Job ID = 1307553 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:22:46 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 ) 2019-06-03T13:26:16 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 ) 2019-06-03T13:26:16 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 ) 2019-06-03T13:27:31 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 ) 2019-06-03T13:27:31 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 ) 2019-06-03T13:27:34 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 : 22,310,526 reads read : 44,621,052 reads written : 22,310,526 reads 0-length : 22,310,526 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: 00:13:02 22310526 reads; of these: 22310526 (100.00%) were unpaired; of these: 971257 (4.35%) aligned 0 times 14577636 (65.34%) aligned exactly 1 time 6761633 (30.31%) aligned >1 times 95.65% overall alignment rate Time searching: 00:13:02 Overall time: 00:13:02 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] 2487090 / 21339269 = 0.1165 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 22:52:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343093/SRX5343093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343093/SRX5343093.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343093/SRX5343093.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343093/SRX5343093.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 22:52:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:52:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:52:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343093/SRX5343093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343093/SRX5343093.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343093/SRX5343093.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343093/SRX5343093.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 22:52:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:52:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:52:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343093/SRX5343093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343093/SRX5343093.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343093/SRX5343093.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343093/SRX5343093.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 22:52:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:52:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:52:28: 1000000 INFO @ Mon, 03 Jun 2019 22:52:28: 1000000 INFO @ Mon, 03 Jun 2019 22:52:28: 1000000 INFO @ Mon, 03 Jun 2019 22:52:36: 2000000 INFO @ Mon, 03 Jun 2019 22:52:36: 2000000 INFO @ Mon, 03 Jun 2019 22:52:36: 2000000 INFO @ Mon, 03 Jun 2019 22:52:44: 3000000 INFO @ Mon, 03 Jun 2019 22:52:44: 3000000 INFO @ Mon, 03 Jun 2019 22:52:44: 3000000 INFO @ Mon, 03 Jun 2019 22:52:51: 4000000 INFO @ Mon, 03 Jun 2019 22:52:52: 4000000 INFO @ Mon, 03 Jun 2019 22:52:52: 4000000 INFO @ Mon, 03 Jun 2019 22:52:59: 5000000 INFO @ Mon, 03 Jun 2019 22:53:00: 5000000 INFO @ Mon, 03 Jun 2019 22:53:00: 5000000 INFO @ Mon, 03 Jun 2019 22:53:07: 6000000 INFO @ Mon, 03 Jun 2019 22:53:07: 6000000 INFO @ Mon, 03 Jun 2019 22:53:08: 6000000 INFO @ Mon, 03 Jun 2019 22:53:14: 7000000 INFO @ Mon, 03 Jun 2019 22:53:15: 7000000 INFO @ Mon, 03 Jun 2019 22:53:16: 7000000 INFO @ Mon, 03 Jun 2019 22:53:22: 8000000 INFO @ Mon, 03 Jun 2019 22:53:23: 8000000 INFO @ Mon, 03 Jun 2019 22:53:24: 8000000 INFO @ Mon, 03 Jun 2019 22:53:30: 9000000 INFO @ Mon, 03 Jun 2019 22:53:31: 9000000 INFO @ Mon, 03 Jun 2019 22:53:32: 9000000 INFO @ Mon, 03 Jun 2019 22:53:38: 10000000 INFO @ Mon, 03 Jun 2019 22:53:39: 10000000 INFO @ Mon, 03 Jun 2019 22:53:40: 10000000 INFO @ Mon, 03 Jun 2019 22:53:46: 11000000 INFO @ Mon, 03 Jun 2019 22:53:47: 11000000 INFO @ Mon, 03 Jun 2019 22:53:48: 11000000 INFO @ Mon, 03 Jun 2019 22:53:54: 12000000 INFO @ Mon, 03 Jun 2019 22:53:54: 12000000 INFO @ Mon, 03 Jun 2019 22:53:55: 12000000 INFO @ Mon, 03 Jun 2019 22:54:01: 13000000 INFO @ Mon, 03 Jun 2019 22:54:02: 13000000 INFO @ Mon, 03 Jun 2019 22:54:03: 13000000 INFO @ Mon, 03 Jun 2019 22:54:09: 14000000 INFO @ Mon, 03 Jun 2019 22:54:10: 14000000 INFO @ Mon, 03 Jun 2019 22:54:11: 14000000 INFO @ Mon, 03 Jun 2019 22:54:17: 15000000 INFO @ Mon, 03 Jun 2019 22:54:17: 15000000 INFO @ Mon, 03 Jun 2019 22:54:19: 15000000 INFO @ Mon, 03 Jun 2019 22:54:24: 16000000 INFO @ Mon, 03 Jun 2019 22:54:25: 16000000 INFO @ Mon, 03 Jun 2019 22:54:26: 16000000 INFO @ Mon, 03 Jun 2019 22:54:32: 17000000 INFO @ Mon, 03 Jun 2019 22:54:33: 17000000 INFO @ Mon, 03 Jun 2019 22:54:34: 17000000 INFO @ Mon, 03 Jun 2019 22:54:39: 18000000 INFO @ Mon, 03 Jun 2019 22:54:40: 18000000 INFO @ Mon, 03 Jun 2019 22:54:42: 18000000 INFO @ Mon, 03 Jun 2019 22:54:47: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:54:47: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:54:47: #1 total tags in treatment: 18852179 INFO @ Mon, 03 Jun 2019 22:54:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:54:47: #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 22:54:47: #1 tags after filtering in treatment: 18852179 INFO @ Mon, 03 Jun 2019 22:54:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:54:47: #1 finished! INFO @ Mon, 03 Jun 2019 22:54:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:54:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:54:48: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:54:48: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:54:48: #1 total tags in treatment: 18852179 INFO @ Mon, 03 Jun 2019 22:54:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:54:48: #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 22:54:48: #1 tags after filtering in treatment: 18852179 INFO @ Mon, 03 Jun 2019 22:54:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:54:48: #1 finished! INFO @ Mon, 03 Jun 2019 22:54:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:54:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:54:49: #2 number of paired peaks: 159 WARNING @ Mon, 03 Jun 2019 22:54:49: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Mon, 03 Jun 2019 22:54:49: start model_add_line... INFO @ Mon, 03 Jun 2019 22:54:49: start X-correlation... INFO @ Mon, 03 Jun 2019 22:54:49: end of X-cor INFO @ Mon, 03 Jun 2019 22:54:49: #2 finished! INFO @ Mon, 03 Jun 2019 22:54:49: #2 predicted fragment length is 57 bps INFO @ Mon, 03 Jun 2019 22:54:49: #2 alternative fragment length(s) may be 57 bps INFO @ Mon, 03 Jun 2019 22:54:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343093/SRX5343093.20_model.r WARNING @ Mon, 03 Jun 2019 22:54:49: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:54:49: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Mon, 03 Jun 2019 22:54:49: #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 22:54:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:54:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:54:49: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:54:49: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:54:49: #1 total tags in treatment: 18852179 INFO @ Mon, 03 Jun 2019 22:54:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:54:49: #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 22:54:49: #1 tags after filtering in treatment: 18852179 INFO @ Mon, 03 Jun 2019 22:54:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:54:49: #1 finished! INFO @ Mon, 03 Jun 2019 22:54:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:54:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:54:50: #2 number of paired peaks: 159 WARNING @ Mon, 03 Jun 2019 22:54:50: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Mon, 03 Jun 2019 22:54:50: start model_add_line... INFO @ Mon, 03 Jun 2019 22:54:50: start X-correlation... INFO @ Mon, 03 Jun 2019 22:54:50: end of X-cor INFO @ Mon, 03 Jun 2019 22:54:50: #2 finished! INFO @ Mon, 03 Jun 2019 22:54:50: #2 predicted fragment length is 57 bps INFO @ Mon, 03 Jun 2019 22:54:50: #2 alternative fragment length(s) may be 57 bps INFO @ Mon, 03 Jun 2019 22:54:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343093/SRX5343093.10_model.r WARNING @ Mon, 03 Jun 2019 22:54:50: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:54:50: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Mon, 03 Jun 2019 22:54:50: #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 22:54:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:54:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:54:51: #2 number of paired peaks: 159 WARNING @ Mon, 03 Jun 2019 22:54:51: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Mon, 03 Jun 2019 22:54:51: start model_add_line... INFO @ Mon, 03 Jun 2019 22:54:51: start X-correlation... INFO @ Mon, 03 Jun 2019 22:54:51: end of X-cor INFO @ Mon, 03 Jun 2019 22:54:51: #2 finished! INFO @ Mon, 03 Jun 2019 22:54:51: #2 predicted fragment length is 57 bps INFO @ Mon, 03 Jun 2019 22:54:51: #2 alternative fragment length(s) may be 57 bps INFO @ Mon, 03 Jun 2019 22:54:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343093/SRX5343093.05_model.r WARNING @ Mon, 03 Jun 2019 22:54:51: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:54:51: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Mon, 03 Jun 2019 22:54:51: #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 22:54:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:54:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:55:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:55:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:55:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:56:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343093/SRX5343093.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:56:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343093/SRX5343093.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:56:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343093/SRX5343093.20_summits.bed INFO @ Mon, 03 Jun 2019 22:56:01: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1030 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:56:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343093/SRX5343093.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:56:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343093/SRX5343093.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:56:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343093/SRX5343093.10_summits.bed INFO @ Mon, 03 Jun 2019 22:56:02: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1396 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:56:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343093/SRX5343093.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:56:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343093/SRX5343093.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:56:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343093/SRX5343093.05_summits.bed INFO @ Mon, 03 Jun 2019 22:56:04: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1789 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。