 03 Jun 2019 20:25:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:25:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:25:12: #2 number of paired peaks: 8061 INFO @ Mon, 03 Jun 2019 20:25:12: start model_add_line... INFO @ Mon, 03 Jun 2019 20:25:12: start X-correlation... INFO @ Mon, 03 Jun 2019 20:25:12: end of X-cor INFO @ Mon, 03 Jun 2019 20:25:12: #2 finished! INFO @ Mon, 03 Jun 2019 20:25:12: #2 predicted fragment length is 190 bps INFO @ Mon, 03 Jun 2019 20:25:12: #2 alternative fragment length(s) may be 190 bps INFO @ Mon, 03 Jun 2019 20:25:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485219/SRX485219.20_model.r INFO @ Mon, 03 Jun 2019 20:25:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:25:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:25:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:25:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:26:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485219/SRX485219.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:26:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485219/SRX485219.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:26:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485219/SRX485219.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:26:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485219/SRX485219.10_summits.bed INFO @ Mon, 03 Jun 2019 20:26:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485219/SRX485219.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:26:00: Done! INFO @ Mon, 03 Jun 2019 20:26:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485219/SRX485219.05_summits.bed INFO @ Mon, 03 Jun 2019 20:26:01: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7002 records, 4 fields): 16 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8557 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:26:07: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 20:26:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485219/SRX485219.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:26:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485219/SRX485219.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:26:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485219/SRX485219.20_summits.bed INFO @ Mon, 03 Jun 2019 20:26:28: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5505 records, 4 fields): 9 millis CompletedMACS2peakCalling BigWig に変換しました。