Job ID = 1294745 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:53:22 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 ) 2019-06-03T00:53:22 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 ) 2019-06-03T00:54:56 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 ) 2019-06-03T00:54:56 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 ) 2019-06-03T00:56:51 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 ) 2019-06-03T00:56:52 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 ) 2019-06-03T00:58:30 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 : 17,637,595 reads read : 17,637,595 reads written : 17,637,595 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: 00:08:47 17637595 reads; of these: 17637595 (100.00%) were unpaired; of these: 1059834 (6.01%) aligned 0 times 10955922 (62.12%) aligned exactly 1 time 5621839 (31.87%) aligned >1 times 93.99% overall alignment rate Time searching: 00:08:47 Overall time: 00:08:47 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] 2408597 / 16577761 = 0.1453 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 10:14:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287854/SRX287854.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287854/SRX287854.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287854/SRX287854.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287854/SRX287854.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 10:14:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:14:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:14:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287854/SRX287854.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287854/SRX287854.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287854/SRX287854.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287854/SRX287854.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 10:14:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:14:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:14:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287854/SRX287854.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287854/SRX287854.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287854/SRX287854.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287854/SRX287854.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 10:14:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:14:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:14:17: 1000000 INFO @ Mon, 03 Jun 2019 10:14:17: 1000000 INFO @ Mon, 03 Jun 2019 10:14:18: 1000000 INFO @ Mon, 03 Jun 2019 10:14:28: 2000000 INFO @ Mon, 03 Jun 2019 10:14:28: 2000000 INFO @ Mon, 03 Jun 2019 10:14:29: 2000000 INFO @ Mon, 03 Jun 2019 10:14:38: 3000000 INFO @ Mon, 03 Jun 2019 10:14:39: 3000000 INFO @ Mon, 03 Jun 2019 10:14:39: 3000000 INFO @ Mon, 03 Jun 2019 10:14:48: 4000000 INFO @ Mon, 03 Jun 2019 10:14:49: 4000000 INFO @ Mon, 03 Jun 2019 10:14:50: 4000000 INFO @ Mon, 03 Jun 2019 10:14:58: 5000000 INFO @ Mon, 03 Jun 2019 10:15:00: 5000000 INFO @ Mon, 03 Jun 2019 10:15:01: 5000000 INFO @ Mon, 03 Jun 2019 10:15:08: 6000000 INFO @ Mon, 03 Jun 2019 10:15:10: 6000000 INFO @ Mon, 03 Jun 2019 10:15:12: 6000000 INFO @ Mon, 03 Jun 2019 10:15:18: 7000000 INFO @ Mon, 03 Jun 2019 10:15:20: 7000000 INFO @ Mon, 03 Jun 2019 10:15:22: 7000000 INFO @ Mon, 03 Jun 2019 10:15:28: 8000000 INFO @ Mon, 03 Jun 2019 10:15:31: 8000000 INFO @ Mon, 03 Jun 2019 10:15:33: 8000000 INFO @ Mon, 03 Jun 2019 10:15:38: 9000000 INFO @ Mon, 03 Jun 2019 10:15:41: 9000000 INFO @ Mon, 03 Jun 2019 10:15:44: 9000000 INFO @ Mon, 03 Jun 2019 10:15:48: 10000000 INFO @ Mon, 03 Jun 2019 10:15:52: 10000000 INFO @ Mon, 03 Jun 2019 10:15:54: 10000000 INFO @ Mon, 03 Jun 2019 10:15:58: 11000000 INFO @ Mon, 03 Jun 2019 10:16:02: 11000000 INFO @ Mon, 03 Jun 2019 10:16:05: 11000000 INFO @ Mon, 03 Jun 2019 10:16:08: 12000000 INFO @ Mon, 03 Jun 2019 10:16:12: 12000000 INFO @ Mon, 03 Jun 2019 10:16:16: 12000000 INFO @ Mon, 03 Jun 2019 10:16:18: 13000000 INFO @ Mon, 03 Jun 2019 10:16:22: 13000000 INFO @ Mon, 03 Jun 2019 10:16:27: 13000000 INFO @ Mon, 03 Jun 2019 10:16:28: 14000000 INFO @ Mon, 03 Jun 2019 10:16:29: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:16:29: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:16:29: #1 total tags in treatment: 14169164 INFO @ Mon, 03 Jun 2019 10:16:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:16:29: #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 10:16:30: #1 tags after filtering in treatment: 14169164 INFO @ Mon, 03 Jun 2019 10:16:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:16:30: #1 finished! INFO @ Mon, 03 Jun 2019 10:16:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:16:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:16:31: #2 number of paired peaks: 280 WARNING @ Mon, 03 Jun 2019 10:16:31: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Mon, 03 Jun 2019 10:16:31: start model_add_line... INFO @ Mon, 03 Jun 2019 10:16:31: start X-correlation... INFO @ Mon, 03 Jun 2019 10:16:31: end of X-cor INFO @ Mon, 03 Jun 2019 10:16:31: #2 finished! INFO @ Mon, 03 Jun 2019 10:16:31: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 10:16:31: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 10:16:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287854/SRX287854.05_model.r WARNING @ Mon, 03 Jun 2019 10:16:31: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:16:31: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 10:16:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 10:16:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:16:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:16:33: 14000000 INFO @ Mon, 03 Jun 2019 10:16:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:16:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:16:34: #1 total tags in treatment: 14169164 INFO @ Mon, 03 Jun 2019 10:16:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:16:34: #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 10:16:35: #1 tags after filtering in treatment: 14169164 INFO @ Mon, 03 Jun 2019 10:16:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:16:35: #1 finished! INFO @ Mon, 03 Jun 2019 10:16:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:16:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:16:36: #2 number of paired peaks: 280 WARNING @ Mon, 03 Jun 2019 10:16:36: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Mon, 03 Jun 2019 10:16:36: start model_add_line... INFO @ Mon, 03 Jun 2019 10:16:36: start X-correlation... INFO @ Mon, 03 Jun 2019 10:16:36: end of X-cor INFO @ Mon, 03 Jun 2019 10:16:36: #2 finished! INFO @ Mon, 03 Jun 2019 10:16:36: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 10:16:36: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 10:16:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287854/SRX287854.10_model.r WARNING @ Mon, 03 Jun 2019 10:16:36: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:16:36: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 10:16:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 10:16:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:16:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:16:38: 14000000 INFO @ Mon, 03 Jun 2019 10:16:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:16:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:16:39: #1 total tags in treatment: 14169164 INFO @ Mon, 03 Jun 2019 10:16:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:16:39: #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 10:16:40: #1 tags after filtering in treatment: 14169164 INFO @ Mon, 03 Jun 2019 10:16:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:16:40: #1 finished! INFO @ Mon, 03 Jun 2019 10:16:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:16:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:16:41: #2 number of paired peaks: 280 WARNING @ Mon, 03 Jun 2019 10:16:41: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Mon, 03 Jun 2019 10:16:41: start model_add_line... INFO @ Mon, 03 Jun 2019 10:16:41: start X-correlation... INFO @ Mon, 03 Jun 2019 10:16:41: end of X-cor INFO @ Mon, 03 Jun 2019 10:16:41: #2 finished! INFO @ Mon, 03 Jun 2019 10:16:41: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 10:16:41: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 10:16:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287854/SRX287854.20_model.r WARNING @ Mon, 03 Jun 2019 10:16:41: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:16:41: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 10:16:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 10:16:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:16:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:17:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:17:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:17:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:17:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287854/SRX287854.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:17:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287854/SRX287854.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:17:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287854/SRX287854.05_summits.bed INFO @ Mon, 03 Jun 2019 10:17:29: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2182 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:17:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287854/SRX287854.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:17:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287854/SRX287854.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:17:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287854/SRX287854.10_summits.bed INFO @ Mon, 03 Jun 2019 10:17:33: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1884 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:17:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287854/SRX287854.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:17:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287854/SRX287854.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:17:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287854/SRX287854.20_summits.bed INFO @ Mon, 03 Jun 2019 10:17:37: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1432 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。