Job ID = 2589941 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T09:52:14 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 ) 2019-08-12T09:52:29 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 ) 2019-08-12T09:52:29 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 : 20,468,883 reads read : 40,937,766 reads written : 20,468,883 reads 0-length : 20,468,883 rm: cannot remove ‘[DSE]RR*’: 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: 00:05:38 20468883 reads; of these: 20468883 (100.00%) were unpaired; of these: 8870767 (43.34%) aligned 0 times 9750030 (47.63%) aligned exactly 1 time 1848086 (9.03%) aligned >1 times 56.66% overall alignment rate Time searching: 00:05:38 Overall time: 00:05:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 10528167 / 11598116 = 0.9077 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, 12 Aug 2019 19:07:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3862416/SRX3862416.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3862416/SRX3862416.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3862416/SRX3862416.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3862416/SRX3862416.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 12 Aug 2019 19:07:05: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:07:05: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:07:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3862416/SRX3862416.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3862416/SRX3862416.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3862416/SRX3862416.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3862416/SRX3862416.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 12 Aug 2019 19:07:06: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:07:06: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:07:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3862416/SRX3862416.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3862416/SRX3862416.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3862416/SRX3862416.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3862416/SRX3862416.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 12 Aug 2019 19:07:07: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:07:07: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:07:17: 1000000 INFO @ Mon, 12 Aug 2019 19:07:17: #1 tag size is determined as 74 bps INFO @ Mon, 12 Aug 2019 19:07:17: #1 tag size = 74 INFO @ Mon, 12 Aug 2019 19:07:17: #1 total tags in treatment: 1069949 INFO @ Mon, 12 Aug 2019 19:07:17: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:07:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:07:17: #1 tags after filtering in treatment: 1069949 INFO @ Mon, 12 Aug 2019 19:07:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:07:17: #1 finished! INFO @ Mon, 12 Aug 2019 19:07:17: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:07:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:07:17: #2 number of paired peaks: 1166 INFO @ Mon, 12 Aug 2019 19:07:17: start model_add_line... INFO @ Mon, 12 Aug 2019 19:07:17: start X-correlation... INFO @ Mon, 12 Aug 2019 19:07:17: end of X-cor INFO @ Mon, 12 Aug 2019 19:07:17: #2 finished! INFO @ Mon, 12 Aug 2019 19:07:17: #2 predicted fragment length is 71 bps INFO @ Mon, 12 Aug 2019 19:07:17: #2 alternative fragment length(s) may be 71 bps INFO @ Mon, 12 Aug 2019 19:07:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3862416/SRX3862416.10_model.r WARNING @ Mon, 12 Aug 2019 19:07:17: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:07:17: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Mon, 12 Aug 2019 19:07:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:07:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:07:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:07:18: 1000000 INFO @ Mon, 12 Aug 2019 19:07:19: #1 tag size is determined as 74 bps INFO @ Mon, 12 Aug 2019 19:07:19: #1 tag size = 74 INFO @ Mon, 12 Aug 2019 19:07:19: #1 total tags in treatment: 1069949 INFO @ Mon, 12 Aug 2019 19:07:19: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:07:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:07:19: #1 tags after filtering in treatment: 1069949 INFO @ Mon, 12 Aug 2019 19:07:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:07:19: #1 finished! INFO @ Mon, 12 Aug 2019 19:07:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:07:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:07:19: #2 number of paired peaks: 1166 INFO @ Mon, 12 Aug 2019 19:07:19: start model_add_line... INFO @ Mon, 12 Aug 2019 19:07:19: start X-correlation... INFO @ Mon, 12 Aug 2019 19:07:19: end of X-cor INFO @ Mon, 12 Aug 2019 19:07:19: #2 finished! INFO @ Mon, 12 Aug 2019 19:07:19: #2 predicted fragment length is 71 bps INFO @ Mon, 12 Aug 2019 19:07:19: #2 alternative fragment length(s) may be 71 bps INFO @ Mon, 12 Aug 2019 19:07:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3862416/SRX3862416.05_model.r WARNING @ Mon, 12 Aug 2019 19:07:19: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:07:19: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Mon, 12 Aug 2019 19:07:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:07:19: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:07:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:07:19: 1000000 INFO @ Mon, 12 Aug 2019 19:07:20: #1 tag size is determined as 74 bps INFO @ Mon, 12 Aug 2019 19:07:20: #1 tag size = 74 INFO @ Mon, 12 Aug 2019 19:07:20: #1 total tags in treatment: 1069949 INFO @ Mon, 12 Aug 2019 19:07:20: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:07:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:07:20: #1 tags after filtering in treatment: 1069949 INFO @ Mon, 12 Aug 2019 19:07:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:07:20: #1 finished! INFO @ Mon, 12 Aug 2019 19:07:20: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:07:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:07:20: #2 number of paired peaks: 1166 INFO @ Mon, 12 Aug 2019 19:07:20: start model_add_line... INFO @ Mon, 12 Aug 2019 19:07:20: start X-correlation... INFO @ Mon, 12 Aug 2019 19:07:20: end of X-cor INFO @ Mon, 12 Aug 2019 19:07:20: #2 finished! INFO @ Mon, 12 Aug 2019 19:07:20: #2 predicted fragment length is 71 bps INFO @ Mon, 12 Aug 2019 19:07:20: #2 alternative fragment length(s) may be 71 bps INFO @ Mon, 12 Aug 2019 19:07:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3862416/SRX3862416.20_model.r WARNING @ Mon, 12 Aug 2019 19:07:20: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:07:20: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Mon, 12 Aug 2019 19:07:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:07:20: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:07:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:07:21: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:07:22: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:07:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3862416/SRX3862416.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:07:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3862416/SRX3862416.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:07:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3862416/SRX3862416.10_summits.bed INFO @ Mon, 12 Aug 2019 19:07:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (321 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:07:23: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:07:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3862416/SRX3862416.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:07:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3862416/SRX3862416.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:07:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3862416/SRX3862416.05_summits.bed INFO @ Mon, 12 Aug 2019 19:07:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (531 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 12 Aug 2019 19:07:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3862416/SRX3862416.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:07:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3862416/SRX3862416.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:07:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3862416/SRX3862416.20_summits.bed INFO @ Mon, 12 Aug 2019 19:07:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (150 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。