Job ID = 1293731 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T16:58:59 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 ) 2019-06-02T17:02:22 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 ) spots read : 13,527,540 reads read : 13,527,540 reads written : 13,527,540 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: 00:05:40 13527540 reads; of these: 13527540 (100.00%) were unpaired; of these: 1086454 (8.03%) aligned 0 times 8348186 (61.71%) aligned exactly 1 time 4092900 (30.26%) aligned >1 times 91.97% overall alignment rate Time searching: 00:05:40 Overall time: 00:05:40 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_rmdupse_core] 2166113 / 12441086 = 0.1741 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 02:19:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111813/SRX111813.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111813/SRX111813.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111813/SRX111813.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111813/SRX111813.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 02:19:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:19:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:19:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111813/SRX111813.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111813/SRX111813.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111813/SRX111813.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111813/SRX111813.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 02:19:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:19:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:19:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111813/SRX111813.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111813/SRX111813.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111813/SRX111813.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111813/SRX111813.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 02:19:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:19:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:19:13: 1000000 INFO @ Mon, 03 Jun 2019 02:19:17: 1000000 INFO @ Mon, 03 Jun 2019 02:19:17: 1000000 INFO @ Mon, 03 Jun 2019 02:19:21: 2000000 INFO @ Mon, 03 Jun 2019 02:19:29: 2000000 INFO @ Mon, 03 Jun 2019 02:19:29: 2000000 INFO @ Mon, 03 Jun 2019 02:19:29: 3000000 INFO @ Mon, 03 Jun 2019 02:19:38: 4000000 INFO @ Mon, 03 Jun 2019 02:19:43: 3000000 INFO @ Mon, 03 Jun 2019 02:19:44: 3000000 INFO @ Mon, 03 Jun 2019 02:19:47: 5000000 INFO @ Mon, 03 Jun 2019 02:19:57: 4000000 INFO @ Mon, 03 Jun 2019 02:19:57: 4000000 INFO @ Mon, 03 Jun 2019 02:19:57: 6000000 INFO @ Mon, 03 Jun 2019 02:20:05: 7000000 INFO @ Mon, 03 Jun 2019 02:20:07: 5000000 INFO @ Mon, 03 Jun 2019 02:20:08: 5000000 INFO @ Mon, 03 Jun 2019 02:20:13: 8000000 INFO @ Mon, 03 Jun 2019 02:20:18: 6000000 INFO @ Mon, 03 Jun 2019 02:20:18: 6000000 INFO @ Mon, 03 Jun 2019 02:20:21: 9000000 INFO @ Mon, 03 Jun 2019 02:20:29: 7000000 INFO @ Mon, 03 Jun 2019 02:20:29: 10000000 INFO @ Mon, 03 Jun 2019 02:20:29: 7000000 INFO @ Mon, 03 Jun 2019 02:20:31: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:20:31: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:20:31: #1 total tags in treatment: 10274973 INFO @ Mon, 03 Jun 2019 02:20:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:20:31: #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 02:20:31: #1 tags after filtering in treatment: 10274973 INFO @ Mon, 03 Jun 2019 02:20:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:20:31: #1 finished! INFO @ Mon, 03 Jun 2019 02:20:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:20:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:20:32: #2 number of paired peaks: 142 WARNING @ Mon, 03 Jun 2019 02:20:32: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Mon, 03 Jun 2019 02:20:32: start model_add_line... INFO @ Mon, 03 Jun 2019 02:20:32: start X-correlation... INFO @ Mon, 03 Jun 2019 02:20:32: end of X-cor INFO @ Mon, 03 Jun 2019 02:20:32: #2 finished! INFO @ Mon, 03 Jun 2019 02:20:32: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 02:20:32: #2 alternative fragment length(s) may be 43,514,557 bps INFO @ Mon, 03 Jun 2019 02:20:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX111813/SRX111813.10_model.r WARNING @ Mon, 03 Jun 2019 02:20:32: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:20:32: #2 You may need to consider one of the other alternative d(s): 43,514,557 WARNING @ Mon, 03 Jun 2019 02:20:32: #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 02:20:32: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:20:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:20:39: 8000000 INFO @ Mon, 03 Jun 2019 02:20:39: 8000000 INFO @ Mon, 03 Jun 2019 02:20:49: 9000000 INFO @ Mon, 03 Jun 2019 02:20:49: 9000000 INFO @ Mon, 03 Jun 2019 02:20:59: 10000000 INFO @ Mon, 03 Jun 2019 02:21:00: 10000000 INFO @ Mon, 03 Jun 2019 02:21:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:21:02: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:21:02: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:21:02: #1 total tags in treatment: 10274973 INFO @ Mon, 03 Jun 2019 02:21:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:21:02: #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 02:21:02: #1 tags after filtering in treatment: 10274973 INFO @ Mon, 03 Jun 2019 02:21:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:21:02: #1 finished! INFO @ Mon, 03 Jun 2019 02:21:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:21:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:21:02: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:21:02: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:21:02: #1 total tags in treatment: 10274973 INFO @ Mon, 03 Jun 2019 02:21:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:21:02: #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 02:21:02: #1 tags after filtering in treatment: 10274973 INFO @ Mon, 03 Jun 2019 02:21:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:21:02: #1 finished! INFO @ Mon, 03 Jun 2019 02:21:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:21:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:21:03: #2 number of paired peaks: 142 WARNING @ Mon, 03 Jun 2019 02:21:03: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Mon, 03 Jun 2019 02:21:03: start model_add_line... INFO @ Mon, 03 Jun 2019 02:21:03: start X-correlation... INFO @ Mon, 03 Jun 2019 02:21:03: end of X-cor INFO @ Mon, 03 Jun 2019 02:21:03: #2 finished! INFO @ Mon, 03 Jun 2019 02:21:03: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 02:21:03: #2 alternative fragment length(s) may be 43,514,557 bps INFO @ Mon, 03 Jun 2019 02:21:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX111813/SRX111813.05_model.r WARNING @ Mon, 03 Jun 2019 02:21:03: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:21:03: #2 You may need to consider one of the other alternative d(s): 43,514,557 WARNING @ Mon, 03 Jun 2019 02:21:03: #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 02:21:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:21:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:21:03: #2 number of paired peaks: 142 WARNING @ Mon, 03 Jun 2019 02:21:03: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Mon, 03 Jun 2019 02:21:03: start model_add_line... INFO @ Mon, 03 Jun 2019 02:21:04: start X-correlation... INFO @ Mon, 03 Jun 2019 02:21:04: end of X-cor INFO @ Mon, 03 Jun 2019 02:21:04: #2 finished! INFO @ Mon, 03 Jun 2019 02:21:04: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 02:21:04: #2 alternative fragment length(s) may be 43,514,557 bps INFO @ Mon, 03 Jun 2019 02:21:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX111813/SRX111813.20_model.r WARNING @ Mon, 03 Jun 2019 02:21:04: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:21:04: #2 You may need to consider one of the other alternative d(s): 43,514,557 WARNING @ Mon, 03 Jun 2019 02:21:04: #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 02:21:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:21:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:21:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX111813/SRX111813.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:21:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX111813/SRX111813.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:21:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX111813/SRX111813.10_summits.bed INFO @ Mon, 03 Jun 2019 02:21:16: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (819 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:21:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:21:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:21:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX111813/SRX111813.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:21:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX111813/SRX111813.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:21:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX111813/SRX111813.05_summits.bed INFO @ Mon, 03 Jun 2019 02:21:46: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1672 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:21:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX111813/SRX111813.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:21:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX111813/SRX111813.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:21:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX111813/SRX111813.20_summits.bed INFO @ Mon, 03 Jun 2019 02:21:47: Done! pass1 - making usageList (5 chroms): 2 millis pass2 - checking and writing primary data (104 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。