Job ID = 1309294 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T14:20:30 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 ) 2019-06-03T14:20:30 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 ) 2019-06-03T14:20:30 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 ) 2019-06-03T14:20:30 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 ) 2019-06-03T14:26:07 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 : 10,479,960 reads read : 20,959,920 reads written : 10,479,960 reads 0-length : 10,479,960 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: 00:00:01 Multiseed full-index search: 00:10:26 10479960 reads; of these: 10479960 (100.00%) were unpaired; of these: 222176 (2.12%) aligned 0 times 8249422 (78.72%) aligned exactly 1 time 2008362 (19.16%) aligned >1 times 97.88% overall alignment rate Time searching: 00:10:27 Overall time: 00:10:27 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] 559036 / 10257784 = 0.0545 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 23:43:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX864532/SRX864532.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX864532/SRX864532.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX864532/SRX864532.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX864532/SRX864532.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 23:43:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:43:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:43:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX864532/SRX864532.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX864532/SRX864532.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX864532/SRX864532.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX864532/SRX864532.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 23:43:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:43:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:43:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX864532/SRX864532.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX864532/SRX864532.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX864532/SRX864532.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX864532/SRX864532.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 23:43:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:43:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:44:04: 1000000 INFO @ Mon, 03 Jun 2019 23:44:05: 1000000 INFO @ Mon, 03 Jun 2019 23:44:06: 1000000 INFO @ Mon, 03 Jun 2019 23:44:18: 2000000 INFO @ Mon, 03 Jun 2019 23:44:19: 2000000 INFO @ Mon, 03 Jun 2019 23:44:20: 2000000 INFO @ Mon, 03 Jun 2019 23:44:31: 3000000 INFO @ Mon, 03 Jun 2019 23:44:31: 3000000 INFO @ Mon, 03 Jun 2019 23:44:34: 3000000 INFO @ Mon, 03 Jun 2019 23:44:44: 4000000 INFO @ Mon, 03 Jun 2019 23:44:45: 4000000 INFO @ Mon, 03 Jun 2019 23:44:48: 4000000 INFO @ Mon, 03 Jun 2019 23:44:57: 5000000 INFO @ Mon, 03 Jun 2019 23:44:58: 5000000 INFO @ Mon, 03 Jun 2019 23:45:03: 5000000 INFO @ Mon, 03 Jun 2019 23:45:08: 6000000 INFO @ Mon, 03 Jun 2019 23:45:10: 6000000 INFO @ Mon, 03 Jun 2019 23:45:18: 7000000 INFO @ Mon, 03 Jun 2019 23:45:19: 6000000 INFO @ Mon, 03 Jun 2019 23:45:22: 7000000 INFO @ Mon, 03 Jun 2019 23:45:29: 8000000 INFO @ Mon, 03 Jun 2019 23:45:35: 7000000 INFO @ Mon, 03 Jun 2019 23:45:35: 8000000 INFO @ Mon, 03 Jun 2019 23:45:40: 9000000 INFO @ Mon, 03 Jun 2019 23:45:47: 9000000 INFO @ Mon, 03 Jun 2019 23:45:47: #1 tag size is determined as 148 bps INFO @ Mon, 03 Jun 2019 23:45:47: #1 tag size = 148 INFO @ Mon, 03 Jun 2019 23:45:47: #1 total tags in treatment: 9698748 INFO @ Mon, 03 Jun 2019 23:45:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:45:47: #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 23:45:47: #1 tags after filtering in treatment: 9698748 INFO @ Mon, 03 Jun 2019 23:45:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:45:47: #1 finished! INFO @ Mon, 03 Jun 2019 23:45:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:45:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:45:48: #2 number of paired peaks: 211 WARNING @ Mon, 03 Jun 2019 23:45:48: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Mon, 03 Jun 2019 23:45:48: start model_add_line... INFO @ Mon, 03 Jun 2019 23:45:48: start X-correlation... INFO @ Mon, 03 Jun 2019 23:45:48: end of X-cor INFO @ Mon, 03 Jun 2019 23:45:48: #2 finished! INFO @ Mon, 03 Jun 2019 23:45:48: #2 predicted fragment length is 145 bps INFO @ Mon, 03 Jun 2019 23:45:48: #2 alternative fragment length(s) may be 145 bps INFO @ Mon, 03 Jun 2019 23:45:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX864532/SRX864532.05_model.r WARNING @ Mon, 03 Jun 2019 23:45:48: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:45:48: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Mon, 03 Jun 2019 23:45:48: #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 23:45:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:45:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:45:50: 8000000 INFO @ Mon, 03 Jun 2019 23:45:55: #1 tag size is determined as 148 bps INFO @ Mon, 03 Jun 2019 23:45:55: #1 tag size = 148 INFO @ Mon, 03 Jun 2019 23:45:55: #1 total tags in treatment: 9698748 INFO @ Mon, 03 Jun 2019 23:45:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:45:55: #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 23:45:55: #1 tags after filtering in treatment: 9698748 INFO @ Mon, 03 Jun 2019 23:45:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:45:55: #1 finished! INFO @ Mon, 03 Jun 2019 23:45:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:45:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:45:56: #2 number of paired peaks: 211 WARNING @ Mon, 03 Jun 2019 23:45:56: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Mon, 03 Jun 2019 23:45:56: start model_add_line... INFO @ Mon, 03 Jun 2019 23:45:56: start X-correlation... INFO @ Mon, 03 Jun 2019 23:45:56: end of X-cor INFO @ Mon, 03 Jun 2019 23:45:56: #2 finished! INFO @ Mon, 03 Jun 2019 23:45:56: #2 predicted fragment length is 145 bps INFO @ Mon, 03 Jun 2019 23:45:56: #2 alternative fragment length(s) may be 145 bps INFO @ Mon, 03 Jun 2019 23:45:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX864532/SRX864532.20_model.r WARNING @ Mon, 03 Jun 2019 23:45:56: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:45:56: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Mon, 03 Jun 2019 23:45:56: #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 23:45:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:45:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:46:06: 9000000 INFO @ Mon, 03 Jun 2019 23:46:16: #1 tag size is determined as 148 bps INFO @ Mon, 03 Jun 2019 23:46:16: #1 tag size = 148 INFO @ Mon, 03 Jun 2019 23:46:16: #1 total tags in treatment: 9698748 INFO @ Mon, 03 Jun 2019 23:46:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:46:16: #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 23:46:16: #1 tags after filtering in treatment: 9698748 INFO @ Mon, 03 Jun 2019 23:46:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:46:16: #1 finished! INFO @ Mon, 03 Jun 2019 23:46:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:46:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:46:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:46:17: #2 number of paired peaks: 211 WARNING @ Mon, 03 Jun 2019 23:46:17: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Mon, 03 Jun 2019 23:46:17: start model_add_line... INFO @ Mon, 03 Jun 2019 23:46:17: start X-correlation... INFO @ Mon, 03 Jun 2019 23:46:17: end of X-cor INFO @ Mon, 03 Jun 2019 23:46:17: #2 finished! INFO @ Mon, 03 Jun 2019 23:46:17: #2 predicted fragment length is 145 bps INFO @ Mon, 03 Jun 2019 23:46:17: #2 alternative fragment length(s) may be 145 bps INFO @ Mon, 03 Jun 2019 23:46:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX864532/SRX864532.10_model.r WARNING @ Mon, 03 Jun 2019 23:46:17: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:46:17: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Mon, 03 Jun 2019 23:46:17: #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 23:46:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:46:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:46:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:46:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX864532/SRX864532.05_peaks.xls INFO @ Mon, 03 Jun 2019 23:46:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX864532/SRX864532.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:46:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX864532/SRX864532.05_summits.bed INFO @ Mon, 03 Jun 2019 23:46:30: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2145 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:46:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX864532/SRX864532.20_peaks.xls INFO @ Mon, 03 Jun 2019 23:46:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX864532/SRX864532.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:46:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX864532/SRX864532.20_summits.bed INFO @ Mon, 03 Jun 2019 23:46:38: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (360 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:46:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:47:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX864532/SRX864532.10_peaks.xls INFO @ Mon, 03 Jun 2019 23:47:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX864532/SRX864532.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:47:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX864532/SRX864532.10_summits.bed INFO @ Mon, 03 Jun 2019 23:47:00: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (745 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。