Job ID = 1295171 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T03:20:50 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 ) 2019-06-03T03:33:13 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 : 30,030,493 reads read : 30,030,493 reads written : 30,030,493 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: 00:13:01 30030493 reads; of these: 30030493 (100.00%) were unpaired; of these: 1839201 (6.12%) aligned 0 times 18333552 (61.05%) aligned exactly 1 time 9857740 (32.83%) aligned >1 times 93.88% overall alignment rate Time searching: 00:13:01 Overall time: 00:13:01 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] 13653252 / 28191292 = 0.4843 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 12:55:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX330271/SRX330271.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX330271/SRX330271.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX330271/SRX330271.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX330271/SRX330271.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 12:55:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:55:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:55:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX330271/SRX330271.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX330271/SRX330271.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX330271/SRX330271.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX330271/SRX330271.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 12:55:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:55:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:55:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX330271/SRX330271.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX330271/SRX330271.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX330271/SRX330271.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX330271/SRX330271.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 12:55:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:55:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:55:40: 1000000 INFO @ Mon, 03 Jun 2019 12:55:40: 1000000 INFO @ Mon, 03 Jun 2019 12:55:42: 1000000 INFO @ Mon, 03 Jun 2019 12:55:50: 2000000 INFO @ Mon, 03 Jun 2019 12:55:50: 2000000 INFO @ Mon, 03 Jun 2019 12:55:55: 2000000 INFO @ Mon, 03 Jun 2019 12:55:59: 3000000 INFO @ Mon, 03 Jun 2019 12:55:59: 3000000 INFO @ Mon, 03 Jun 2019 12:56:07: 3000000 INFO @ Mon, 03 Jun 2019 12:56:07: 4000000 INFO @ Mon, 03 Jun 2019 12:56:08: 4000000 INFO @ Mon, 03 Jun 2019 12:56:15: 5000000 INFO @ Mon, 03 Jun 2019 12:56:16: 5000000 INFO @ Mon, 03 Jun 2019 12:56:18: 4000000 INFO @ Mon, 03 Jun 2019 12:56:24: 6000000 INFO @ Mon, 03 Jun 2019 12:56:24: 6000000 INFO @ Mon, 03 Jun 2019 12:56:29: 5000000 INFO @ Mon, 03 Jun 2019 12:56:32: 7000000 INFO @ Mon, 03 Jun 2019 12:56:32: 7000000 INFO @ Mon, 03 Jun 2019 12:56:40: 6000000 INFO @ Mon, 03 Jun 2019 12:56:41: 8000000 INFO @ Mon, 03 Jun 2019 12:56:41: 8000000 INFO @ Mon, 03 Jun 2019 12:56:50: 9000000 INFO @ Mon, 03 Jun 2019 12:56:50: 9000000 INFO @ Mon, 03 Jun 2019 12:56:51: 7000000 INFO @ Mon, 03 Jun 2019 12:56:58: 10000000 INFO @ Mon, 03 Jun 2019 12:56:58: 10000000 INFO @ Mon, 03 Jun 2019 12:57:02: 8000000 INFO @ Mon, 03 Jun 2019 12:57:06: 11000000 INFO @ Mon, 03 Jun 2019 12:57:07: 11000000 INFO @ Mon, 03 Jun 2019 12:57:13: 9000000 INFO @ Mon, 03 Jun 2019 12:57:14: 12000000 INFO @ Mon, 03 Jun 2019 12:57:15: 12000000 INFO @ Mon, 03 Jun 2019 12:57:22: 13000000 INFO @ Mon, 03 Jun 2019 12:57:23: 13000000 INFO @ Mon, 03 Jun 2019 12:57:24: 10000000 INFO @ Mon, 03 Jun 2019 12:57:31: 14000000 INFO @ Mon, 03 Jun 2019 12:57:32: 14000000 INFO @ Mon, 03 Jun 2019 12:57:35: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:57:35: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:57:35: #1 total tags in treatment: 14538040 INFO @ Mon, 03 Jun 2019 12:57:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:57:35: #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 12:57:35: #1 tags after filtering in treatment: 14538040 INFO @ Mon, 03 Jun 2019 12:57:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:57:35: #1 finished! INFO @ Mon, 03 Jun 2019 12:57:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:57:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:57:36: 11000000 INFO @ Mon, 03 Jun 2019 12:57:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:57:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:57:37: #1 total tags in treatment: 14538040 INFO @ Mon, 03 Jun 2019 12:57:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:57:37: #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 12:57:37: #2 number of paired peaks: 2186 INFO @ Mon, 03 Jun 2019 12:57:37: start model_add_line... INFO @ Mon, 03 Jun 2019 12:57:37: #1 tags after filtering in treatment: 14538040 INFO @ Mon, 03 Jun 2019 12:57:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:57:37: #1 finished! INFO @ Mon, 03 Jun 2019 12:57:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:57:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:57:37: start X-correlation... INFO @ Mon, 03 Jun 2019 12:57:37: end of X-cor INFO @ Mon, 03 Jun 2019 12:57:37: #2 finished! INFO @ Mon, 03 Jun 2019 12:57:37: #2 predicted fragment length is 52 bps INFO @ Mon, 03 Jun 2019 12:57:37: #2 alternative fragment length(s) may be 2,52 bps INFO @ Mon, 03 Jun 2019 12:57:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX330271/SRX330271.10_model.r WARNING @ Mon, 03 Jun 2019 12:57:37: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:57:37: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Mon, 03 Jun 2019 12:57:37: #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 12:57:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:57:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:57:38: #2 number of paired peaks: 2186 INFO @ Mon, 03 Jun 2019 12:57:38: start model_add_line... INFO @ Mon, 03 Jun 2019 12:57:39: start X-correlation... INFO @ Mon, 03 Jun 2019 12:57:39: end of X-cor INFO @ Mon, 03 Jun 2019 12:57:39: #2 finished! INFO @ Mon, 03 Jun 2019 12:57:39: #2 predicted fragment length is 52 bps INFO @ Mon, 03 Jun 2019 12:57:39: #2 alternative fragment length(s) may be 2,52 bps INFO @ Mon, 03 Jun 2019 12:57:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX330271/SRX330271.05_model.r WARNING @ Mon, 03 Jun 2019 12:57:39: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:57:39: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Mon, 03 Jun 2019 12:57:39: #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 12:57:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:57:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:57:46: 12000000 INFO @ Mon, 03 Jun 2019 12:57:57: 13000000 INFO @ Mon, 03 Jun 2019 12:58:07: 14000000 INFO @ Mon, 03 Jun 2019 12:58:13: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:58:13: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:58:13: #1 total tags in treatment: 14538040 INFO @ Mon, 03 Jun 2019 12:58:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:58:13: #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 12:58:13: #1 tags after filtering in treatment: 14538040 INFO @ Mon, 03 Jun 2019 12:58:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:58:13: #1 finished! INFO @ Mon, 03 Jun 2019 12:58:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:58:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:58:15: #2 number of paired peaks: 2186 INFO @ Mon, 03 Jun 2019 12:58:15: start model_add_line... INFO @ Mon, 03 Jun 2019 12:58:15: start X-correlation... INFO @ Mon, 03 Jun 2019 12:58:15: end of X-cor INFO @ Mon, 03 Jun 2019 12:58:15: #2 finished! INFO @ Mon, 03 Jun 2019 12:58:15: #2 predicted fragment length is 52 bps INFO @ Mon, 03 Jun 2019 12:58:15: #2 alternative fragment length(s) may be 2,52 bps INFO @ Mon, 03 Jun 2019 12:58:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX330271/SRX330271.20_model.r WARNING @ Mon, 03 Jun 2019 12:58:15: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:58:15: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Mon, 03 Jun 2019 12:58:15: #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 12:58:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:58:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:58:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:58:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:58:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX330271/SRX330271.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:58:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX330271/SRX330271.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:58:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX330271/SRX330271.10_summits.bed INFO @ Mon, 03 Jun 2019 12:58:36: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3310 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:58:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX330271/SRX330271.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:58:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX330271/SRX330271.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:58:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX330271/SRX330271.05_summits.bed INFO @ Mon, 03 Jun 2019 12:58:38: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4868 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:58:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:59:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX330271/SRX330271.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:59:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX330271/SRX330271.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:59:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX330271/SRX330271.20_summits.bed INFO @ Mon, 03 Jun 2019 12:59:14: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2110 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。