Job ID = 1303384 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T11:22:38 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 ) 2019-06-03T11:24:20 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 ) 2019-06-03T11:24:20 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 ) 2019-06-03T11:24:20 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 ) 2019-06-03T11:26:56 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 ) 2019-06-03T11:28:37 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 ) 2019-06-03T11:28:37 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 ) 2019-06-03T11:30:27 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 ) 2019-06-03T11:33:16 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 21,013,092 reads read : 21,013,092 reads written : 21,013,092 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: 00:08:26 21013092 reads; of these: 21013092 (100.00%) were unpaired; of these: 1684781 (8.02%) aligned 0 times 13981722 (66.54%) aligned exactly 1 time 5346589 (25.44%) aligned >1 times 91.98% overall alignment rate Time searching: 00:08:26 Overall time: 00:08:26 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] 11060520 / 19328311 = 0.5722 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 20:48:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933906/SRX4933906.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933906/SRX4933906.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933906/SRX4933906.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933906/SRX4933906.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 20:48:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:48:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:48:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933906/SRX4933906.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933906/SRX4933906.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933906/SRX4933906.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933906/SRX4933906.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 20:48:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:48:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:48:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933906/SRX4933906.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933906/SRX4933906.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933906/SRX4933906.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933906/SRX4933906.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 20:48:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:48:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:48:07: 1000000 INFO @ Mon, 03 Jun 2019 20:48:09: 1000000 INFO @ Mon, 03 Jun 2019 20:48:10: 1000000 INFO @ Mon, 03 Jun 2019 20:48:14: 2000000 INFO @ Mon, 03 Jun 2019 20:48:18: 2000000 INFO @ Mon, 03 Jun 2019 20:48:19: 2000000 INFO @ Mon, 03 Jun 2019 20:48:21: 3000000 INFO @ Mon, 03 Jun 2019 20:48:26: 3000000 INFO @ Mon, 03 Jun 2019 20:48:27: 4000000 INFO @ Mon, 03 Jun 2019 20:48:28: 3000000 INFO @ Mon, 03 Jun 2019 20:48:35: 4000000 INFO @ Mon, 03 Jun 2019 20:48:35: 5000000 INFO @ Mon, 03 Jun 2019 20:48:36: 4000000 INFO @ Mon, 03 Jun 2019 20:48:42: 6000000 INFO @ Mon, 03 Jun 2019 20:48:43: 5000000 INFO @ Mon, 03 Jun 2019 20:48:45: 5000000 INFO @ Mon, 03 Jun 2019 20:48:50: 7000000 INFO @ Mon, 03 Jun 2019 20:48:52: 6000000 INFO @ Mon, 03 Jun 2019 20:48:54: 6000000 INFO @ Mon, 03 Jun 2019 20:48:56: 8000000 INFO @ Mon, 03 Jun 2019 20:48:58: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:48:58: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:48:58: #1 total tags in treatment: 8267791 INFO @ Mon, 03 Jun 2019 20:48:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:48:58: #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 20:48:58: #1 tags after filtering in treatment: 8267791 INFO @ Mon, 03 Jun 2019 20:48:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:48:58: #1 finished! INFO @ Mon, 03 Jun 2019 20:48:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:48:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:48:59: #2 number of paired peaks: 568 WARNING @ Mon, 03 Jun 2019 20:48:59: Fewer paired peaks (568) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 568 pairs to build model! INFO @ Mon, 03 Jun 2019 20:48:59: start model_add_line... INFO @ Mon, 03 Jun 2019 20:48:59: start X-correlation... INFO @ Mon, 03 Jun 2019 20:48:59: end of X-cor INFO @ Mon, 03 Jun 2019 20:48:59: #2 finished! INFO @ Mon, 03 Jun 2019 20:48:59: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 20:48:59: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 20:48:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933906/SRX4933906.20_model.r WARNING @ Mon, 03 Jun 2019 20:48:59: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:48:59: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 20:48:59: #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 20:48:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:48:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:49:00: 7000000 INFO @ Mon, 03 Jun 2019 20:49:03: 7000000 INFO @ Mon, 03 Jun 2019 20:49:09: 8000000 INFO @ Mon, 03 Jun 2019 20:49:11: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:49:11: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:49:11: #1 total tags in treatment: 8267791 INFO @ Mon, 03 Jun 2019 20:49:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:49:11: #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 20:49:11: #1 tags after filtering in treatment: 8267791 INFO @ Mon, 03 Jun 2019 20:49:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:49:11: #1 finished! INFO @ Mon, 03 Jun 2019 20:49:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:49:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:49:11: 8000000 INFO @ Mon, 03 Jun 2019 20:49:12: #2 number of paired peaks: 568 WARNING @ Mon, 03 Jun 2019 20:49:12: Fewer paired peaks (568) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 568 pairs to build model! INFO @ Mon, 03 Jun 2019 20:49:12: start model_add_line... INFO @ Mon, 03 Jun 2019 20:49:12: start X-correlation... INFO @ Mon, 03 Jun 2019 20:49:12: end of X-cor INFO @ Mon, 03 Jun 2019 20:49:12: #2 finished! INFO @ Mon, 03 Jun 2019 20:49:12: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 20:49:12: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 20:49:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933906/SRX4933906.10_model.r WARNING @ Mon, 03 Jun 2019 20:49:12: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:49:12: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 20:49:12: #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 20:49:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:49:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:49:14: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:49:14: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:49:14: #1 total tags in treatment: 8267791 INFO @ Mon, 03 Jun 2019 20:49:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:49:14: #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 20:49:14: #1 tags after filtering in treatment: 8267791 INFO @ Mon, 03 Jun 2019 20:49:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:49:14: #1 finished! INFO @ Mon, 03 Jun 2019 20:49:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:49:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:49:15: #2 number of paired peaks: 568 WARNING @ Mon, 03 Jun 2019 20:49:15: Fewer paired peaks (568) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 568 pairs to build model! INFO @ Mon, 03 Jun 2019 20:49:15: start model_add_line... INFO @ Mon, 03 Jun 2019 20:49:15: start X-correlation... INFO @ Mon, 03 Jun 2019 20:49:15: end of X-cor INFO @ Mon, 03 Jun 2019 20:49:15: #2 finished! INFO @ Mon, 03 Jun 2019 20:49:15: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 20:49:15: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 20:49:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933906/SRX4933906.05_model.r WARNING @ Mon, 03 Jun 2019 20:49:15: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:49:15: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 20:49:15: #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 20:49:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:49:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:49:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:49:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933906/SRX4933906.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:49:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933906/SRX4933906.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:49:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933906/SRX4933906.20_summits.bed INFO @ Mon, 03 Jun 2019 20:49:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1033 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:49:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:49:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:49:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933906/SRX4933906.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:49:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933906/SRX4933906.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:49:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933906/SRX4933906.10_summits.bed INFO @ Mon, 03 Jun 2019 20:49:49: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1481 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:49:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933906/SRX4933906.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:49:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933906/SRX4933906.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:49:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933906/SRX4933906.05_summits.bed INFO @ Mon, 03 Jun 2019 20:49:51: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2223 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。